Phylogeographic methods facilitate inference of the geographical history of genetic lineages. Recent examples explore human migration and the origins of viral pandemics. There is longstanding disagreement over the use and validity of certain phylogeographic inference methodologies. In this paper, we highlight three distinct frameworks for phylogeographic inference to give a taste of this disagreement. Each of the three approaches presents a different viewpoint on phylogeography, most fundamentally on how we view the relationship between the inferred history of a sample and the history of the population the sample is embedded in. Satisfactory resolution of this relationship between history of the tree and history of the population remains a challenge for all but the most trivial models of phylogeographic processes. Intriguingly, we believe that some recent methods that entirely avoid inference about the history of the population will eventually help to reach a resolution.

The impact of barriers to dispersal and gene flow is often inferred to be the primary cause of lineage divergence and phylogeographic structure in terrestrial organisms. In particular, the Mississippi River has been implicated as a barrier to gene flow in many species, including aquatic taxa. However, if barriers are permeable to organisms, then phylogeographic structure may be difficult to detect due to gene flow between lineages. Using time-calibrated Bayesian phylogenetic analyses of mtDNA, and phylogeographic coalescent simulations, we determine if the Mississippi River operates as a barrier to gene flow in the aquatic diamond-backed watersnake (Nerodia rhombifer). The phylogenetic analyses support a basal division within N. rhombifer mtDNA lineages that coincides with populations generally east and west of the Mississippi River. These results, and that of the divergence dating analyses, therefore suggest that the river was a significant barrier to gene flow in the Pleistocene similar to 1.4 million years ago, presumably during an interglacial period when the river was much wider. However, we also detect western haplotypes in the eastern clade, and vice versa, thereby indicating that this barrier has not been complete. Nonetheless, the coalescent simulations that account for limited migration suggest that the Mississippi River was an important feature that shaped the phylogeographic history of this aquatic snake in the USA despite limited gene flow. (C) 2010 Elsevier Inc. All rights reserved.

Explosive speciation in ancient lakes has fascinated biologists for centuries and has inspired classical work on the tempo and modes of speciation. Considerable attention has been directed towards the extrinsic forces of speciation-the geological, geographical and ecological peculiarities of ancient lakes. Recently, there has been a resurgence of interest in the intrinsic nature of these radiations, the biological characteristics conducive to speciation. While new species are thought to arise mainly by the gradual enhancement of reproductive isolation among geographically isolated populations, ancient lakes provide little evidence for a predominant role of geography in speciation. Recent phylogenetic work provides strong evidence that multiple colonization waves were followed by parallel intralacustrine radiations that proceeded at relatively rapid rates despite long-term gene flow through hybridization and introgression. Several studies suggest that hybridization itself might act as a key evolutionary mechanism by triggering major genomic reorganization/revolution and enabling the colonization of new ecological niches in ancient lakes. These studies propose that hybridization is not only of little impediment to diversification but could act as an important force in facilitating habitat transitions, promoting postcolonization adaptations and accelerating diversification. Emerging ecological genomic approaches are beginning to shed light on the long-standing evolutionary dilemma of speciation in the face of gene flow. We propose an integrative programme for future studies on speciation in ancient lakes.

Theoretical work focused on microsatellite variation has produced a number of important results, including the expected distribution of repeat sizes and the expected squared difference in repeat size between two randomly selected samples. However, closed-form expressions for the sampling distribution and frequency spectrum of microsatellite variation have not been identified. Here, we use coalescent simulations of the stepwise mutation model to develop gamma and exponential approximations of the microsatellite allele frequency spectrum, a distribution central to the description of microsatellite variation across the genome. For both approximations, the parameter of biological relevance is the number of alleles at a locus, which we express as a function of theta, the population-scaled mutation rate, based on simulated data. Discovered relationships between theta, the number of alleles, and the frequency spectrum support the development of three new estimators of microsatellite theta. The three estimators exhibit roughly similar mean squared errors (MSEs) and all are biased. However, across a broad range of sample sizes and theta values, the MSEs of these estimators are frequently lower than all other estimators tested. The new estimators are also reasonably robust to mutation that includes step sizes greater than one. Finally, our approximation to the microsatellite allele frequency spectrum provides a null distribution of microsatellite variation. In this context, a preliminary analysis of the effects of demographic change on the frequency spectrum is performed. We suggest that simulations of the microsatellite frequency spectrum under evolutionary scenarios of interest may guide investigators to the use of relevant and sometimes novel summary statistics.

Although dispersal is recognized as a key issue in several fields of population biology (such as behavioral ecology population genetics metapopulation dynamics or evolutionary modeling) these disciplines focus on different aspects of the concept and often make different implicit assumptions regarding migration models Using simulations we investigate how such assumptions translate into effective gene flow and fixation probability of selected alleles Assumptions regarding migration type (e g source-sink resident pre-emption or balanced dispersal) and patterns (e g stepping-stone versus island dispersal) have large impacts when demes differ in sizes or selective pressures The effects of fragmentation as well as the spatial localization of newly arising mutations also strongly depend on migration type and patterns Migration rate also matters depending on the migration type fixation probabilities at an intermediate migration rate may he outside the range defined by the low- and high-migration limits when demes differ in sizes Given the extreme sensitivity of fixation probability to characteristics of dispersal we underline the Importance of making explicit (and documenting empirically) the crucial ecological/ behavioral assumptions underlying migration models (C) 2010 Elsevier Inc All rights reserved.

Background: Past and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae) which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ in several phenotypic traits (including morphology, behavior and life history). We investigated whether phenotypic divergence is accompanied by genetic divergence between populations of different landscapes along a 700 km latitudinal gradient. Methodology/Principal Findings: Populations (23) along the latitudinal gradient in both landscape types were analyzed using microsatellite and allozyme markers. A general decrease in genetic diversity with latitude was detected, likely due to post-glacial colonization effects. Contrary to expectations, agricultural landscapes were not less diverse and no significant bottlenecks were detected. Nonetheless, a genetic signature of recent colonization is reflected in the absence of clinal genetic differentiation within the agricultural landscape, significantly lower gene flow between agricultural populations (3.494) than between woodland populations (4.183), and significantly higher genetic differentiation between agricultural (0.050) than woodland (0.034) pairwise comparisons, likely due to multiple founder events. Globally, the genetic data suggest multiple long distance dispersal/colonization events and subsequent high intra-and inter-landscape gene flow in this species. Phosphoglucomutase deviated from other enzymes and microsatellite markers, and hence may be under selection along the latitudinal gradient but not between landscape types. Phenotypic divergence was greater than genetic divergence, indicating directional selection on some flight morphology traits. Main Conclusions/Significance: Clinal differentiation characterizes the population structure within the original woodland habitat. Genetic signatures of recent habitat expansion remain, notwithstanding high gene flow. After differentiation through drift was excluded, both latitude and landscape were significant factors inducing spatially variable phenotypic variation.

Microsatellite markers were used to characterize the structure of genetic diversity in natural Moroccan Aleppo pine (Pinus halepensis Mill.) populations, the most southwesterly marginal populations of the species in the Mediterranean Basin. Twenty-two natural populations and one artificial population, located in four regions covering most of the natural range of P. halepensis in the country, were sampled. Across this range, towards the south and west (and towards high altitudes) the populations become increasingly discrete and discontinuous. The nuclear microsatellite marker analysis suggests that a large proportion of the Aleppo pines in Morocco have derived from a single genetic lineage, represented by a central group of 11 of the examined populations located in the High and Middle Atlas Mountains. In addition, two smaller groups, represented by the marginal southwestern High Atlas populations, and three still smaller north / northeastern groups of populations located in the Rif and northeast Middle Atlas Mountains, could be genetically distinguished. Further, coalescence analysis of historical demographic population patterns suggests that ancient bottlenecks occurred in all of the natural populations. However, the population differentiation and genetic diversity levels we found were good (F-st = 15.47), presumably because of the species' good potential for long-distance dispersal of seeds and high invasive capacity, which appear to have maintained a state of stable near-equilibrium, meta-population dynamics since ancient times.

The idea that molecular data should contain information on the recent evolutionary history of populations is rather old. However, much of the work carried out today owes to the work of the statisticians and theoreticians who demonstrated that it was possible to detect departures from equilibrium conditions (e. g., panmictic population/mutation-drift equilibrium) and interpret them in terms of deviations from neutrality or stationarity. During the last 20 years the detection of population size changes has usually been carried out under the assumption that samples were obtained from populations that can be approximated by a Wright-Fisher model (i.e., assuming panmixia, demographic stationarity, etc.). However, natural populations are usually part of spatial networks and are interconnected through gene flow. Here we simulated genetic data at mutation and migration-drift equilibrium under an n-island and a stepping-stone model. The simulated populations were thus stationary and not subject to any population size change. We varied the level of gene flow between populations and the scaled mutation rate. We also used several sampling schemes. We then analyzed the simulated samples using the Bayesian method implemented in MSVAR, the Markov Chain Monte Carlo simulation program, to detect and quantify putative population size changes using microsatellite data. Our results show that all three factors (genetic differentiation/gene flow, genetic diversity, and the sampling scheme) play a role in generating false bottleneck signals. We also suggest an ad hoc method to counter this effect. The confounding effect of population structure and of the sampling scheme has practical implications for many conservation studies. Indeed, if population structure is creating “spurious” bottleneck signals, the interpretation of bottleneck signals from genetic data might be less straightforward than it would seem, and several studies may have overestimated or incorrectly detected bottlenecks in endangered species.

We assessed genetic differentiation among populations of weathervane scallop (Patinopecten caurinus) in the northeastern Pacific, extending over 2500 km in the Gulf of Alaska and southeastern Bering Sea. Variability was surveyed at nuclear loci with allozyme, microsatellite, and single nucleotide polymorphism (SNP) methods, and at mitochondrial (mt)DNA loci with SNPs and nucleotide sequencing. High levels of gene diversity were detected for allozymes (H = 0.080), microsatellites (H = 0.734), and mtDNA (h = 0.781). Genotypes at nuclear loci generally fit Hardy-Weinberg proportions, except for some microsatellite loci, for which null-allele frequencies of 0.02 to 0.34 were estimated. No allele-frequency differences were detected among samples, except for the allozyme loci Gpi and Pep-4. Overall levels of differentiation ranged from F-ST = 0.0004 for allozymes, F-ST = 0.0008 for mtDNA to F-ST = 0.0004 for microsatellites. No isolation by distance was found for any of the markers. A unimodal mtDNA mismatch distribution and significant excesses of low-frequency variants for allozymes, microsatellites, and mtDNA may reflect a post-glacial population expansion. The lack of genetic differentiation measured by neutral markers does not preclude the existence of locally adapted, self-sustaining populations that are important in the harvest management of this species.

Background: Relaxed molecular clock models allow divergence time dating and “relaxed phylogenetic” inference, in which a time tree is estimated in the face of unequal rates across lineages. We present a new method for relaxing the assumption of a strict molecular clock using Markov chain Monte Carlo to implement Bayesian modeling averaging over random local molecular clocks. The new method approaches the problem of rate variation among lineages by proposing a series of local molecular clocks, each extending over a subregion of the full phylogeny. Each branch in a phylogeny (subtending a clade) is a possible location for a change of rate from one local clock to a new one. Thus, including both the global molecular clock and the unconstrained model results, there are a total of 2(2n-2) possible rate models available for averaging with 1, 2, ... , 2n - 2 different rate categories. Results: We propose an efficient method to sample this model space while simultaneously estimating the phylogeny. The new method conveniently allows a direct test of the strict molecular clock, in which one rate rules them all, against a large array of alternative local molecular clock models. We illustrate the method's utility on three example data sets involving mammal, primate and influenza evolution. Finally, we explore methods to visualize the complex posterior distribution that results from inference under such models. Conclusions: The examples suggest that large sequence datasets may only require a small number of local molecular clocks to reconcile their branch lengths with a time scale. All of the analyses described here are implemented in the open access software package BEAST 1.5.4 (http://beast-mcmc.googlecode.com/).

The Oregon spotted frog (Rana pretiosa) is one of the most threatened amphibians in the Pacific Northwest. Here we analyzed data from 13 microsatellite loci and 298 bp of mitochondrial DNA in frogs collected from 23 of the remaining R. pretiosa populations in order to (1) assess levels of genetic diversity within populations of R. pretiosa, (2) identify the major genetic groups in the species, (3) estimate levels of genetic differentiation and gene flow among populations within each major group, and (4) compare the pattern of differentiation among R. pretiosa populations with that among populations of R. cascadae, a non-endangered congener that also occurs in Oregon and Washington. There is a strong, hierarchical genetic structure in R. pretiosa. That structure includes six major genetic groups, one of which is represented by a single remaining population. R. pretiosa populations have low genetic diversity (average H (e) = 0.31) compared to R. cascadae (average H (e) = 0.54) and to other ranid frogs. Genetic subdivision among populations is much higher in R. pretiosa than in R. cascadae, particularly over the largest geographic distances (hundreds of kilometers). A joint analysis of migration rates among populations and of effective sizes within populations (using MIGRATE) suggests that both species have extremely low migration rates, and that R. pretiosa have slightly smaller effective sizes. However, the slight difference in effective sizes between species appears insufficient to explain the large difference in genetic diversity and in large-scale genetic structure. We therefore hypothesize that low connectivity among the more widely-spaced R. pretiosa populations (owing to their patchier habitat), is the main cause of their lower genetic diversity and higher among-population differentiation. Conservation recommendations for R. pretiosa include maintaining habitat connectivity to facilitate gene flow among populations that are still potentially connected, and either expanding habitat or founding additional `backup' populations to maintain diversity in the isolated populations. We recommend that special consideration be given to conservation of the Camas Prairie population in Northern Oregon. It is the most geographically isolated population, has the lowest genetic diversity (H (e) = 0.14) and appears to be the only remaining representative of a major genetic group that is now almost extinct. Finally, because the six major groups within R. pretiosa are strongly differentiated, occupy different habitat types, and are geographically separate, they should be recognized as evolutionarily significant units for purposes of conservation planning.

P>Recently, there has been a debate about whether the temperate forests of East Asia merged or fragmented during glacial periods in the Pleistocene. Here, we tested these two opposing views through phylogeographical studies of the temperate-deciduous walnut tree, Juglans mandshurica (Juglandaceae) in northern and northeastern China, as well as Japan and Korea. We assessed the genetic structure of 33 natural populations using 10 nuclear microsatellite loci and seven chloroplast DNA (cpDNA) fragments. The cpDNA data showed the complete fixation of two different haplotype lineages in northeastern vs northern populations. This pronounced phylogeographic break was also indicated by nuclear microsatellite data, but there were disparities regarding individual populations. Among those populations fixed for haplotype A (the northeastern group), three were clustered in the northern group and four showed evidence of mixed ancestry based on microsatellite data. Our results support the hypothesis that two independent refugia were maintained across the range of J. mandshurica in the north of China during the last glacial maximum, contrary to the inference that all temperate forests migrated to the south (25-30 degrees N). The discordance between the patterns revealed by cpDNA and microsatellite data indicate that asymmetrical gene flow has occurred between the two refugia.

Che, X. and Xu, S. 2010. Bayesian data analysis for agricultural experiments. Can. J. Plant Sci. 90: 575-603. Data collected in agricultural experiments can be analyzed in many different ways using different models. The most commonly used models are the linear model and the generalized linear model. The maximum likelihood method is often used for data analysis. However, this method may not be able to handle complicated models, especially multiple level hierarchical models. The Bayesian method partitions complicated models into simple components, each of which may be formulated analytically. Therefore, the Bayesian method is capable of handling very complicated models. The Bayesian method itself may not be more complicated than the maximum likelihood method, but the analysis is time consuming, because numerical integration involved in Bayesian analysis is almost exclusively accomplished based on Monte Carlo simulations, the so called Markov Chain Monte Carlo (MCMC) algorithm. Although the MCMC algorithm is intuitive and straightforward to statisticians, it may not be that simple to agricultural scientists, whose main purpose is to implement the method and interpret the results. In this review, we provide the general concept of Bayesian analysis and the MCMC algorithm in a way that can be understood by non-statisticians. We also demonstrate the implementation of the MCMC algorithm using professional software packages such as the MCMC procedure in SAS. Three datasets from agricultural experiments were analyzed to demonstrate the MCMC algorithm.

Characterization of the fine-scale population dynamics of the mosquito Aedes taeniorhynchus is needed to improve our understanding of its role as a disease vector in the Galapagos Islands. We used microsatellite data to assess the genetic structure of coastal and highland mosquito populations and patterns of gene flow between the two habitats through time on Santa Cruz Island. In addition, we assessed possible associations of mosquito abundance and genetic diversity with environmental variables. The coastal and highland mosquito populations were highly differentiated from each other all year round, with some gene flow detected only during periods of increased precipitation. The results support the hypothesis that selection arising from ecological differences between habitats is driving adaptation and divergence in A. taeniorhynchus, and maintaining long-term genetic differentiation of the populations against gene flow. The highland and lowland populations may constitute an example of incipient speciation in progress. Highland populations were characterized by lower observed heterozygosity and allelic richness, suggesting a founder effect and/or lower breeding site availability in the highlands. A lack of reduction in genetic diversity over time in highland populations suggests that they survive dry periods as dormant eggs. Association between mosquito abundance and precipitation was strong in the highlands, whereas tide height was the main factor affecting mosquito abundance on the coast. Our findings suggests differences in the infection dynamics of mosquito-borne parasites in the highlands compared to the coast, and a higher risk of mosquito-driven disease spread across these habitats during periods of increased precipitation.

Intertidal and subtidal communities of the western and eastern coasts of the North Atlantic Ocean were greatly affected by Pleistocene glaciations, with some taxa persisting on both coasts, and others recolonizing after being extirpated on one coast during the Last Glacial Maximum. In the original spirit of comparative phylogeography, we conducted a comparative analysis using mtDNA sequence data and a hierarchical approximate Bayesian computation (ABC) approach for testing these two scenarios across 12 intertidal and subtidal coastal invertebrates spanning the North Atlantic to determine the temporal dynamics of species membership of these two ephemeral communities. Conditioning on a low gene-flow model, our results suggested that a colonization or mitochondrial selective sweep history was predominant across all taxa, with only the bivalve mollusc Mytilus edulis showing a history of trans-Atlantic persistence. Conditioning on a high gene-flow model weakened the support for this assemblage-level demographic history. The predominance of a colonization-type history also highlights concerns about analyses based on single-locus data where genetic hitchhiking may be incorrectly inferred as colonization. In conclusion, driving factors in shifting species range distributions and membership of ephemeral coastal communities could be species-specific environmental tolerances, species interactions, and/or stochastic demographic extinction. Through a re-examination of a long-standing question of North Atlantic phylogeography, we highlight the flexibility and statistical honesty of using a model-based ABC approach.

Background: Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations. Results: To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor (Mc1r) to investigate molecular genetic differentiation among three B. jamaicensis subspecies (B. j. borealis, B. j. calurus, B. j. harlani). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between B. j. harlani and B. j. borealis. Differences observed between B. j. harlani and B. j. borealis in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, B. j. borealis and B. j. calurus, and estimates of migration rates among all three subspecies were high. No consistent differences were observed in Mc1r data between B. j. harlani and other B. jamaicensis subspecies or between light and dark color morphs within B. j. calurus, suggesting that Mc1r does not play a significant role in B. jamaicensis melanism. Conclusions: These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.

P>Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. Flow cytometry analyses detected ploidy polymorphisms of 2x and 4x in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.

Differences in larval developmental mode are predicted to affect ecological and evolutionary processes ranging from gene flow and population bottlenecks to rates of population recovery from anthropogenic disturbance and capacity for local adaptation. The most powerful tests of these predictions use comparisons among species to ask how phylogeographic patterns are correlated with the evolution and loss of prolonged planktonic larval development. An important and largely untested assumption of these studies is that interspecific differences in population genetic structure are mainly caused by differences in dispersal and gene flow (rather than by differences in divergence times among populations or changes in effective population sizes), and that species with similar patterns of spatial genetic variation have similar underlying temporal demographic histories. Teasing apart these temporal and spatial patterns is important for understanding the causes and consequences of evolutionary changes in larval developmental mode. New analytical methods that use the coalescent history of allelic diversity can reveal these temporal patterns, test the strength of traditional population-genetic explanations for variation in spatial structure based on differences in dispersal, and identify strongly supported alternative explanations for spatial structure based on demographic history rather than on gene flow alone. We briefly review some of these recent analytical developments, and show their potential for refining ideas about the correspondence between the evolution of larval developmental mode, population demographic history, and spatial genetic variation.

Premise of the study: The Frullania tamarisci complex includes eight Holarctic liverwort species. One of these, F. asagrayana, is distributed broadly throughout eastern North America from Canada to the Gulf Coast. Preliminary genetic data suggested that the species includes two groups of populations. This study was designed to test whether the two groups are reproductively isolated biological species. Methods: Eighty-eight samples from across the range of F. asagrayana, plus 73 samples from one population, were genotyped for 13 microsatellite loci. Sequences for two plastid loci and nrITS were obtained from 13 accessions. Genetic data were analyzed using coalescent models and Bayesian inference. Key results: Frullania asagrayana is sequence-invariant at the two plastid loci and ITS2, but two clear groups were resolved by microsatellites. The two groups are largely reproductively isolated, but there is a low level of gene flow from the southern to the northern group. No gene flow was detected in the other direction. A local population was heterogeneous but displayed strong genetic structure. Conclusions: The genetic structure of F. asagrayana in eastern North America reflects morphologically cryptic differentiation between reproductively isolated groups of populations, near-panmixis within groups, and clonal propagation at local scales. Reproductive isolation between groups that are invariant at the level of nucleotide sequences shows that caution must be exercised in making taxonomic and evolutionary inferences from reciprocal monophyly (or lack thereof) between putative species.

We will soon have complete genome sequences from thousands of species, as well as from many individuals within species. This coming explosion of information will transform our understanding of the amount, distribution and functional significance of genetic variation in natural populations. Now is a crucial time to explore the potential implications of this information revolution for conservation genetics and to recognize limitations in applying genomic tools to conservation issues. We identify and discuss those problems for which genomics will be most valuable for curbing the accelerating worldwide loss of biodiversity. We also provide guidance on which genomics tools and approaches will be most appropriate to use for different aspects of conservation.

Most methods for studying divergence with gene flow rely upon data from many individuals at few loci. Such data can be useful for inferring recent population history but they are unlikely to contain sufficient information about older events. However, the growing availability of genome sequences suggests a different kind of sampling scheme, one that may be more suited to studying relatively ancient divergence. Data sets extracted from whole-genome alignments may represent very few individuals but contain a very large number of loci. To take advantage of such data we developed a new maximum-likelihood method for genomic data under the isolation-with-migration model. Unlike many coalescent-based likelihood methods, our method does not rely on Monte Carlo sampling of genealogies, but rather provides a precise calculation of the likelihood by numerical integration over all genealogies. We demonstrate that the method works well on simulated data sets. We also consider two models for accommodating mutation rate variation among loci and find that the model that treats mutation rates as random variables leads to better estimates. We applied the method to the divergence of Drosophila melanogaster and D. simulans and detected a low, but statistically significant, signal of gene flow from D. simulans to D. melanogaster.

For many biological investigations, groups of individuals are genetically sampled from several geographic locations. These sampling locations often do not reflect the genetic population structure. We describe a framework using marginal likelihoods to compare and order structured population models, such as testing whether the sampling locations belong to the same randomly mating population or comparing unidirectional and multidirectional gene flow models. In the context of inferences employing Markov chain Monte Carlo methods, the accuracy of the marginal likelihoods depends heavily on the approximation method used to calculate the marginal likelihood. Two methods, modified thermodynamic integration and a stabilized harmonic mean estimator, are compared. With finite Markov chain Monte Carlo run lengths, the harmonic mean estimator may not be consistent. Thermodynamic integration, in contrast, delivers considerably better estimates of the marginal likelihood. The choice of prior distributions does not influence the order and choice of the better models when the marginal likelihood is estimated using thermodynamic integration, whereas with the harmonic mean estimator the influence of the prior is pronounced and the order of the models changes. The approximation of marginal likelihood using thermodynamic integration in MIGRATE allows the evaluation of complex population genetic models, not only of whether sampling locations belong to a single panmictic population, but also of competing complex structured population models.

An emerging pattern is that population densities of generalist rodents are higher in small compared to large forest patches in fragmented landscapes. We used genetically based measures of migration between patches to test two dispersal-based hypotheses for this negative density-area relationship: (1) emigration rates from small patches should be relatively lower compared to large patches (”inhibited dispersal hypothesis”), or (2) immigration rates should be higher into small than large patches (”immigration hypothesis”). Neither hypothesis was supported using data on dispersal inferred from eight microsatellite loci for 12 populations of Peromyscus leucopus in six small (1.3-2.7 ha) and six large (8-150 ha) forest patches. Emigration rates were not lower from and immigration rates were not higher into small than large patches. In fact, contrary to both hypotheses, emigration rates were higher from populations of P. leucopus in small compared to large patches. Based on a combination of genetic and field data, we speculate that higher reproduction in smaller patches resulted in higher densities which led to higher emigration rates from those patches. Rates of reproduction (presumably driven by better habitat conditions in smaller patches), rather than dispersal, seems to drive density differences in forest patches. We conclude that smaller forest patches within an agricultural matrix act as a source of individuals, and that migration rates are fairly high among forest patches regardless of size.

Conservation geneticists make inferences about their focal species from genetic data, and then use these inferences to inform conservation decisions. Since different biological processes can produce similar patterns of genetic diversity, we advocate an approach to data analysis that considers the full range of evolutionary forces and attempts to evaluate their relative contributions in an objective manner. Here we collect data from microsatellites and chloroplast loci and use these data to explore models of historical demography in the carnivorous Pitcher Plant, Sarracenia alata. Findings indicate that populations of S. alata exhibit high degrees of population genetic structure, likely caused by dispersal limitation, and that population sizes have decreased in western populations and increased in eastern populations. These results provide new insight to the management and conservation of plants restricted to small, declining populations isolated in increasingly scarce and highly threatened habitat, including other rare and endangered species of Sarracenia.

Marine species frequently show weak and/or complex genetic structuring that is commonly dismissed as `chaotic' genetic patchiness and ecologically uninformative. Here, using three datasets that individually feature weak chaotic patchiness, we demonstrate that combining inferences across species and incorporating environmental data can greatly improve the predictive value of marine population genetics studies on small spatial scales. Significant correlations in genetic patterns of microsatellite markers among three species, kelp bass Paralabrax clathratus, Kellet's whelk Kelletia kelletii and California spiny lobster Panulirus interruptus, in the Southern California Bight suggest that slight differences in diversity and pairwise differentiation across sampling sites are not simply noise or chaotic patchiness, but are ecologically meaningful. To test whether interspecies correlations potentially result from shared environmental drivers of genetic patterns, we assembled data on kelp bed size, sea surface temperature and estimates of site-to-site migration probability derived from a high resolution multi-year ocean circulation model. These data served as predictor variables in linear models of genetic diversity and linear mixed models of genetic differentiation that were assessed with information-theoretic model selection. Kelp was the most informative predictor of genetics for all three species, but ocean circulation also played a minor role for kelp bass. The shared patterns suggest a single spatial marine management strategy may effectively protect genetic diversity of multiple species. This study demonstrates the power of environmental and ecological data to shed light on weak genetic patterns and highlights the need for future focus on a mechanistic understanding of the links between oceanography, ecology and genetic structure.

We assayed genetic variations at five microsatellite loci of dolphinfish captured at five sites in 2005 and eight sites in 2006 to detect genetic population structure of dolphinfish Coryphaena hippurus in the Gulf of California and surrounding waters. Results show high genetic variation, similar to other pelagic fishes with large populations. Pairwise F-ST values and hierarchical AMOVA detected subtle but significant spatial and temporal heterogeneity, mainly in samples of 2005 and some of 2006. However, Bayesian assignment analysis failed to detect genetic differentiation, which was also supported by the Mantel test and gene flow estimates among the sampled sites. This suggests that, despite the slight heterogeneity detected in this region, the dolphinfish forms a single panmictic population with high genetic variation and gene flow. (C) 2010 Elsevier B.V. All rights reserved.

The concept of effective population size (N-e) is based on an elegantly simple idea which, however, rapidly becomes very complex when applied to most real-world situations. In natural populations, spatial and temporal stratifications create different classes of individuals with different vital rates, and this in turn affects (generally reduces) N-e in complex ways. I consider how these natural stratifications influence our understanding of effective size and how to estimate it, and what the consequences are for conservation and management of natural populations. Important points that emerge include the following: The relative influences of local vs metapopulation N-e depend on a variety of factors, including the time frame of interest. Levels of diversity in local populations are strongly influenced by even low levels of migration, so these measures are not reliable indicators of local N-e. For long-term effective size, obtaining a reliable estimate of mutation rate is the most important consideration; unless this is accomplished, estimates can be biased by orders of magnitude. At least some estimators of contemporary N-e appear to be robust to relatively high (approximately 10%) equilibrium levels of migration, so under many realistic scenarios they might yield reliable estimates of local N-e. Age structure probably has little effect on long-term estimators of N-e but can strongly influence contemporary estimates. More research is needed in several key areas: (i) to disentangle effects of selection and drift in metapopulations connected by intermediate levels of migration; (ii) to elucidate the relationship between N-b (effective number of breeders per year) and N-e per generation in age-structured populations; (iii) to perform rigorous sensitivity analyses of new likelihood and coalescent-based methods for estimating demographic and evolutionary histories.

Identifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Issues arise with most current population genetic inference methods when the genetic divergence is low among putative populations. Low levels of genetic divergence may be as a result of either high ongoing migration or historic high migration but no current, ongoing migration. We direct attention to recent developments in the use of the tempo-spatial distribution of closely related individuals to detect population structure or estimate current migration rates. These `kinship-based' approaches complement more traditional population-based genetic inference methods by providing a means to detect population structure and estimate current migration rates when genetic divergence is low. However, for kinship-based methods to become widely adopted, formal estimation procedures applicable to a range of species life histories are needed.

`No-take' marine protected areas (MPAs) are successful in protecting populations of many exploited fish species, but it is often unclear whether networks of MPAs are adequately spaced to ensure connectivity among reserves, and whether there is spillover into adjacent exploited areas. Such issues are particularly important in species with low dispersal potential, many of which exist as genetically distinct regional stocks. The roman, Chrysoblephus laticeps, is an overexploited, commercially important sparid endemic to South Africa. Post-recruits display resident behavior and occupy small home ranges, making C. laticeps a suitable model species to study genetic structure in marine teleosts with potentially low dispersal ability. We used multilocus data from two types of highly variable genetic markers (mitochondrial DNA control region and seven microsatellite markers) to clarify patterns of genetic connectivity and population structure in C. laticeps using samples from two MPAs and several moderately or severely exploited regions. Despite using analytical tools that are sensitive to detect even subtle genetic structure, we found that this species exists as a single, well-mixed stock throughout its core distribution. The high levels of connectivity identified among sites support the findings of previous studies that have indicated that inshore MPAs are an adequate tool for managing overexploited temperate reef fishes. Even though dispersal of adult C. laticeps out of MPAs is limited, the fact that the large adults in these reserves produce exponentially more offspring than their smaller counterparts in exploited areas makes MPAs a rich source of recruits. We nonetheless caution against concluding that the lack of structure identified in C. laticeps and several other southern African teleosts can be considered to be representative of marine teleosts in this region in general. Many such species are represented in more than one marine biogeographic province and may be comprised of regionally adapted stocks that require individual management.

Population structure in many Arctic marine mammal species reflects a dynamic interplay between physical isolating mechanisms and the extent to which dispersal opportunities are met. We examined variation within mtDNA and eight microsatellite markers to investigate population structure and demographic history in beluga whales in the North Atlantic. Genetic heterogeneity was observed between Svalbard and West Greenland that reveals limited gene flow over ecological time scales. Differentiation was also recorded between Atlantic belugas and two previously studied populations in the North Pacific, the Beaufort Sea and Gulf of Alaska. However, Bayesian cluster analysis of the nDNA data identified two population clusters that did not correspond to the respective ocean basins, as predicted, but to: (1) Arctic (Svalbard-White Sea-Greenland-Beaufort Sea) and (2) Subarctic (Gulf of Alaska) regions. Similarly, the deepest phylogeographic signal was between the Arctic populations and the Gulf of Alaska. Fitting an isolation-with-migration model yielded genetic abundance estimates that match census estimates and revealed that Svalbard and the Beaufort Sea likely diverged 7,600-35,400 years ago but have experienced recurrent periods with gene flow since then, most likely via the Russian Arctic during subsequent warm periods. Considering current projections of continued sea ice losses in the Arctic, this study identified likely routes of future contact among extant beluga populations, and other mobile marine species, which have implications for genetic introgression, health, ecology and behavior.

Vinas, J., Perez-Serra, A., Vidal, O., Alvarado Bremer, J. R., and Pla, C. 2010. Genetic differentiation between eastern and western Mediterranean swordfish revealed by phylogeographic analysis of the mitochondrial DNA control region. - ICES Journal of Marine Science, 67: 1222-1229. Despite there being evidence of several discrete breeding grounds, Mediterranean populations of swordfish have been considered a single panmictic unit with no genetic substructure. Sequence analysis of the mitochondrial DNA ( mtDNA) control region of five Mediterranean locations (n = 251) reveals for the first time a clear genetic differentiation between eastern and western Mediterranean populations. This differentiation was detected only after conducting separate phylogeographic analyses on two previously described mtDNA clades. Although the frequencies of these clades are similar throughout the Mediterranean Sea, the levels of intra-clade genetic variation drop substantially towards the eastern end. This, together with clear differences in past demographic history and uneven migration rates between Mediterranean basins, suggests that the two populations experienced different effects during the Pleistocene. Subsequently, the mtDNA distinctiveness of eastern and western Mediterranean swordfish populations has been maintained probably by homing towards breeding areas.

We investigated demographic history and population structuring of Colossoma macropomum sampled from 14 localities in the Amazon basin and the Bolivian sub-basin; the two basins are separated by a series of 16 rapids. Although genetically differentiated, IMa analyses suggest non-zero bi-directional migration rates, and inter-basin divergence of approximately 17 thousand years ago. Analyses in BEAST indicated that Bolivian C. macropomum has been demographically stable except for a moderate population increase in the last 12 thousand years, while Amazonian C. macropomum has been experiencing demographic growth over the last 350 thousand years, resulting in approximately one order of magnitude increase in coalescent N-e. (C) 2010 Elsevier Inc. All rights reserved.

Genetic data are often used to assess `population connectivity' because it is difficult to measure dispersal directly at large spatial scales. Genetic connectivity, however, depends primarily on the absolute number of dispersers among populations, whereas demographic connectivity depends on the relative contributions to population growth rates of dispersal vs. local recruitment (i.e. survival and reproduction of residents). Although many questions are best answered with data on genetic connectivity, genetic data alone provide little information on demographic connectivity. The importance of demographic connectivity is clear when the elimination of immigration results in a shift from stable or positive population growth to negative population growth. Otherwise, the amount of dispersal required for demographic connectivity depends on the context (e.g. conservation or harvest management), and even high dispersal rates may not indicate demographic interdependence. Therefore, it is risky to infer the importance of demographic connectivity without information on local demographic rates and how those rates vary over time. Genetic methods can provide insight on demographic connectivity when combined with these local demographic rates, data on movement behaviour, or estimates of reproductive success of immigrants and residents. We also consider the strengths and limitations of genetic measures of connectivity and discuss three concepts of genetic connectivity that depend upon the evolutionary criteria of interest: inbreeding connectivity, drift connectivity, and adaptive connectivity. To conclude, we describe alternative approaches for assessing population connectivity, highlighting the value of combining genetic data with capture-mark-recapture methods or other direct measures of movement to elucidate the complex role of dispersal in natural populations.

Historical records suggest that the petrels of Round Island (near Mauritius, Indian Ocean) represent a recent, long-distance colonization by species originating from the Atlantic and Pacific Oceans. The majority of petrels on Round Island appear most similar to Pterodroma arminjoniana, a species whose only other breeding locality is Trindade Island in the South Atlantic. Using nine microsatellite loci, patterns of genetic differentiation in petrels from Round and Trindade Islands were analysed. The two populations exhibit low but significant levels of differentiation in allele frequencies and estimates of migration rate between islands using genetic data are also low, supporting the hypothesis that these populations have recently separated but are now isolated from one another. A second population of petrels, most similar in appearance to the Pacific species P. neglecta, is also present on Round Island and observations suggest that the two petrel species are hybridizing. Vocalizations recorded on the island also suggest that hybrid birds may be present within the population. Data from microsatellite genotypes support this hypothesis and indicate that there may have been many generations of hybridization and back-crossing between P. arminjoniana and P. neglecta on Round Island. Our results provide an insight into the processes of dispersal and the consequences of secondary contact in Procellariiformes.

Geographic range differences among species may result from differences in their physiological tolerances. In the intertidal zone, marine and terrestrial environments intersect to create a unique habitat, across which physiological tolerance strongly influences range. Traits to cope with environmental extremes are particularly important here because many species live near their physiological limits and environmental gradients can be steep. The snail Melampus bidentatus occurs in coastal salt marshes in the western Atlantic and the Gulf of Mexico. We used sequence data from one mitochondrial (COI) and two nuclear markers (histone H3 and a mitochondrial carrier protein, MCP) to identify three cryptic species within this broad-ranging nominal species, two of which have partially overlapping geographic ranges. High genetic diversity, low population structure, and high levels of migration within these two overlapping species suggest that historical range limitations do not entirely explain their different ranges. To identify microhabitat differences between these two species, we modelled their distributions using data from both marine and terrestrial environments. Although temperature was the largest factor setting range limits, other environmental components explained features of the ranges that temperature alone could not. In particular, the interaction of precipitation and salinity likely sets physiological limits that lead to range differences between these two cryptic species. This suggests that the response to climatic change in these snails will be mediated by changes to multiple environmental factors, and not just to temperature alone.

Larval dispersal may have an important effect on genetic structure of benthic fishes. To examine the population genetic structure of spottedtail goby Synechogobius ommaturus, a 478 base pair (bp) fragment of the hypervariable portion of the mtDNA control region was sequenced and used to interpret life-history characteristics and larval dispersal strategy. Individuals (n = 186) from 10 locations on the coasts of China and Korea were analysed and 44 haplotypes were obtained. The levels of haplotype and nucleotide diversity were higher in East China Sea populations than in other populations. Both the phylogenetic tree and the minimum spanning tree showed that no significant genealogical structures corresponding to sampling locations existed. AMOVA and pair-wise F-ST revealed significant genetic differentiation between populations from Korea and China. A significant isolation by distance pattern was observed in this species (r = 0 center dot 53, P < 0 center dot 001). Both mismatch distribution analysis and neutrality tests showed S. ommaturus to have experienced a recent population expansion. These results suggest that the Pleistocene ice ages had a major effect on the phylogeographic pattern of S. ommaturus, that larvae might avoid offshore dispersal and that dispersal of larvae may maintain a migration-drift equilibrium.

Phylogenetic, phylogeographic, population genetic and coalescence analyses were combined to examine the recent evolutionary history of the widespread Indo-Pacific parrotfish, Scarus psittacus, over a geographic range spanning three marine biogeographic realms. We sequenced 164 individuals from 12 locations spanning 17,000 km, from 55A(0)E to 143A(0)W, using 322 base pairs of mitochondrial control region (D-loop). S. psittacus displayed high haplotype (h = 0.83-0.98), but low nucleotide (< 1%) diversity. Most (> 83%) genetic variation was within populations. AMOVA revealed significant partitioning and identified five geographic groups. These included one central population and four populations peripheral to the centre. The central population occupied reefs from Western Australia to Tahiti and represented the central Indo-Pacific biogeographic realm. Cocos Keeling was distinct from central and western Indo-Pacific biogeographic realms occupying a position intermediate to these. Peripheral populations (Hawaii, Marquesas) represented the eastern Indo-Pacific biogeographic realm, while Seychelles represented the western Indo-Pacific biogeographic realm. All but the central population expanded (< 163 kya). Whilst all populations experienced major sea level and SST changes associated with Pleistocene glaciation cycles, the genetic structure of the central population was relatively homogenous unlike the remaining genetically distinctive populations.

Identifying biological trends and threats to organisms that make long distance migrations are often the limiting factors in their conservation. Indeed, Laysan albatross Phoebastria immutabilis are highly vagile seabirds, foraging throughout the North Pacific Ocean. Despite mark-recapture data indicating natal philopatry, Laysan albatross recently re-colonized several anthropogenically extirpated breeding locations. At the same time, a breeding population in the north-western Hawaiian Islands was lost to erosion and it was hypothesized that the colonization events were due to displacement rather than dispersal. Nuclear and mitochondrial markers were used in a range wide survey to test whether natal philopatry corresponded to population structure in Laysan albatross, and to determine whether recent colonization events were a result of displacement from vanishing breeding habitat. Five microsatellite loci found little population structure (F-ST=0.01, P=0.001), and sequences from the mitochondrial control region revealed low population structure (pi(ST)=0.05, P < 0.001). The results were consistent with male-mediated dispersal and strong, but not absolute, philopatry by females. Mixed stock analyses and banding records from the newly colonized sites indicated contributions from multiple source populations, which contradicted the displacement hypothesis of a single source population and instead supported species-wide dispersal from all source colonies. High genetic diversity (pi=0.045, h=0.989), rapid colonization, and great dispersal potential bode well for the conservation of Laysan albatross. However, it may be necessary to protect high-island nesting sites, preserve genetic diversity and maintain breeding populations in the face of projected sea level rises and persistent bycatch.

Aim We examined genetic structure and long-distance gene flow in two lichenized ascomycetes, Flavocetraria cucullata and Flavocetraria nivalis, which are widespread in arctic and alpine tundra. Location Circumpolar North. Methods DNA sequences were obtained for 90 specimens (49 for F. cucullata and 41 for F. nivalis) collected from various locations in Europe, Asia and North America. Sequences of the nuclear internal transcribed spacer (ITS) + 5.8S ribosomal subunit gene region were generated for 89 samples, and supplemented by beta-tubulin (BTUB) and translation elongation factor 1-alpha gene (EF1) sequences for a subset of F. cucullata specimens. Phylogenetic, nonparametric permutation methods and coalescent analyses were used to assess population divergence and to estimate the extent and direction of migration among continents. Results Both F. cucullata and F. nivalis were monophyletic, supporting their morphology-based delimitation, and had high and moderately high intraspecific genetic diversity, respectively. Clades within each species contained specimens from both North America and Eurasia. We found only weak genetic differentiation among North American and Eurasian populations, and evidence for moderate to high transoceanic gene flow. Main conclusions Our results suggest that both F. cucullata and F. nivalis have been able to migrate over large distances in response to climatic fluctuations. The high genetic diversity observed in the Arctic indicates long-term survival at high latitudes, whereas the estimated migration rates and weak geographic population structure suggest a continuing long-distance gene flow between continents that has prevented pronounced genetic differentiation. The mode of long-distance dispersal is unknown, but wind dispersal of conidia and/or ascospores is probably important in the open arctic landscapes. The high genetic diversity and efficient long-distance dispersal capability of F. cucullata and F. nivalis suggest that these species, and perhaps other arctic lichens as well, will be able to track their potential niche in the changing Arctic.

Background: After a volcano erupts, a lake may form in the cooled crater and become an isolated aquatic ecosystem. This makes fishes in crater lakes informative for understanding sympatric evolution and ecological diversification in barren environments. From a geological and limnological perspective, such research offers insight about the process of crater lake ecosystem establishment and speciation. In the present study we use genetic and coalescence approaches to infer the colonization history of Midas cichlid fishes (Amphilophus cf. citrinellus) that inhabit a very young crater lake in Nicaragua-the ca. 1800 year-old Lake Apoyeque. This lake holds two sympatric, endemic morphs of Midas cichlid: one with large, hypertrophied lips (similar to 20% of the total population) and another with thin lips. Here we test the associated ecological, morphological and genetic diversification of these two morphs and their potential to represent incipient speciation. Results: Gene coalescence analyses [11 microsatellite loci and mitochondrial DNA (mtDNA) sequences] suggest that crater lake Apoyeque was colonized in a single event from the large neighbouring great lake Managua only about 100 years ago. This founding in historic times is also reflected in the extremely low nuclear and mitochondrial genetic diversity in Apoyeque. We found that sympatric adult thin-and thick-lipped fishes occupy distinct ecological trophic niches. Diet, body shape, head width, pharyngeal jaw size and shape and stable isotope values all differ significantly between the two lip-morphs. The eco-morphological features pharyngeal jaw shape, body shape, stomach contents and stable isotopes (delta N-15) all show a bimodal distribution of traits, which is compatible with the expectations of an initial stage of ecological speciation under disruptive selection. Genetic differentiation between the thin-and thick-lipped population is weak at mtDNA sequence (F-ST = 0.018) and absent at nuclear microsatellite loci (F-ST < 0.001). Conclusions: This study provides empirical evidence of eco-morphological differentiation occurring very quickly after the colonization of a new and vacant habitat. Exceptionally low levels of neutral genetic diversity and inference from coalescence indicates that the Midas cichlid population in Apoyeque is much younger (ca. 100 years or generations old) than the crater itself (ca. 1 800 years old). This suggests either that the crater remained empty for many hundreds of years after its formation or that remnant volcanic activity prevented the establishment of a stable fish population during the early life of the crater lake. Based on our findings of eco-morphological variation in the Apoyeque Midas cichlids, and known patterns of adaptation in Midas cichlids in general, we suggest that this population may be in a very early stage of speciation (incipient species), promoted by disruptive selection and ecological diversification.

The South American tern Sterna hirundinacea is a migratory species for which dispersal, site fidelity and migratory routes are largely unknown. Here, we used five microsatellite loci and 799 bp partial mitochondrial DNA sequences (Cytochrome b and ND2) to investigate the genetic structure of South American terns from the South Atlantic Ocean (Brazilian and Patagonian colonies). Brazilian and Patagonian colonies have two distinct breeding phenologies (austral winter and austral summer, respectively) and are under the influence of different oceanographic features (e.g. Brazil and Falklands/Malvinas ocean currents, respectively), that may promote genetic isolation between populations. Results show that the Atlantic populations are not completely panmictic, nevertheless, contrary to our expectations, low levels of genetic structure were detected between Brazilian and Patagonian colonies. Such low differentiation (despite temporal isolation of the colonies) could be explained by demographic history of these populations coupled with ongoing levels of gene flow. Interestingly, estimations of gene flow through Maximum likelihood and Bayesian approaches has indicated asymmetrical long term and contemporary gene flow from Brazilian to Patagonian colonies, approaching a source-sink metapopulation dynamic. Genetic analysis of other South American tern populations (especially those from the Pacific coast and Falklands-Malvinas Islands) and other seabird species showing similar geographical distribution (e.g. royal tern Thalasseus maximus), are fundamental in gaining a better understanding of the main processes involved in the diversification of seabirds in the southern hemisphere.

Coalescent model based methods for phylogeny estimation force systematists to confront issues related to the identification of species boundaries. Unlike conventional phylogenetic analysis, where species membership can be assessed qualitatively after the phylogeny is estimated, the phylogenies that are estimated under a coalescent model treat aggregates of individuals as the operational taxonomic units and thus require a priori definition of these sets because the models assume that the alleles in a given lineage are sampled from a single panmictic population. Fortunately, the use of coalescent model based approaches allows systematists to conduct probabilistic tests of species limits by calculating the probability of competing models of lineage composition. Here, we conduct the first exploration of the issues related to applying such tests to a complex empirical system. Sequence data from multiple loci were used to assess species limits and phylogeny in it elide of North American Myotis bats. After estimating gene trees at each locus, the likelihood of models representing all hierarchical permutations of lineage composition was calculated and Akaike information criterion scores were computed. Metrics borrowed from information theory suggest that there is strong support for several models that include multiple evolutionary lineages within the currently described species Myotis lucifugus and M. evotis. Although these results are preliminary, they illustrate the practical importance of coupled species delimitation and phylogeny estimation.

To assess the effects of altitude on the level and structure of genetic diversity, a genetic survey was conducted in 12 populations of sessile oak (Quercus petraea) located between 130 and 1660 m in two parallel valleys on the northern side of the Pyrenees Mountains. Genetic diversity was monitored at 16 nuclear microsatellite loci and 5 chloroplast DNA (cpDNA) markers. The cpDNA survey suggested that extant populations in both valleys shared the same source populations from the plain. There was no visible trend of nuclear genetic diversity along altitude, even if indirect estimates of effective population sizes revealed a consistent reduction at higher altitudes. Population differentiation, although low, was mostly present among populations of the same valleys and reached similar levels than differentiation across the range of distribution of sessile oak. Contribution to the overall differentiation in the valleys was mostly due to the genetic divergence of the highest populations and the altitudinal variation of allelic frequencies at a few loci. Bayesian inference of migration between groups of populations showed that gene flow is preferentially unidirectional from lower altitudes in one valley to other groups of populations. Finally, we found evidence of clonal reproduction in high altitude populations. The introgression of Quercus robur and Quercus pubescens was also more frequent at the altitudinal margin suggesting that this mechanism may have contributed to the present migration and adaptation of Q. petraea and may also facilitate its future upslope shift in the context of climate change.

Viral strain evolution and disease emergence are influenced by anthropogenic change to the environment. We investigated viral characteristics, host ecology, and landscape features in the rabies-striped skunk disease system of the central Great Plains to determine how these factors interact to influence disease emergence. We amplified portions of the N and G genes of rabies viral RNA from 269 samples extracted from striped skunk brains throughout the distribution of two different rabies strains for which striped skunks were the reservoir. Because the distribution of these two strains overlapped on the landscape and were present in the same host population, we could evaluate how viral properties influenced epidemiological patterns in the area of sympatry. We found that South Central Skunk rabies (SCSK) exhibited intense purifying selection and high infectivity, which are both characteristics of an epizootic virus. Conversely, North Central Skunk rabies (NCSK) exhibited relaxed purifying selection and comparatively lower infectivity, suggesting the presence of an enzootic virus. The host population in the area of sympatry was highly admixed, and skunks among allopatric and sympatric areas had similar effective population sizes. Spatial analysis indicated that landscape features had minimal influence on NCSK movement across the landscape, but those same features were partial barriers to the spread of SCSK. We conclude that NCSK and SCSK have different epidemiological properties that interact differently with both host and landscape features to influence rabies spread in the central Great Plains. We suggest a holistic approach for future studies of emerging infectious diseases that includes studies of viral properties, host characteristics, and spatial features.

The repeated formation and loss of land-bridges during the Pleistocene have had lasting impacts on population genetic structure. In the tropics, where island populations persisted through multiple glacial cycles, alternating periods of isolation and contact are expected to have driven population and taxonomic divergence. Here, we combine mitochondrial and nuclear sequence data with microsatellites to dissect the impact of Pleistocene climate change on intra-specific diversification in the horseshoe bat Rhinolophus affinis. This taxon shows considerable morphological and acoustic variation: two parapatric subspecies (himalayanus and macrurus) occur on mainland China and a third (hainanus) on Hainan Island. Our phylogeographic reconstruction and coalescent analyses suggest the island subspecies formed from an ancestral population of himalayanus via two colonization events c. 800 000 years before present. R. a. hainanus then recolonized the mainland, forming macrurus and thus a secondary contact zone with himalayanus. Finally, macrurus recolonized Hainan following the LGM. We found that all three biological events corresponded to known periods of land-bridge formation. Evidence of introgression was detected between macrurus and both its sister taxa, with geographical proximity rather than length of separation appearing to be the biggest determinant of subsequent genetic exchange. Our study highlights the important role of climate-mediated sea level changes have had in shaping current processes and patterns of population structure and taxonomic diversification.

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and UST under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (5 Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements UST/FST, SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

The global migration patterns of influenza viruses have profound implications for the evolutionary and epidemiological dynamics of the disease. We developed a novel approach to reconstruct the genetic history of human influenza A (H3N2) collected worldwide over 1998 to 2009 and used it to infer the global network of influenza transmission. Consistent with previous models, we find that China and Southeast Asia lie at the center of this global network. However, we also find that strains of influenza circulate outside of Asia for multiple seasons, persisting through dynamic migration between northern and southern regions. The USA acts as the primary hub of temperate transmission and, together with China and Southeast Asia, forms the trunk of influenza's evolutionary tree. These findings suggest that antiviral use outside of China and Southeast Asia may lead to the evolution of long-term local and potentially global antiviral resistance. Our results might also aid the design of surveillance efforts and of vaccines better tailored to different geographic regions.

Studies on genetic connectivity are essential for the design of management strategies for coral reef fisheries. In this study we used a mitochondrial DNA marker to investigate population structure of the reef-associated parrotfish, Scarus ghobban, from four countries, Kenya, Mauritius, Seychelles and Tanzania, in the western Indian Ocean. We obtained nucleotide sequences of the mitochondrial control region for 117 individuals. Measures of haplotype diversity were relatively high. Pairwise population differentiation (F (ST)) was low, but not always non-significant. Analysis of molecular variance (AMOVA) showed genetic differentiation between groups, when the data was partitioned into two groups consisting of samples from Mauritius and Tanzania in one group, and samples from Kenya and Seychelles in another group. Direction of gene flow was estimated using a Bayesian approach. Migration was sometimes asymmetric or directional, coinciding with the flow of major oceanic and coastal currents in the region. Mismatch distributions, based on the observed number of differences among haplotype pairs, produced a unimodal distribution, indicative of recent demographic expansion. Phylogenetic analyses revealed three clades without any geographic structure, suggesting recent migration between historically isolated lineages. We reconstructed the historical demography of S. ghobban and examined it in the context of Pleistocene climate stages and changes in relative sea level. Overall, these results showed that populations of S. ghobban are genetically diverse and have relatively high gene flow, with some genetic structuring in the western Indian Ocean.

Aim To elucidate the historical phylogeography of the dusky pipefish (Syngnathus floridae) in the North American Atlantic and Gulf of Mexico ocean basins. Location Southern Atlantic Ocean and northern Gulf of Mexico within the continental United States. Methods A 394-bp fragment of the mitochondrial cytochrome b gene and a 235-bp fragment of the mitochondrial control region were analysed from individuals from 10 locations. Phylogenetic reconstruction, haplotype network, mismatch distributions and analysis of molecular variance were used to infer population structure between ocean basins and time from population expansion within ocean basins. Six microsatellite loci were also analysed to estimate population structure and gene flow among five populations using genetic distance methods (F-ST, Nei's genetic distance), isolation by distance (Mantel's test), coalescent-based estimates of genetic diversity and migration patterns, Bayesian cluster analysis and bottleneck simulations. Results Mitochondrial analyses revealed significant structuring between ocean basins in both cytochrome b (Theta(ST) = 0.361, P < 0.0001; Theta(CT) = 0.312, P < 0.02) and control region (Theta(ST) = 0.166, P < 0.0001; Theta(CT) = 0.128, P < 0.03) sequences. However, phylogenetic reconstructions failed to show reciprocal monophyly in populations between ocean basins. Microsatellite analyses revealed significant population substructuring between all locations sampled except for the two locations that were in closest proximity to each other (global F-ST value = 0.026). Bayesian analysis of microsatellite data also revealed significant population structuring between ocean basins. Coalescent-based analyses of microsatellite data revealed low migration rates among all sites. Mismatch distribution analysis of mitochondrial loci supports a sudden population expansion in both ocean basins in the late Pleistocene, with the expansion of Atlantic populations occurring more recently. Main conclusions Present-day populations of S. floridae do not bear the mitochondrial DNA signature of the strong phylogenetic discontinuity between the Atlantic and Gulf coasts of North America commonly observed in other species. Rather, our results suggest that Atlantic and Gulf of Mexico populations of S. floridae are closely related but nevertheless exhibit local and regional population structure. We conclude that the present-day phylogeographic pattern is the result of a recent population expansion into the Atlantic in the late Pleistocene, and that life-history traits and ecology may play a pivotal role in shaping the realized geographical distribution pattern of this species.

At least four species of New Zealand snipes (Coenocorypha) became extinct following the introduction of predatory mammals, and another two species suffered massive range reductions. To investigate species limits and population differentiation in six of the seven remaining offshore populations, we assayed variation in nine microsatellite loci and 1,980 base pairs of four mitochondrial DNA (mtDNA) genes. Genetic diversity in all populations except the largest one on Adams Island in the Auckland Islands was very low in both genomes. Alleles were fixed at many microsatellite loci and for single mtDNA haplotypes, particularly in the populations in the Chathams, Snares, Antipodes and Campbell Islands. Strong population structure has developed, and Chathams and Snares Islands populations are effectively genetically isolated from one another and from the more southern island populations. Based on reciprocal monophyly of lineages and their morphological distinctiveness we recommend that three phylogenetic species should be recognized, C. pusilla in the Chatham Islands, C. huegeli in the Snares Islands and C. aucklandica in the southern islands. The populations of C. aucklandica in the Auckland Islands, Antipodes Island and Campbell Island may warrant recognition as subspecies, and all should be managed as separate conservation units.

A previous mtDNA study indicated that female-mediated gene flow was extremely rare among alligator snapping turtle populations in different drainages of the Gulf of Mexico. In this study, we used variation at seven microsatellite DNA loci to assess the possibility of male-mediated gene flow, we augmented the mtDNA survey with additional sampling of the large Mississippi River System, and we evaluated the hypothesis that the consistently low within-population mtDNA diversity reflects past population bottlenecks. The results show that dispersal between drainages of the Gulf of Mexico is rare (F (STmsat) = 0.43, I broken vertical bar(STmtDNA) = 0.98). Past range-wide bottlenecks are indicated by several genetic signals, including low diversity for microsatellites (1.1-3.9 alleles/locus; H (e) = 0.06-0.53) and mtDNA (h = 0.00 for most drainages; pi = 0.000-0.001). Microsatellite data reinforce the conclusion from mtDNA that the Suwannee River population might eventually be recognized as a distinct taxonomic unit. It was the only population showing fixation or near fixation for otherwise rare microsatellite alleles. Six evolutionarily significant units are recommended on the basis of reciprocal mtDNA monophyly and high levels of microsatellite DNA divergence.

Tuber borchii (Ascomycota, Pezizales) is a highly valued truffle sold in local markets in Italy. Despite its economic importance, knowledge on its distribution and genetic structure is scarce. The objective of this work was to investigate the factors shaping the genetic structure of T. borchii using 61 representative specimens with a broad distribution throughout Italy. In spite of the lack of morphological differences, phylogenetic and coalescent-based analyses using four loci identified two genetically isolated groups sympatrically distributed. The low levels of divergence between the two clades may be the result of recent range expansions from geographically distinct refugia, potentially mediated by reforestation using coniferous species that are common ectomycorrhizal symbionts for both groups.

Most native red foxes (Vulpes vulpes) in the western contiguous United States appear to be climatically restricted to colder regions in the major mountain ranges and, in some areas, have suffered precipitous declines in abundance that may be linked to warming trends. However, another population of unknown origin has occurred in arid habitats in the Sacramento Valley of California well outside this narrow bioclimatic niche since at least 1880. If native, this population would be ecologically distinct among indigenous North American red foxes. We used mitochondrial and microsatellite markers from historical and modern samples (modes: 1910-1930 and 2000-2008, respectively) obtained throughout the western United States to determine the origins of the Sacramento Valley red fox, and assess the historical and modern connectivity and genetic effective population sizes of Sacramento Valley and montane red foxes. We found clear and consistent evidence supporting the indigenous origin of the Sacramento Valley population, including the phylogenetic positioning of the dominant, endemic mtDNA clade and microsatellite clustering of the Sacramento Valley population with the nearest montane population. Based on both mitochondrial and microsatellite AMOVAs, connectivity among Western populations of red foxes declined substantially between historical and modern time periods. Estimates based on temporal losses in gene diversity for both marker types suggest that both the Sierra Nevada (including the Southern Cascades population) and the Sacramento Valley populations have small genetic effective population sizes. Significant heterozygote excesses also indicate the occurrence of recent bottlenecks in these populations. Both substitutions distinguishing the 2 endemic Sacramento Valley haplotypes from the dominant montane haplotype were in the coding region and nonsynonymous, consistent with adaptive differences. These findings along with previously reported body size distinctions between Sacramento Valley and montane red foxes argue for distinct subspecific status for the Sacramento Valley red fox, for which we propose the designation V. v. patwin n. subsp. The small genetic effective population size estimates for the Sierra Nevada red fox and Sacramento Valley red fox are cause for concern, as is the possibility of genetic introgression into the latter population from an adjacent, recently established nonnative population.

Population loss is often a harbinger of species extinction, but few opportunities exist to follow a species' demography and genetics through both time and space while this occurs. Previous research has shown that the northern fur seal (Callorhinus ursinus) was extirpated from most of its range over the past 200-800 years and that some of the extirpated populations had unique life history strategies. In this study, widespread availability of subfossils in the eastern Pacific allowed us to examine temporal changes in spatial genetic structure during massive population range contraction and partial recovery. We sequenced the mitochondrial control region from 40 ancient and 365 modern samples and analyzed them through extensive simulations within a serial Approximate Bayesian Computation framework. These analyses suggest that the species maintained a high abundance, probably in subarctic refugia, that dispersal rates are likely 85% per generation into new breeding colonies, and that population structure was not higher in the past. Despite substantial loss of breeding range, this species' high dispersal rates and refugia appear to have prevented a loss of genetic diversity. High dispersal rates also suggest that previous evidence for divergent life history strategies in ancient populations likely resulted from behavioral plasticity. Our results support the proposal that panmictic, or nearly panmictic, species with large ranges will be more resilient to future disturbance and environmental change. When appropriately verified, evidence of low population structure can be powerful information for conservation decision-making.

Genetic diversity at the S-locus controlling self-incompatibility (SI) is often high because of negative frequency-dependent selection. In species with highly patchy spatial distributions, genetic drift can overwhelm balancing selection and cause stochastic loss of S-alleles. Natural selection may favor the breakdown of SI in populations with few S-alleles because low S-allele diversity constrains the seed production of self-incompatible plants. We estimated S-allele diversity, effective population sizes, and migration rates in Leavenworthia alabamica, a self-incompatible mustard species restricted to discrete habitat patches in rocky glades. Patterns of polymorphism were investigated at the S-locus and 15 neutral microsatellites in three large and three small populations with 100-fold variation in glade size. Populations on larger glades maintained more S-alleles, but all populations were estimated to harbor at least 20 S-alleles, and mate availabilities typically exceeded 0.80, which is consistent with little mate limitation in nature. Estimates of the effective size (N-e) in each population ranged from 600 to 1600, and estimated rates of migration (m) ranged from 3 x 10-4 to nearly 1 x 10-3. According to theoretical models, there is limited opportunity for genetic drift to reduce S-allele diversity in populations with these attributes. Although pollinators or resources limit seed production in small glades, limited S-allele diversity does not appear to be a factor promoting the incipient breakdown of SI in populations of this species that were studied.

Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration versus recent common ancestry are only recently available. Using past volcanic eruption times as a framework, we combine morphological analyses of traits important to reproduction with a coalescent-based genetic analysis of two proximate sockeye salmon (Oncorhynchus nerka) populations. We find that this is the most recent (similar to 500 years, 100 generations) natural ecological divergence recorded in a fish species, and report that this divergence is occurring despite migration. Although studies of fish divergence following the retreat of glaciers (10,000-15,000 years ago) have contributed extensively to our understanding of speciation, the Aniakchak system of sockeye salmon provides a rare example of the initial stages of ecological divergence following natural colonization. Our results show that even in the face of continued migration, populations may diverge in the absence of a physical barrier.

Background: A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been investigated. We evaluated the haplotype reconstruction method implemented by PHASE in the context of phylogeographic applications. Empirical sequence datasets from five non-coding nuclear loci with gametic phase ascribed by molecular approaches were coupled with simulated datasets to investigate three key issues: (1) haplotype reconstruction error rates and the nature of inference errors, (2) dataset features and genotypic configurations that drive haplotype reconstruction uncertainty, and (3) impacts of omitting unresolved genotypes on levels of observed phylogenetic diversity and the accuracy of downstream phylogeographic analyses. Results: We found that PHASE usually had very low false-positives (i.e., a low rate of confidently inferring haplotype pairs that were incorrect). The majority of genotypes that could not be resolved with high confidence included an allele occurring only once in a dataset, and genotypic configurations involving two low-frequency alleles were disproportionately represented in the pool of unresolved genotypes. The standard practice of omitting unresolved genotypes from downstream analyses can lead to considerable reductions in overall phylogenetic diversity that is skewed towards the loss of alleles with larger-than-average pairwise sequence divergences, and in turn, this causes systematic bias in estimates of important population genetic parameters. Conclusions: A combination of experimental and computational approaches for resolving phase of segregating sites in phylogeographic applications is essential. We outline practical approaches to mitigating potential impacts of computational haplotype reconstruction on phylogeographic inferences. With targeted application of laboratory procedures that enable unambiguous phase determination via physical isolation of alleles from diploid PCR products, relatively little investment of time and effort is needed to overcome the observed biases.

The northern spotted owl (Strix occidentalis caurina) is one of the most controversial threatened subspecies ever listed under the US Endangered Species Act. Despite protection of its remaining forest habitat, recent field studies show continued declines of northern spotted owls. One potential threat to northern spotted owls which has not yet been shown is loss of genetic variation from population bottlenecks. Bottlenecks can increase the probability of mating among related individuals, potentially causing inbreeding depression, and can decrease adaptive potential. Here we report evidence for recent bottlenecks in northern spotted owls using a large genetic dataset (352 individuals and 10 microsatellite loci). The signature of bottlenecks was strongest in the Washington Cascade Mountains, in agreement with field data. Our results provide independent evidence that northern spotted owls have recently declined, and suggest that loss of genetic variation is an emerging threat to the subspecies' persistence. Reduced effective population size (N (e)) shown here in addition to field evidence for demographic decline highlights the increasing vulnerability of this bird to extinction.

In the absence of recent admixture between species, bipartitions of individuals in gene trees that are shared across loci can potentially be used to infer the presence of two or more species. This approach to species delimitation via molecular sequence data has been constrained by the fact that genealogies for individual loci are often poorly resolved and that ancestral lineage sorting, hybridization, and other population genetic processes can lead to discordant gene trees. Here we use a Bayesian modeling approach to generate the posterior probabilities of species assignments taking account of uncertainties due to unknown gene trees and the ancestral coalescent process. For tractability, we rely on a user-specified guide tree to avoid integrating over all possible species delimitations. The statistical performance of the method is examined using simulations, and the method is illustrated by analyzing sequence data from rotifers, fence lizards, and human populations.

The sandbar shark, Carcharhinus plumbeus, is a large, cosmopolitan, coastal species. Females are thought to show philopatry to nursery grounds while males potentially migrate long distances, creating an opportunity for male-mediated gene flow that may lead to discordance in patterns revealed by mitochondrial DNA (mtDNA) and nuclear markers. While this dynamic has been investigated in elasmobranchs over small spatial scales, it has not been examined at a global level. We examined patterns of historical phylogeography and contemporary gene flow by genotyping 329 individuals from nine locations throughout the species' range at eight nuclear microsatellite markers and sequencing the complete mtDNA control region. Pairwise comparisons often resulted in fixation indices and divergence estimates of greater magnitude using mtDNA sequence data than microsatellite data. In addition, multiple methods of estimation suggested fewer populations based on microsatellite loci than on mtDNA sequence data. Coalescent analyses suggest divergence and restricted migration among Hawaii, Taiwan, eastern and western Australia using mtDNA sequence data and no divergence and high migration rates, between Taiwan and both Australian sites using microsatellite data. Evidence of secondary contact was detected between several localities and appears to be discreet in time rather than continuous. Collectively, these data suggest complex spatial/temporal relationships between shark populations that may feature pulses of female dispersal and more continuous male-mediated gene flow.

Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.

Long pelagic larval phases and the absence of physical barriers impede.rapid speciation and contrast the high diversity observed in marine ecosystems such as coral reefs. In this study, we used the three-spot dascyllus (Dascyllus trimaculatus) species complex to evaluate speciation modes at the spatial scale of the Indo-Pacific. The complex includes four recognized species and four main color morphs that differ in distribution Previous studies of the group using mitochondrial DNA revealed a noncongruence between color morphs and genetic groupings; with two of the color morphs grouped together and one color morph separated into three clades. Using extensive geographic sampling of 563 individuals and a combination of mitochondrial DNA sequences and 13 nuclear microsatellites, we defined population/species boundaries and inferred different speciation modes. The complex is composed of seven genetically distinct entities, some of which are distinct morphologically. Despite extensive dispersal abilities and an apparent lack of barriers, observed genetic partitions are consistent with allopatric speciation. However, ecological pressure, assortative mating, and sexual selection, were likely important during periods of geographical isolation. This study therefore suggests that primarily historical factors later followed by ecological factors caused divergence and speciation in this group of coral reef fish.

Aim Ascophyllum nodosum (L.) Le Jolis is a dominant fucoid seaweed occurring along sheltered, rocky shores throughout the North Atlantic (but not in the Pacific), where it is a foundational species of the intertidal community. Its large size and vulnerability to ice-scour have led to the hypothesis that contemporary populations in the north-west Atlantic may be the result of de novo recolonization from the north-east Atlantic since the Last Glacial Maximum (LGM) (c. 20 ka). We tested this hypothesis. Location Temperate North Atlantic rocky intertidal between c. 42 and 65 degrees N latitude. Methods More than 1300 individuals from 28 populations were sampled from across the entire range of A. nodosum and genotyped for six microsatellite loci, and > 500 individuals were genotyped for two mitochondrial loci, an intergenic spacer (IGS) and the tRNA (W) gene (trnW). Population structure and historical demography were analysed in a standard population genetics and coalescence framework. Results Based on the presence of private alleles and haplotypes, we found that A. nodosum has survived on both sides of the Atlantic (since before the LGM, dating back to at least the penultimate Eemian interglacial) with similar effective population sizes and divergence times (1.2 and 0.8 Ma). Dispersal has been predominantly from Europe to North America, and there is very weak present-day population differentiation across the North Atlantic. Diversity measures provided additional support for determining the location of refugia. Main conclusions Ascophyllum nodosum was apparently little affected by the LGM, although contemporary climate change is likely to have major effects on its latitudinal distribution on both sides of the North Atlantic. It is a very long-lived species, analogous in virtually all demographic aspects to a tree - resistant to extinction but vulnerable to catastrophic events. The Brittany peninsula is a hotspot of genetic diversity worthy of conservation.

Genomes conceal a vast intricate record of their carriers' descent and evolution. To disclose this information, biologists need phylogenetic models that integrate various levels of organization, ranging from nucleotide sequences to ecological interactions. Rates of duplication and horizontal gene transfer, organism trees and ancestral population sizes can all be inferred through statistical models of gene family evolution and population genetics. Similarly, phylogenomics combined with other fields of natural sciences can reveal the nature of ancient phenotypes and paleoenvironments. These computationally intensive approaches now benefit from progress in statistics and algorithmics. In this article, we review the recent advances and discuss possible developments towards a comprehensive reconstruction of the history of life.

The extreme environmental variability of coastal lagoons suggests that physical and ecological factors could contribute to the genetic divergence among populations occurring in lagoon and open-coast environments. In this study we analysed the genetic variability of lagoon and marine samples of the sand goby, Pomatoschistus marmoratus (Risso, 1810) (Pisces: Gobiidae), on the SW Spain coast. A fragment of mitochondrial DNA control region (570 bp) was sequenced for 196 individuals collected in five localities: Lo Pagan, Los Urrutias and Playa Honda (Mar Menor coastal lagoon), and Veneziola and Mazarron (Mediterranean Sea). The total haplotype diversity was h = 0.9424 +/- 0.0229, and the total nucleotide diversity was pi = 0.0108 +/- 0.0058. Among-sample genetic differentiation was not significant and small-scale patterns in the distribution of haplotypes were not apparent. Gene flow and dispersal-related life history traits may account for low genetic structure at a small spatial scale. The high genetic diversity found in P. marmoratus increases its potential to adapt to changing conditions of the Mar Menor coastal lagoon.

The fungal pathogen Verticillium dahliae has resulted in significant losses in numerous crops in coastal California, but lettuce remained unaffected until the mid-1990s. Since then outbreaks have decimated entire fields, but the causes of this sudden susceptibility of lettuce remain elusive. The population structure of V. dahliae isolated from coastal California (n = 123) was investigated with 22 microsatellite markers, and compared with strains from tomato in central California (n = 60), spinach seed imported from Washington State and Northern Europe (n = 43), and ornamentals from Wisconsin (n = 17). No significant differentiation was measured among hosts in coastal California or with the spinach and Wisconsin ornamental sampling groups. In contrast, the tomato sampling group was significantly differentiated. Significant gene flow was measured among the various geographic and host sampling groups, with the exception of tomato. Evidence of recombination in V. dahliae was identified through gametic disequilibrium and an exceedingly high genotypic diversity. The high incidence of V. dahliae in spinach seed and high planting density of the crop are sources of recurrent gene flow into coastal California, and may be associated with the recent outbreaks in lettuce. (C) 2010 Elsevier Inc. All rights reserved.

Chih-Shin Chen, Chih-Hsiang Tzeng, and Tai-Sheng Chiu (2010) Morphological and molecular analyses reveal separations among spatiotemporal populations of anchovy (Engraulis japonicus) in the southern East China Sea. Zoological Studies 49(2): 270-282. Coastal and oceanic populations of Japanese anchovy (Engraulis japonicus) occur in the southern East China Sea. The distributions of the larval stages of these populations provide a bases for subdividing anchovy into 3 spatiotemporal stocks for the management of local Taiwanese fisheries: spring coastal (sprW) and oceanic (sprE) stocks respectively in the western and eastern seas of Taiwan, and an autumn stock (autE) in Ilan Bay, northeastern Taiwan. Using larval morphological analyses to evaluate population similarities, we found subtle differences between the sprE and sprW geographic stocks, but strong intra-geographic differences between sprE and autE seasonal stocks. Molecular analyses, based on fragments of 740 bp (positions 200-939) of the mitochondrial DNA cytochrome b gene, revealed a substantial amount of genetic variations among populations. Analysis of molecular variance indicated significant differences among stocks, primarily due to the sympatric contrast between sprE and autE (F-ST = 0.073, p < 0.001), rather than due to geographic subdivisions, such as sprE vs. sprW (F-ST = 0.039) or sprW vs. autE (F-ST = 0.007). These results indicate the presence of a unique oceanic stock in eastern Taiwan in spring that is separated from the other populations. This spatiotemporal heterogeneity suggests a dynamic state of larval recruitment along the coast of northern Taiwan. We propose a dispersal route for larval anchovy from the Taiwan Strait to the northern coast, or active migration by adult anchovies in accordance with oceanographic patterns in the southern East China Sea. http://zoolstud.sinica.edu.tw/Journals/49.21270.pdf

Understanding the influence of habitat alteration on population structure and persistence is critical for effective conservation strategies. Timber harvest and wildfire are two of the most prevalent disturbances across temperate forests, yet the long-term effects of these two forces on population connectivity have rarely been studied. We studied populations of the Rocky Mountain tailed frog (Ascaphus montanus) across landscapes that have experienced either timber harvest or broad scale fires. Rocky Mountain tailed frogs generally require forested habitat, and are a species of concern in managed forests. We used landscape genetic techniques to test the explanatory power of alternative paths of connectivity across both burned and harvested forests and identified topographical and climatic variables that significantly influenced gene flow. We found that timber harvest and fire led to different patterns of genetic connectivity. Widespread terrestrial gene flow was maintained across previously burned areas and connectivity was primarily limited by solar radiation. In contrast, gene flow among populations in managed forests followed riparian corridors, presumably to avoid the loss of cover due to timber harvest. Gene flow along riparian corridors in Rocky Mountain tailed frogs differs from a population of the closely related coastal tailed frog (Ascaphus truei), for which gene flow appears to occur primarily over land. These results suggest management of Rocky Mountain tailed frogs should focus on maintaining riparian buffer zones, which may be less effective for the coastal species. Thus, consideration of landscape differences is essential even for conservation of closely related, morphologically similar species. (C) 2009 Elsevier Ltd. All rights reserved.

Background: Despite its key location between the rest of the continent and Europe, research on the phylogeography of north African species remains very limited compared to European and North American taxa. The Mediterranean land mollusc Cornu aspersum (= Helix aspersa) is part of the few species widely sampled in north Africa for biogeographical analysis. It then provides an excellent biological model to understand phylogeographical patterns across the Mediterranean basin, and to evaluate hypotheses of population differentiation. We investigated here the phylogeography of this land snail to reassess the evolutionary scenario we previously considered for explaining its scattered distribution in the western Mediterranean, and to help to resolve the question of the direction of its range expansion ( from north Africa to Europe or vice versa). By analysing simultaneously individuals from 73 sites sampled in its putative native range, the present work provides the first broad-scale screening of mitochondrial variation (cyt b and 16S rRNA genes) of C. aspersum. Results: Phylogeographical structure mirrored previous patterns inferred from anatomy and nuclear data, since all haplotypes could be ascribed to a B ( West) or a C ( East) lineage. Alternative migration models tested confirmed that C. aspersum most likely spread from north Africa to Europe. In addition to Kabylia in Algeria, which would have been successively a centre of dispersal and a zone of secondary contacts, we identified an area in Galicia where genetically distinct west and east type populations would have regained contact. Conclusions: Vicariant and dispersal processes are reviewed and discussed in the light of signatures left in the geographical distribution of the genetic variation. In referring to Mediterranean taxa which show similar phylogeographical patterns, we proposed a parsimonious scenario to account for the “east-west” genetic splitting and the northward expansion of the western ( B) clade which roughly involves (i) the dispersal of ancestral ( eastern) types through Oligocene terranes in the Western Mediterranean (ii) the Tell Atlas orogenesis as gene flow barrier between future west and east populations, (iii) the impact of recurrent climatic fluctuations from mid-Pliocene to the last ice age, (iv) the loss of the eastern lineage during Pleistocene northwards expansion phases.

Background: The Yakuts contrast strikingly with other populations from Siberia due to their cattle- and horse-breeding economy as well as their Turkic language. On the basis of ethnological and linguistic criteria as well as population genetic studies, it has been assumed that they originated from South Siberian populations. However, many questions regarding the origins of this intriguing population still need to be clarified ( e. g. the precise origin of paternal lineages and the admixture rate with indigenous populations). This study attempts to better understand the origins of the Yakuts by performing genetic analyses on 58 mummified frozen bodies dated from the 15(th) to the 19(th) century, excavated from Yakutia ( Eastern Siberia). Results: High quality data were obtained for the autosomal STRs, Y-chromosomal STRs and SNPs and mtDNA due to exceptional sample preservation. A comparison with the same markers on seven museum specimens excavated 3 to 15 years ago showed significant differences in DNA quantity and quality. Direct access to ancient genetic data from these molecular markers combined with the archaeological evidence, demographical studies and comparisons with 166 contemporary individuals from the same location as the frozen bodies helped us to clarify the microevolution of this intriguing population. Conclusion: We were able to trace the origins of the male lineages to a small group of horse-riders from the Cis-Baikal area. Furthermore, mtDNA data showed that intermarriages between the first settlers with Evenks women led to the establishment of genetic characteristics during the 15(th) century that are still observed today.

The genetic structure of contemporary populations can be shaped by both their history and current ecological conditions. We assessed the relative importance of postglacial colonization history and habitat type in the patterns and degree of genetic diversity and differentiation in northern European nine-spined sticklebacks (Pungitius pungitius), using mitochondrial DNA (mtDNA) sequences and 12 nuclear microsatellite and insertion/deletion loci. The mtDNA analyses identified - and microsatellite analyses supported - the existence of two historically distinct lineages (eastern and western). The analyses of nuclear loci among 51 European sites revealed clear historically influenced and to minor degree habitat dependent, patterns of genetic diversity and differentiation. While the effect of habitat type on the levels of genetic variation (coastal > freshwater) and differentiation (freshwater > coastal) was clear, the levels of genetic variability and differentiation in the freshwater sites were independent of habitat type (viz. river, lake and pond). However, levels of genetic variability, together with estimates of historical effective population sizes, decreased dramatically and linearly with increasing latitude. These geographical patterns of genetic variability and differentiation suggest that the contemporary genetic structure of freshwater nine-spined sticklebacks has been strongly impacted by the founder events associated with postglacial colonization and less by current ecological conditions (cf. habitat type). In general, the results highlight the strong and persistent effects of postglacial colonization history on genetic structuring of northern European fauna and provide an unparalleled example of latitudinal trends in levels of genetic diversity.

Understanding the factors that limit recombination in bacteria is critical in order to better understand and assess its effects on genetic variation and bacterial population genetic structure. Transformation in the naturally competent bacterium, Streptococcus pneumoniae, is regulated by a polymorphic competence (com) apparatus. It has been suggested that polymorphic types, called pherotypes, generate and maintain subpopulation genetic structure within this species. We test predictions stemming from this hypothesis using a cosmopolitan sample of clinical pneumococcal isolates. We sequenced the locus encoding the peptide that induces competence (comC) to assign clones to each known pherotype class and then used multilocus sequence typing to determine whether there is significant genetic differentiation between pherotypes subgroups. We find two dominant pherotypes within our sample, and both are maintained at high frequencies (CSP1 74%, CSP2 26%). Our analyses fail to detect significant genetic differentiation between pherotype groups and find strong evidence, from a coalescent analysis, for interpherotype recombination. In addition, our analyses indicate that positive selection may account for the maintenance of the fixed polymorphism in this locus (comC). Altogether, these results fail to support the prediction that the polymorphism in the competence system acts to limit recombination within S. pneumoniae populations. We discuss why this result is expected given the mechanism underlying transformation and outline a scenario to explain the evolution of polymorphism in the competence system.

Species delimitation has long been a difficult and controversial process, and different operational criteria often lead to different results. In particular, investigators using phenotypic vs. molecular data to delineate species may recognize different boundaries, especially if morphologically or ecologically differentiated populations have only recently diverged. Here we examine the genetic relationship between the widespread sunflower species Helianthus petiolaris and its narrowly distributed sand dune endemic sister species H. neglectus using sequence data from nine nuclear loci. The two species were initially described as distinct based on a number of minor morphological differences, somewhat different ecological tolerances, and at least one chromosomal rearrangement distinguishing them; but detailed molecular data has not been available until now. We find that, consistent with previous work, H. petiolaris is exceptionally genetically diverse. Surprisingly, H. neglectus harbors very similar levels of genetic diversity (average diversity across loci is actually slightly higher in H. neglectus). It is extremely unlikely that such a geographically restricted species could maintain these levels of genetic variation in isolation. In addition, the two species show very little evidence of any genetic divergence, and estimates of interspecific gene flow are comparable to gene flow estimates among regions within H. petiolaris. These results indicate that H. petiolaris and H. neglectus likely do not represent two distinct, isolated gene pools; H. neglectus is probably more accurately thought of as a geographically restricted, morphologically and ecologically distinct subspecies of H. petiolaris rather than a separate species.

Many alpine species are under threat from global climate change, as their geographic ranges become increasingly fragmented and unsuitable. Understanding rates and determinants of gene flow among such fragmented populations, over historical as well as recent timescales, can help to identify populations under threat. It is also important to clarify the degree to which loss of local populations reduces overall genetic diversity within the taxon. The endangered Blue Mountains Water Skink (Eulamprus leuraensis) is restricted to < 40 small swamps in montane south-eastern Australia. Our analyses of seven microsatellite loci of 241 animals from 13 populations show strong geographic structure, with major genetic divergence even between populations separated by < 0.5 km. Dispersal between populations is scarce, and appears to involve mostly males. Our analyses suggest potential recent bottleneck events in all the identified populations, and lower genetic diversity and population size parameter at lower-elevation sites than at higher-elevation sites. Management of this endangered taxon thus needs to treat most populations separately, because of their genetic distinctiveness and low rates of genetic exchange.

Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n=256) and historical (n=99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96-80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddledon theminimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations.

The basidiomycetous fungus, Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen in Latin America causing sheath blight (SB) of rice Particularly in Venezuela. the fungus also Causes banded leaf and sheath blight (BLSB) oil maize, which is considered all emerging disease problem where maize replaced traditional rice-cropping areas or is now planted in adjacent. fields Our goals in this study Were 10 elucidate (i) the effects of host specialization on gene flow between sympatric and allopatric rice and maize-infecting fungal populations and (ii) the reproductive mode of the fungus, looking for evidence of recombination in total, 375 isolates of R. solani AG1 IA sampled from three sympatric rice and maize fields in Venezuela (Porutuguesa State) and two allopatric rice fields from Colombia (Meta State) and Panama (Chiriqui State) were genotyped Using, 10 microsatellite loci Allopatric populations from Venezuela. Colombia. and Panama were significantly differentiated (Phi(ST), of 0 16 to 0 34). Partitioning of the genetic diversity indicated differentiation between sympatric populations from different host species, with 17% of the total genetic variation distributed between hosts while only 3 to 6% wits distributed geographically among the sympatric Venezuelan Fields We detected symmetrical historical migration between the rice- and the maize-infecting populations from Venezuela Rice- and maize-derived isolates were able to infect built rice and maize but were more aggressive Oil their original hosts, consistent with host specialization. Because the maize- and rice-infecting populations are still cross-pathogenic, we postulate that the genetic differentiation was relatively recent and mediated via a host shift. An isolation with nu.-ration analysis indicated that the maize-infecting population diverged from the rice-infecting population between 40 and 240 years ago Our findings also suggest that maize-infecting Populations have a mainly recombining reproductive system whereas the rice-infecting Populations have a Mixed reproductive system in Latin America

When combined with haplotype fusion PCR (HF-PCR), ligation haplotyping is a robust, high-throughput method for empirical determination of haplotypes, which can be applied to assaying both sequence and structural variation over long distances. Unlike alternative approaches to haplotype determination, such as allele-specific PCR and long PCR, HF-PCR and ligation haplotyping do not suffer from mispriming or template-switching errors. In this method, HF-PCR is used to juxtapose DNA sequences from single-molecule templates, which contain single-nucleotide polymorphisms (SNPs) or paralogous sequence variants (PSVs) separated by several kilobases. HF-PCR uses an emulsion-based fusion PCR, which can be performed rapidly and in a 96-well format. Subsequently, a ligation-based assay is performed on the HF-PCR products to determine haplotypes. Products are resolved by capillary electrophoresis. Once optimized, the procedure can be performed quickly, taking a day and a half to generate phased haplotypes from genomic DNA.

The genetic population structure of the common branching vase sponge, Callyspongia vaginalis, was determined along the entire length (465 km) of the Florida reef system from Palm Beach to the Dry Tortugas based on sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Populations of C. vaginalis were highly structured (overall I broken vertical bar(ST) = 0.33), in some cases over distances as small as tens of kilometers. However, nonsignificant pairwise I broken vertical bar(ST) values were also found between a few relatively distant sampling sites suggesting that some long distance larval dispersal may occur via ocean currents or transport in sponge fragments along continuous, shallow coastlines. Indeed, sufficient gene flow appears to occur along the Florida reef tract to obscure a signal of isolation by distance, but not to homogenize COI haplotype frequencies. The strong genetic differentiation among most of the sampling locations suggests that recruitment in this species is largely local source-driven, pointing to the importance of further elucidating general connectivity patterns along the Florida reef tract to guide the spatial scale of management efforts.

We investigate the degree of between-population genetic differentiation in the Mediterranean field cricket Gryllus bimaculatus, as well as the possible causes of such differentiation. Using cytochrome b mtDNA sequences, we estimate genetic variation in G. bimaculatus from seven South African and two Mediterranean populations. Within-population genetic variation in Europe (two haplotypes, one unique to a single individual) suggest low effective population size and strong bottlenecks with associated founder effects, probably due to cold winter environments in Europe that limit reproduction to a short part of the summer. The likely cause for this is the daily maxima in winter temperatures that fall below the critical level of 16 degrees C (enabling normal calling and courtship behaviour in Mediterranean Europe, whereas the equivalent temperatures Southern Africa are above this limit and enable reproduction over a large part of the year. European genetic variants were either shared with Africa or closely related to African haplotypes. For survival, European populations are probably dependent on immigration from other areas, including Africa. South African populations have low but measurable gene flow with Europe and show significant between-population genetic differentiation (30 haplotypes). Isolation-by-distance is not sufficient to explain the degree of between-population genetic differences observed, and a large degree of dispersal is also required in order to account for the observed patterns. Differences in morphology and calling behaviour among these populations are underlied by these genetic differences.

The frog Leptodactylus validus occurs in northern South America, Trinidad and Tobago, and the southern Lesser Antilles (Grenada and St. Vincent). Mitochondrial DNA sequences were used to perform a nested clade phylogeographic analysis (NCPA), to date colonization events, and to analyze colonization patterns using on a relaxed molecular clock and coalescent simulations. L. validus originated on the mainland and first colonized Trinidad with subsequent independent colonizations of Tobago and the Lesser Antilles from Trinidad. The NCPA suggests a historical vicariant event between populations in Trinidad and Tobago from those in the Lesser Antilles. The colonization of Trinidad occurred similar to 1 million years ago (mya) and the colonization of the Lesser Antillean islands occurred similar to 0.4 mya. The coalescent approach supported the scenario where L. validus dispersed from Trinidad to St. Vincent and from there to Grenada, a dispersal event that could have been mediated by human introduction as recent as 1600 years ago. (C) 2009 Elsevier Inc. All rights reserved.

Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.

Although the sexual transfer of genetic material between species (i.e. introgression) has been documented in many groups of plants and animals, genome-wide patterns of introgression are poorly understood. Is most of the genome permeable to interspecific gene flow, or is introgression typically restricted to a handful of genomic regions? Here, we assess the genomic extent and direction of introgression between three sunflowers from the south-central USA: the common sunflower, Helianthus annuus ssp. annuus; a near-endemic to Texas, Helianthus debilis ssp. cucumerifolius; and their putative hybrid derivative, thought to have recently colonized Texas, H. annuus ssp. texanus. Analyses of variation at 88 genetically mapped microsatellite loci revealed that long-term migration rates were high, genome-wide and asymmetric, with higher migration rates from H. annuus texanus into the two parental taxa than vice versa. These results imply a longer history of intermittent contact between H. debilis and H. annuus than previously believed, and that H. annuus texanus may serve as a bridge for the transfer of alleles between its parental taxa. They also contradict recent theory suggesting that introgression should predominantly be in the direction of the colonizing species. As in previous studies of hybridizing sunflower species, regions of genetic differentiation appear small, whether estimated in terms of FST or unidirectional migration rates. Estimates of recent immigration and admixture were inconsistent, depending on the type of analysis. At the individual locus level, one marker showed striking asymmetry in migration rates, a pattern consistent with tight linkage to a Bateson-Dobzhansky-Muller incompatibility.

Methods developed over the past decade have made it possible to estimate molecular demographic parameters such as effective population size, divergence time, and gene flow with unprecedented accuracy and precision. However, they make simplifying assumptions about certain aspects of the species' histories and the nature of the genetic data, and it is not clear how robust they are to violations of these assumptions. Here, we use simulated data sets to examine the effects of a number of violations of the “Isolation with Migration” (IM) model, including intralocus recombination, population structure, gene flow from an unsampled species, linkage among loci, and divergent selection, on demographic parameter estimates made using the program IMA. We also examine the effect of having data that fit a nucleotide substitution model other than the two relatively simple models available in IMA. We find that IMA estimates are generally quite robust to small to moderate violations of the IM model assumptions, comparable with what is often encountered in real-world scenarios. In particular, population structure within species, a condition encountered to some degree in virtually all species, has little effect on parameter estimates even for fairly high levels of structure. Likewise, most parameter estimates are robust to significant levels of recombination when data sets are pared down to apparently nonrecombining blocks, although substantial bias is introduced to several estimates when the entire data set with recombination is included. In contrast, a poor fit to the nucleotide substitution model can result in an increased error rate, in some cases due to a predictable bias and in other cases due to an increase in variance in parameter estimates among data sets simulated under the same conditions.

Patterns of genetic variation of Albinaria caerulea, a land snail that was probably transported by humans to Vravrona (Attica, Greece), were analysed using the mitochondrial ATPase8 gene. The analysis of molecular variance indicated significant local differentiation at the subpopulation level. This considerable population subdivision and genetic differentiation in a short time is possibly related to life history and population structure of the species. The population structure and demographic history suggest a recent single colonization event, by a single or a few lineages, at the first site inhabited by humans in Vravrona (about 5,000 years before present). This was followed by population expansion and subsequent intra-colonization events (accompanied by bottlenecks) to more recently inhabited sites. The estimated small effective population size/census population size ratio further implies considerable population fluctuations. Bayesian inference and statistical parsimony analyses indicate that the population of Vravrona is associated with a species subgroup which includes populations found in the Cycladic islands of Sikinos, Folegandros and Thira; its source is probably related to certain samples from Sikinos.

In heterogeneous landscapes, divergent selection can favor the evolution of locally adapted ecotypes, especially when interhabitat gene flow is minimal. However, if habitats differ in size or quality, source-sink dynamics can shape evolutionary trajectories. Upland and bottomland forests of the southeastern USA differ in water table depth, light availability, edaphic conditions, and plant community. We conducted a multiyear reciprocal transplant experiment to test whether Elliott's blueberry (Vaccinium elliottii) is locally adapted to these contrasting environments. Additionally, we exposed seedlings and cuttings to prolonged drought and flooding in the greenhouse to assess fitness responses to abiotic stress. Contrary to predictions of local adaptation, V. elliottii families exhibited significantly higher survivorship and growth in upland than in bottomland forests and under drought than flooded conditions, regardless of habitat of origin. Neutral population differentiation was minimal, suggesting widespread interhabitat migration. Population density, reproductive output, and genetic diversity were all significantly greater in uplands than in bottomlands. These disparities likely result in asymmetric gene flow from uplands to bottomlands. Thus, adaptation to a marginal habitat can be constrained by small populations, limited fitness, and immigration from a benign habitat. Our study highlights the importance of demography and genetic diversity in the evolution of local (mal)adaptation.

We used demographic, spatial, and microsatellite data to assess fine-scale genetic structure in Ethiopian wolves found in the Bale Mountains and evaluated the impact of historical versus recent demographic processes on genetic variation. We applied several analytical methods, assuming equilibrium and nonequilibrium conditions, to assess demography and genetic structure. Genetic variation (H-E = 0.584-0.607, allelic richness = 4.2-4.3) was higher than previously reported for this species and genetic structure was influenced by geography and social structure. Statistically significant F-ST values (0.06-0.08) implied differentiation among subpopulations. STRUCTURE analyses showed that neighbouring packs often have shared coancestry and spatial autocorrelation showed higher genetic similarity between individuals within packs and between individuals in neighbouring packs compared to random pairs of individuals. Recent effective population sizes were lower than 2n (where n is the number of packs) and lower than the number of breeding individuals with Ne/N ratios near 0.20. All subpopulations have experienced bottlenecks, one occurring due to a rabies outbreak in 2003. Nevertheless, differentiation among these subpopulations is consistent with long-term migration rates and fragmentation at the end of the Pleistocene. Enhanced drift due to population bottlenecks may be countered by higher migration into disease-affected subpopulations. Contemporary factors such as social structure and population bottlenecks are clearly influencing the level and distribution of genetic variation in this population, which has implications for its conservation.

The Yarkand hare, Lepus yarkandensis, is an endemic, endangered species restricted to the Tarim Basin of the Xinjiang Uygur Autonomous Region, China. The Yarkand hare is distributed in scattered oases which are physically isolated by the desert. Its natural fragmentation habitat makes it an ideal object for studying effect of habitat fragmentation on its genetic structure. To evaluate the effects of habitat fragmentation on genetic diversity of the species, we assessed genetic diversity for 20 sampling populations based on control region and Cytb markers. Relatively low levels of gene diversity are found in most of isolated populations in the southern margin of the Taklamakan Desert. Furthermore, a positive correlation is found between gene diversity and the size of historical effective population. Significant genetic differentiation is detected among most populations by pairwise F-ST analyses, which is characterized by an isolation by distance pattern. Additionally, the AMOVA results show highly significant population structure among seven geographical groups. High migration rates are found among continuous populations, while very low levels of migration rates are found among the relatively isolated populations, suggesting that the desert may make an effective barrier against gene flow. Finally, the control region shows four clades by the phylogenetic analyses, three of which are present in nearly all sampling populations. The observed pattern of the lineage mixing, also shown by the Cytb data, may be caused by extensive gene flow among populations, and could be explained by possible demographical expansion of the Yarkand hare during the late Pleistocene interglacial period.

Sharp declines in population size, known as genetic bottlenecks, increase the level of inbreeding and reduce genetic diversity threatening population sustainability in both short- and long-term. We evaluated the presence, severity and approximate time of bottlenecks in 34 European grayling (Thymallus thymallus) populations covering the majority of the species distribution using microsatellite markers. We identified footprints of population decline in all grayling populations using the M ratio test. In contrast to earlier simulation studies assuming isolated populations, forward simulations allowing low levels of migration demonstrated that bottleneck footprints measured using the M ratio can persist within small populations much longer (up to thousands of generations) than previously anticipated. Using a coalescence approach, the beginning of population reduction was dated back to 1,000-10,000 years ago which suggests that the extremely low M ratio in European grayling is most likely caused by the last glaciation and subsequent post-glacial recolonization processes. In contrast to the M ratio, two alternative methods for bottleneck detection identified more recent bottlenecks in six populations and thus, from a conservation perspective, these populations warrant future monitoring. Based on a single time-point analysis using approximate Bayesian computation methodology, all grayling populations exhibited very small effective population sizes with the majority of Ne estimates below 50. Taken together, our results demonstrate the predominate role of genetic drift in European grayling populations in the short term but also emphasize the importance of gene flow counteracting the effects of genetic drift and loss of variation over longer evolutionary timescales.

Security infrastructure along international boundaries threatens to degrade connectivity for wildlife. To explore potential effects of a fence under construction along the U.S.-Mexico border on wildlife, we assessed movement behavior of two species with different life histories whose regional persistence may depend on transboundary movements. We used radiotelemetry to assess how vegetation and landscape structure affect flight and natal dispersal behaviors of Ferruginous Pygmy-Owls (Glaucidium brasilianum), and satellite telemetry, gene-flow estimates, and least-cost path models to assess movement behavior and interpopulation connectivity of desert bighorn sheep (Ovis canadensis mexicana). Flight height of Pygmy-Owls averaged only 1.4 m (SE 0.1) above ground, and only 23% of flights exceeded 4 m. Juvenile Pygmy-Owls dispersed at slower speeds, changed direction more, and had lower colonization success in landscapes with larger vegetation openings or higher levels of disturbance (p <= 0.047), which suggests large vegetation gaps coupled with tall fences may limit transboundary movements. Female bighorn sheep crossed valleys up to 4.9 km wide, and microsatellite analyses indicated relatively high levels of gene flow and migration (95% CI for F-ST = 0.010-0.115, Nm = 1.9-24.8, M = 10.4-15.4) between populations divided by an 11-km valley. Models of gene flow based on regional topography and movement barriers suggested that nine populations of bighorn sheep in northwestern Sonora are linked by dispersal with those in neighboring Arizona. Disruption of transboundary movement corridors by impermeable fencing would isolate some populations on the Arizona side. Connectivity for other species with similar movement abilities and spatial distributions may be affected by border development, yet mitigation strategies could address needs of wildlife and humans.

To explore the impact of history on selection and genetic structure at functional loci, we compared patterns of major histocompatibility complex (MHC) variability in two sympatric species of ctenomyid rodents with different demographic backgrounds. Although Ctenomys talarum has experienced a stable demographic history, Ctenomys australis has undergone a recent demographic expansion. Accordingly, we predicted that MHC allele frequency distributions should be more skewed, differences between coding and noncoding regions should be less pronounced, and evidence of current selection on MHC loci should be reduced in C. australis relative to C. talarum. To test these predictions, we compared variation at the MHC class II DRB and DQA genes with that at multiple neutral markers, including DQA intron 2, the mitochondrial control region, and 8-12 microsatellite loci. These analyses supported the first two of our predictions but indicated that estimates of selection (based on omega-values) were greater for C. australis. Further exploration of these data, however, revealed differences in the time frames over which selection appears to have acted on each species, with evidence of contemporary selection on MHC loci being limited to C. talarum. Collectively, these findings indicate that demographic history can substantially influence genetic structure at functional loci and that the effects of history on selection may be temporally complex and dynamic. (C) 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 260-277.

Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phylogeography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally conceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of “likelihood-free” approximate Bayesian methods should permit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the concurrent rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evolutionary biology. (C) 2009 Elsevier Inc. All rights reserved.

Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Pleistocene for the Qinghai-Tibetan (Tibetan) plateau, a region where glaciation was not synchronous with the North Hemisphere ice sheet maxima, remains poorly understood. Here, we compared the phylogeographical patterns of five avian species on the Qinghai-Tibetan plateau by three mitochondrial DNA fragments: the Tibetan snow finch (Montifringilla adamsi), the Blanford's snow finch (Pyrgilauda blanfordi), the horned lark (Eremophila alpestris), the twite (Carduelis flavirostris) and the black redstart (Phoenicurus ochruros). Our results revealed the three species mostly distributed on the platform region of the plateau that experienced population expansion following the retreat of the extensive glaciation period (0.5-0.175 Ma). These results are at odds with the results from avian species of Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023-0.018 Ma). A single refugium was identified in a restricted semi-continuous area around the eastern margin of the plateau, instead of multiple independent refugia for European and North American species. For the other two species distributed on the edges of the plateau (the twite and black redstart), populations were maintained at stable levels. Edge areas are located on the eastern margin, which might have had little or no ice cover during the glaciation period. Thus, milder climate may have mitigated demographic stresses for edge species relative to the extremes experienced by platform counterparts, the present-day ranges of which were heavily ice covered during the glaciation period. Finally, various behavioural and ecological characteristics, including dispersal capacities, habitat preference and altitude specificity along with evolutionary history might have helped to shape different phylogeographical structures appearing in these five species.

Premise of the study: Microsatellite primers were developed in the South African sclerophyllous shrub Protea punctata to investigate the degree of population differentiation within and between P. punctata and closely related species. Methods and Results: 10 primer pairs were identified from three individuals of Protea punctata. The primers amplified di-and tri-nucleotide repeats. Across all P. punctata samples, the loci have 8-49 alleles. All primers also amplified in Protea section Exsertae (P. aurea, P. aurea subsp. potbergensis, P. mundii, P. venusta, P. lacticolor, and P. subvestita). The loci had 14-69 alleles across the subgenus. Conclusions: These results show the broad utility of microsatellite loci for future studies of population genetics in the white proteas and their potential utility across the entire genus.

Molecular studies have demonstrated a deep lineage split between the two gorilla species, as well as divisions within these taxa; estimates place this divergence in the mid-Pleistocene, with gene flow continuing until approximately 80,000 years ago. Here, we present analyses of skeletal data indicating the presence of substantial recent gene flow among gorillas at all taxonomic levels: between populations, subspecies, and species. Complementary analyses of DNA sequence variation suggest that low-level migration occurred primarily in awesterly-to-easterly direction. In western gorillas, the locations of hybrid phenotypes map closely to expectations based on population refugia and riverine barrier hypotheses, supporting the presence of significant vicariance-driven structuring and occasional admixture within this taxon. In eastern lowland gorillas, the high frequency of hybrid phenotypes is surprising, suggesting that this region represents a zone of introgression between eastern gorillas and migrants from the west, and underscoring the conservation priority of this critically endangered group. These results highlight the complex nature of evolutionary divergence in this genus, indicate that historical gene flow has played a major role in structuring gorilla diversity, and demonstrate that our understanding of the evolutionary processes responsible for shaping biodiversity can benefit immensely from consideration of morphological and molecular data in conjunction.

Background: Sample size is one of the critical factors affecting the accuracy of the estimation of population genetic diversity parameters. Small sample sizes often lead to significant errors in determining the allelic richness, which is one of the most important and commonly used estimators of genetic diversity in populations. Correct estimation of allelic richness in natural populations is challenging since they often do not conform to model assumptions. Here, we introduce a simple and robust approach to estimate the genetic diversity in large natural populations based on the empirical data for finite sample sizes. Results: We developed a non-linear regression model to infer genetic diversity estimates in large natural populations from finite sample sizes. The allelic richness values predicted by our model were in good agreement with those observed in the simulated data sets and the true allelic richness observed in the source populations. The model has been validated using simulated population genetic data sets with different evolutionary scenarios implied in the simulated populations, as well as large microsatellite and allozyme experimental data sets for four conifer species with contrasting patterns of inherent genetic diversity and mating systems. Our model was a better predictor for allelic richness in natural populations than the widely-used Ewens sampling formula, coalescent approach, and rarefaction algorithm. Conclusions: Our regression model was capable of accurately estimating allelic richness in natural populations regardless of the species and marker system. This regression modeling approach is free from assumptions and can be widely used for population genetic and conservation applications.

Venturia inaequalis is an ascomycete fungus responsible for apple scab, a disease that has invaded almost all apple growing regions worldwide, with the corresponding adverse effects on apple production. Monitoring and predicting the effectiveness of intervention strategies require knowledge of the origin, introduction pathways, and population biology of pathogen populations. Analysis of the variation of genetic markers using the inferential framework of population genetics offers the potential to retrieve this information. Methodology/Principal Findings. Here, we present a population genetic analysis of microsatellite variation in 1,273 strains of V. inaequalis representing 28 orchard samples from seven regions in five continents. Analysis of molecular variance revealed that most of the variation (88%) was distributed within localities, which is consistent with extensive historical migrations of the fungus among and within regions. Despite this shallow population structure, clustering analyses partitioned the data set into separate groups corresponding roughly to geography, indicating that each region hosts a distinct population of the fungus. Comparison of the levels of variability among populations, along with coalescent analyses of migration models and estimates of genetic distances, was consistent with a scenario in which the fungus emerged in Central Asia, where apple was domesticated, before its introduction into Europe and, more recently, into other continents with the expansion of apple growing. Across the novel range, levels of variability pointed to multiple introductions and all populations displayed signatures of significant post-introduction increases in population size. Most populations exhibited high genotypic diversity and random association of alleles across loci, indicating recombination both in native and introduced areas. Conclusions/Significance. Venturia inaequalis is a model of invasive phytopathogenic fungus that has now reached the ultimate stage of the invasion process with a broad geographic distribution and well-established populations displaying high genetic variability, regular sexual reproduction, and demographic expansion.

Natural populations of known detailed past demographic history are extremely valuable to evaluate methods of historical inference, yet are extremely rare. As an alternative approach, we have generated multiple replicate microsatellite data sets from laboratory-cultured populations of a gonochoric free-living nematode, Caenorhabditis remanei, that were constrained to pre-defined demographic histories featuring different levels of migration among populations or bottleneck events of different magnitudes. These data sets were then used to evaluate the performances of two recently developed population genetics methods, BAYESASS+, that estimates recent migration rates among populations, and BOTTLENECK, that detects the occurrence of recent bottlenecks. Migration rates inferred by BAYESASS+ were generally over-estimates, although these were often included within the confidence interval. Analyses of data sets simulated in-silico, using a model mimicking the laboratory experiments, produced less biased estimates of the migration rates, and showed increased efficiency of the program when the number of loci and sampled genotypes per population was higher. In the replicates for which the prebottleneck laboratory-cultured populations did not significantly depart from a mutation/drift equilibrium, an important assumption of the program BOTTLENECK, only a portion of the bottleneck events were detected. This result was confirmed by in-silico simulations mirroring the laboratory bottleneck experiments. More generally, our study demonstrates the feasibility, and highlights some of the limits, of the approach that consists in generating molecular genetic data sets by controlling the evolution of laboratory-reared nematode populations, for the purpose of validating methods inferring population history.

Background: Female-biased dispersal (FBD) is predicted to occur in monogamous species due to local resource competition among females, but evidence for this association in mammals is scarce. The predicted relationship between FBD and monogamy may also be too simplistic, given that many pair-living mammals exhibit substantial extra-pair paternity. Methodology/Principal Findings: I examined whether dispersal and gene flow are female-biased in the large treeshrew (Tupaia tana) in Borneo, a behaviorally monogamous species with a genetic mating system characterized by high rates (50%) of extra-pair paternity. Genetic analyses provided evidence of FBD in this species. As predicted for FBD, I found lower mean values for the corrected assignment index for adult females than for males using seven microsatellite loci, indicating that female individuals were more likely to be immigrants. Adult female pairs were also less related than adult male pairs. Furthermore, comparison of Bayesian coalescent-based estimates of migration rates using maternally and bi-parentally inherited genetic markers suggested that gene flow is female-biased in T. tana. The effective number of migrants between populations estimated from mitochondrial DNA sequence was three times higher than the number estimated using autosomal microsatellites. Conclusions/Significance: These results provide the first evidence of FBD in a behaviorally monogamous species without mating fidelity. I argue that competition among females for feeding territories creates a sexual asymmetry in the costs and benefits of dispersal in treeshrews.

Background: The harpy eagle (Harpia harpyja) is the largest Neotropical bird of prey and is threatened by human persecution and habitat loss and fragmentation. Current conservation strategies include local education, captive rearing and reintroduction, and protection or creation of trans-national habitat blocks and corridors. Baseline genetic data prior to reintroduction of captive-bred stock is essential for guiding such efforts but has not been gathered previously. Methodology/Findings: We assessed levels of genetic diversity, population structure and demographic history for harpy eagles using samples collected throughout a large portion of their geographic distribution in Central America (n = 32) and South America (n = 31). Based on 417 bp of mitochondrial control region sequence data, relatively high levels of haplotype and nucleotide diversity were estimated for both Central and South America, although haplotype diversity was significantly higher for South America. Historical restriction of gene flow across the Andes (i.e. between our Central and South American subgroups) is supported by coalescent analyses, the haplotype network and significant F-ST values, however reciprocally monophyletic lineages do not correspond to geographical locations in maximum likelihood analyses. A sudden population expansion for South America is indicated by a mismatch distribution analysis, and further supported by significant (p<0.05) negative values of Fu and Li's D-F and F, and Fu's F-S. This expansion, estimated at approximately 60 000 years BP (99 000-36 000 years BP 95% CI), encompasses a transition from a warm and dry time period prior to 50 000 years BP to an interval of maximum precipitation (50 000-36 000 years BP). Notably, this time period precedes the climatic and habitat changes associated with the last glacial maximum. In contrast, a multimodal distribution of haplotypes was observed for Central America suggesting either population equilibrium or a recent decline. Significance: High levels of mitochondrial genetic diversity in combination with genetic differentiation among subgroups within regions and between regions highlight the importance of local population conservation in order to preserve maximal levels of genetic diversity in this species. Evidence of historically restricted female-mediated gene flow is an important consideration for captive-breeding programs.

Broad scale patterns of genetic structure in coastal communities are strongly affected by both ecological transitions and larval dispersal. Along the Chilean coast, we examined 2 species of co-distributed barnacles, Jehlius cirratus and Notochthamalus scabrosus, which span an ecological transition associated with a sharp increase in larval recruitment. A distinct break in haplotype frequencies in the mitochondrial cytochrome oxidase I (mtCOI) gene was detected in N. scabrosus, with only marginal genetic structure observed in J. cirratus, suggesting significant differences in either selective pressures or dispersal ability between the species. The nuclear gene elongation factor la was also analyzed in N. scabrosus, and similarly suggested limited gene flow. The sharp genetic transition is downstream of the described ecological transition, effectively mirroring a genetic cline described in a different barnacle species along the North American Pacific coast.

Species delimitation and species tree inference are difficult problems in cases of recent divergence, especially when different loci have different histories. This paper quantifies the difficulty of jointly finding the division of samples to species and estimating a species tree without constraining the possible assignments a priori. It introduces a parametric and a nonparametric method, including new heuristic search strategies, to do this delimitation and tree inference using individual gene trees as input. The new methods were evaluated using thousands of simulations and 4 empirical data sets. These analyses suggest that the new methods, especially the nonparametric one, may provide useful insights for systematists working at the species level with molecular data. However, they still often return incorrect results.

We compared morphology and sequenced nuclear and mitochondrial genes from 11 populations of a previously genetically unstudied “Baja California disjunct” species, the diamond turbot (Hypsopsetta guttulata). This species exhibits very limited adult movement and restriction to soft-bottom habitats but has a moderately long pelagic larval duration. Therefore, if pelagic larval duration is correlated with gene flow between Gulf of California and Pacific populations, we expect a reduced level of genetic and morphological differentiation. However, if adult habitat and ecology have more effect on gene flow, we expect the populations in the two bodies of water to be more highly differentiated. We used logistic regression to compare morphological features and phylogenetic and population genetic analyses to compare nucleotide sequence data. Gulf of California H. guttulata are different from Pacific populations in morphology and both mitochondrial and nuclear gene sequences. MtDNA shows reciprocal monophyly, and nuclear sequences from the Gulf of California formed a monophyletic group. Population genetic analyses also suggest further population subdivision within the Pacific and within the Gulf of California. We argue that adult ecology has a significant effect on migration rates among populations in the Pacific Ocean and the Gulf of California.

The marine environment provides an opportunity to examine population structure in species with high dispersal capabilities and often no obvious barriers to genetic exchange. In coastal waters of the western North Atlantic, common bottlenose dolphins, Tursiops truncatus, are a highly mobile species with a continuous distribution from New York to Florida. We examine if the highly mobile nature coupled with no obvious geographic barriers to movement in this region result in a large panmictic population. Mitochondrial control region sequences and 18 microsatellite loci indicate dolphins are partitioning the habitat both latitudinally and longitudinally. A minimum of five genetically differentiated populations were identified among 404 samples collected in the range of New Jersey to northern Florida using both genetic marker types, some inhabiting nearshore coastal waters and others utilizing inshore estuarine waters. The genetic results reject the hypothesis of a single stock of coastal bottlenose dolphins put forth after the 1987-1988 epizootic that caused a large-scale die-off of dolphins and suggest instead the disease vector was transferred from one population to the next as a result of seasonal migratory movements of some populations. These coastal Atlantic populations also differ significantly from bottlenose dolphin samples collected in coastal waters of the northern Gulf of Mexico, implying a long-term barrier to movement between the two basins.

The dispersal process, by which individuals or other dispersing agents such as gametes or seeds move from birthplace to a new settlement locality, has important consequences for the dynamics of genes, individuals, and species. Many of the questions addressed by ecology and evolutionary biology require a good understanding of species' dispersal patterns. Much effort has thus been devoted to overcoming the difficulties associated with dispersal measurement. In this context, genetic tools have long been the focus of intensive research, providing a great variety of potential solutions to measuring dispersal. This methodological diversity is reviewed here to help (molecular) ecologists find their way toward dispersal inference and interpretation and to stimulate further developments.

Although range expansions have Occurred recurrently in the history of most species, their genetic consequences have been little investigated. Theoretical studies show that range expansions are quite different from pure demographic expansions and that the extent of recent gene flow conditions expected patterns of molecular diversity within and between populations. Spatially explicit simulation studies have led to unexpected and fascinating results about genetic patterns emerging after a range expansion. For instance, spatial expansions can generate allele frequency gradients, promote the surfing of rare variants into newly occupied territories, induce the structuring of newly colonized areas into distinct sectors of low genetic diversity, or lead to massive introgression of local genes into the genome of an invading species. Interestingly, most of these patterns had been previously attributed to distinct selective processes, showing that taking into account the dynamic nature of a species range can lead to a paradigm shift in our perception of evolutionary processes.

We studied 1616 bp of mtDNA sequence in plateau pika Ochotona curzoniae sampled from 10 geographical regional groups to study the population history as well as long-term gene flow of O. curzoniae. We detected 153 haplotypes in 245 individuals. Mismatch analyses detected rapid population expansion in nine regional groups. Long-term estimates of gene flow revealed a unidirectional manner from peripheral groups towards central plateau groups. In contrast, gene flow among central plateau groups was bidirectional. Our results indicate that the population expansion of most groups occurred 0.24-0.03 Mya, which mostly coincides with the interglacial period before the last glacial maximum. Gene flow of O. curzoniae was closely related to the different effects of the extensive glacial period (EGP) and the last glacial period (LGP) on the species. The EGP had caused extinction of all central populations, while the LGP had very limited influence on the populations that recolonized the central region. However, the glaciers in the relatively humid areas surrounding the interior of the plateau during the LGP were substantial and had prevented or greatly reduced the `counter' gene flow from the central populations to the edge populations, resulting in a unidirectional gene flow. A hierarchical analysis of molecular variance showed that 55.1% of the total variance was explained by among-groups structuring while 34.2% was explained by the differences among individuals within populations. Compared with other endemic species on the Qinghai-Tibetan Plateau, O. curzoniae has a moderate level of the population genetic structure, which is higher than birds and lower than lizard, due to its limited dispersal ability.

Genetic diversity population structure, average long-term effective population size (N-e), and average long-term genetic migration rate of red drum Sciaenops ocellatus in each of four Texas bays were assessed using variation in 13 nuclear-encoded microsatellites among samples front the 2004 and 2005 cohorts. No significant differences in genetic diversity were detected among bays. Levels of gene diversity of red drum in each bay were equal to or greater than estimates reported for microsatellites in red drum sampled previously from two of the four bays and from other bays in the southeastern USA. including some that had not yet been Supplemented with hatchery-raised fish. Tests of the homogeneity of allele and genotype distributions (including analysis of molecular variance) among the four bays were nonsignificant. Estimates of the migration rate (m) between bays ranged front 0.08% to 0.15%, with the average long-term number of migrants (calculated as N-e X m) between bays estimated to range from 1.04 to 2.37 fish/generation. Estimates of average long-term N-e in the four bays ranged from 1,302 to 1,581 fish and collectively were well within the range hypothesized to support sustained, long-term persistence. The estimates of N-e also were, on average, five to six times higher than comparable estimates reported for the 1986-1989 red drum cohorts sampled from seven bays across the northern Gulf of Mexico. Adjustment of long-term N-e in each of the four bays relative to bay-specific spatial parameters revealed a positive relationship with red drum abundance as measured by catch-per-unit-effort statistics compiled by the Texas Parks and Wildlife Department between 1982 and 2005. The observed high levels of genetic diversity, estimates of average long-term N-e, and increased N-e over the past 15-20 years are consistent with the hypothesis that the Texas Parks and Wildlife Department's stock enhancement program has not genetically compromised the resident red drum subpopulations in the four bays.

The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls.

Patiria miniata, a broadcast-spawning sea star species with high dispersal potential, has a geographic range in the intertidal zone of the northeast Pacific Ocean from Alaska to California that is characterized by a large range gap in Washington and Oregon. We analyzed spatial genetic variation across the P. miniata range using multilocus sequence data (mtDNA, nuclear introns) and multilocus genotype data (microsatellites). We found a strong phylogeographic break at Queen Charlotte Sound in British Columbia that was not in the location predicted by the geographical distribution of the populations. However, this population genetic discontinuity does correspond to previously described phylogeographic breaks in other species. Northern populations from Alaska and Haida Gwaii were strongly differentiated from all southern populations from Vancouver Island and California. Populations from Vancouver Island and California were undifferentiated with evidence of high gene flow or very recent separation across the range disjunction between them. The surprising and discordant spatial distribution of populations and alleles suggests that historical vicariance (possibly caused by glaciations) and contemporary dispersal barriers (possibly caused by oceanographic conditions) both shape population genetic structure in this species.

Gag (Mycteroperca microlepis) from the eastern Gulf of Mexico and northwestern Atlantic are managed as separate stocks, although evidence for their demographic isolation remains equivocal. Several hundred individuals were genotyped at 11 microsatellite loci and it wits found that gag across these regions were genetically indistinguishable (F-ST < 0.001). A coalescent-based computer Simulation was employed to quantitatively assess the relative importance of dispersal rate. population size, and time since divergence on gag genetic homogeneity. Using empirical estimates of long-term effective Population size (16500), it range of dispersal rates and divergence times (500 to 500000 generations) wits modeled, and it was concluded that present-clay genetic homogeneity must be maintained by dispersal rates of at least 20-30 migrants per generation and up to hundreds or thousands per generation. This Study also documents the absence of significant temporal genetic structure and inbreeding in the Atlantic when comparing cohorts separated in time from weeks to 20 years. This suggests that the long-standing practice of overfishing gag has yet to manifest as in inbreeding effect. Overall, gag dispersal rates remain uncertain, and consequently, this Study can neither Support nor refute management schemes that independently regulate gag in the eastern Gulf of Mexico and northwestern Atlantic.

A total of 669 isolates of Phytophthora ramorum, the pathogen responsible for Sudden Oak Death, were collected from 34 Californian forests and from the ornamental plant-trade. Seven microsatellite markers revealed 82 multilocus genotypes (MGs) of which only three were abundant (> 10%). Iteratively collapsing based upon minimum Theta(ST), yielded five meta-samples and five singleton populations. Populations in the same meta-sample were geographically contiguous, with one exception, possibly explained by the trade of infected plants from the same source into different locations. Multidimensional scaling corroborated this clustering and identified nursery populations as genetically most distant from the most recent outbreaks. A minimum-spanning network illustrated the evolutionary relationships among MGs, with common genotypes at the centre and singletons at the extremities; consistent with colonization by a few common genotypes followed by local evolution. Coalescent migration analyses used the original data set and a data set in which local genotypes were collapsed into common ancestral genotypes. Both analyses suggested that meta-samples 1 (Santa Cruz County) and 3 (Sonoma and Marin Counties), act as sources for most of the other forests. The untransformed data set best explains the first phases of the invasion, when the role of novel genotypes may have been minimal, whereas the second analysis best explains migration patterns in later phases of the invasion, when prevalence of novel genotypes was likely to have become more significant. Using this combined approach, we discuss possible migration routes based on our analyses, and compare them to historical and field observations from several case studies.

The comparative genetic structure of hosts and their parasites has important implications for their coevolution, but has been investigated in relatively few systems. In this study, we analysed the genetic structure and diversity of the New Zealand intertidal snail Zeacumantus subcarinatus (n = 330) and two of its trematode parasites, Maritrema novaezealandensis (n = 269) and Philophthalmus sp. (n = 246), using cytochrome c oxidase subunit I gene (COI) sequences. Snails and trematodes were examined from 11 collection sites representing three regions on the South Island of New Zealand. Zeacumantus subcarinatus displayed low genetic diversity per geographic locality, strong genetic structure following an isolation by distance pattern, and low migration rates at the scale of the study. In contrast, M. novaezealandensis possessed high genetic diversity, genetic homogeneity among collection sites and high migration rates. Genetic diversity and migration rates were typically lower for Philophthalmus sp. compared to M. novaezealandensis and it displayed weak to moderate genetic structure. The observed patterns likely result from the limited dispersal ability of the direct developing snail and the utilization of bird definitive hosts by the trematodes. In addition, snails may occasionally experience long-distance dispersal. Discrepancies between trematode species may result from differences in their effective population sizes and/or life history traits.

Genome assemblies are now available for nine primate species, and large-scale sequencing projects are underway or approved for six others. An explicitly evolutionary and phylogenetic approach to comparative genomics, called phylogenomics, will be essential in unlocking the valuable information about evolutionary history and genomic function that is contained within these genomes. However, most phylogenomic analyses so far have ignored the effects of variation in ancestral populations on patterns of sequence divergence. These effects can be pronounced in the primates, owing to large ancestral effective population sizes relative to the intervals between speciation events. In particular, local genealogies can vary considerably across loci, which can produce biases and diminished power in many phylogenomic analyses of interest, including phylogeny reconstruction, the identification of functional elements, and the detection of natural selection. At the same time, this variation in genealogies can be exploited to gain insight into the nature of ancestral populations. In this Perspective, I explore this area of intersection between phylogenetics and population genetics, and its implications for primate phylogenomics. I begin by “lifting the hood” on the conventional tree-like representation of the phylogenetic relationships between species, to expose the population-genetic processes that operate along its branches. Next, I briefly review an emerging literature that makes use of the complex relationships among coalescence, recombination, and speciation to produce inferences about evolutionary histories, ancestral populations, and natural selection. Finally, I discuss remaining challenges and future prospects at this nexus of phylogenetics, population genetics, and genomics.

The spatial scale of dispersal in coral reef fishes eludes ecologists despite the importance of this parameter for understanding the dynamics of ecological and evolutionary processes. Genetic isolation by distance (IBD) has been used to estimate dispersal in coral reef fishes, but its application in marine systems has been limited by insufficient sampling at different spatial scales and a lack of information regarding population density. Here, we present an analysis of IBD in the barred hamlet (Hypoplectrus puella, Serranidae) at spatial scales ranging from 10 to 3200 km complemented with SCUBA surveys of population densities covering 94 000 m(2) of reef. We used 10 hypervariable DNA markers to genotype 854 fish from 15 locations, and our results establish that IBD in H. puella emerges at a spatial scale of 175 km and is preserved up to the regional scale (3200 km). Assuming a normal or a Laplace dispersal function, our data are consistent with mean dispersal distances in H. puella that range between 2 and 14 km. Such small mean dispersal distances is a surprising result given the three-week pelagic larval duration of H. puella and the low level of genetic structure at the Caribbean scale (Wright's fixation index, F-ST, estimate = 0.005). Our data reinforce the importance of considering population density when estimating dispersal from IBD and underscore the relevance of sampling at local scales, even when genetic structure is weak at the regional scale.

Human mediated biological invasions are seen as an increasing danger for biodiversity. On the other hand, range expansions are natural processes. It is often practically not possible to tell these processes apart, like in the case of the freshwater crab Potamon fluviatile. This species has a disjunct distribution on the Balkan Peninsula, Italy, Sicily and Malta. An innovative analysis framework involving phylogeographic model selection and temporal coalescent analyses on a mitochondrial dataset (COI and NADH1) could clarify that the origin of the species was on the Balkans and the colonisation of Italy proceeded from the northern Balkans via southern Italy in the Otranto Strait region. The population expansion associated with this invasion was estimated to have taken place 15,000 years before present (95% c.f. 10,000-24,000 years BP). An anthropogenic introduction is therefore implausible and a natural expansion likely. We argue that the species should thus be included in the national conservation management in Italy.

Data on genetic structure of corals living in the Mediterranean Sea are very scarce. Leptopsammia pruvoti Lacaze-Duthiers, 1897, is a gonochoric and brooding solitary coral that colonizes shaded rocky habitats. It is very abundant under overhangs, in caverns, and in small crevices, with typical densities of thousands of polyps per square meter. In the present study, a hierarchical survey of spatial models of genetic structure and potential gene flow was conducted within and among seven shallow water Mediterranean populations, which ranged from 2 to 872 km apart. Within each population, polyps were randomly collected from three patches 5 m apart. Seven allozyme loci indicated a genetic structure characterized by (1) a marked departure from Hardy-Weinberg equilibrium, with a considerable deficit of heterozygotes; (2) most genetic differentiation occurring between patches within populations (F-ST = 0.118 to 0.206), rather than among distant populations (F-ST = 0.052); and (3) no significant correlation between genetic differentiation and geographic distance. Localized recruitment with consequent biparental inbreeding or Wahlund effect, associated with a proportion of larvae that undergo long-distance dispersal, could explain the observed pattern of genetic structure.

Estimating dispersal distances from population genetic data provides an important alternative to logistically taxing methods for directly observing dispersal. Although methods for estimating dispersal rates between a modest number of discrete demes are well developed, methods of inference applicable to “isolation-by-distance” models are much less established. Here, we present a method for estimating rho sigma(2), the product of population density (rho) and the variance of the dispersal displacement distribution (sigma(2)). The method is based on the assumption that low-frequency alleles are identical by descent. Hence, the extent of geographic clustering of such alleles, relative to their frequency in the population, provides information about rho sigma(2). We show that a novel likelihood-based method can infer this composite parameter with a modest bias in a lattice model of isolation-by-distance. For calculating the likelihood, we use an importance sampling approach to average over the unobserved intraallelic genealogies, where the intraallelic genealogies are modeled as a pure birth process. The approach also leads to a likelihood-ratio test of isotropy of dispersal, that is, whether dispersal distances on two axes are different. We test the performance of our methods using simulations of new mutations in a lattice model and illustrate its use with a dataset from Arabidopsis thaliana.

Recently introduced, exotic plant pathogens may exhibit low genetic diversity and be limited to clonal reproduction. However, rapidly mutating molecular markers such as microsatellites can reveal genetic variation within these populations and be used to model putative migration patterns. Phytophthora ramorum is the exotic pathogen, discovered in the late 1990s, that is responsible for sudden oak death in California forests and ramorum blight of common ornamentals. The nursery trade has moved this pathogen from source populations on the West Coast to locations across the United States, thus risking introduction to other native forests. We examined the genetic diversity of P. ramorum in United States nurseries by microsatellite genotyping 279 isolates collected from 19 states between 2004 and 2007. Of the three known P. ramorum clonal lineages, the most common and genetically diverse lineage in the sample was NA1. Two eastward migration pathways were revealed in the clustering of NA1 isolates into two groups, one containing isolates from Connecticut, Oregon, and Washington and the other isolates from California and the remaining states. This finding is consistent with trace forward analyses conducted by the US Department of Agriculture's Animal and Plant Health Inspection Service. At the same time, genetic diversities in several states equaled those observed in California, Oregon, and Washington and two-thirds of multilocus genotypes exhibited limited geographic distributions, indicating that mutation was common during or subsequent to migration. Together, these data suggest that migration, rapid mutation, and genetic drift all play a role in structuring the genetic diversity of P. ramorum in US nurseries. This work demonstrates that fast-evolving genetic markers can be used to examine the evolutionary processes acting on recently introduced pathogens and to infer their putative migration patterns, thus showing promise for the application of forensics to plant pathogens.

Documentation of spatial genetic discordance among breeding populations of Arctic-nesting avian species is important, because anthropogenic change is altering environmental linkages at micro- and macrogeographic scales. We estimated levels of population subdivision within Pacific Common Eiders (Somateria mollissima v-nigrum) breeding on 12 barrier islands in the western Beaufort Sea, Alaska, using molecular markers and capture-mark-recapture (CMR) data. Common Eider populations were genetically structured on a microgeographic scale. Regional comparisons between populations breeding on island groups separated by 90 km (Mikkelsen Bay and Simpson Lagoon) revealed structuring at 1.4 microsatellite loci (F-ST = 0.004, P < 0.01), a nuclear intron (F-ST = 0.022, P = 0.02), and mitochondrial DNA (Phi(ST) = 0.082, P < 0.05). The CMR data (n = 34) did not indicate female dispersal between island groups. Concordance between genetic and CMR data indicates that females breeding in the western Beaufort Sea are strongly philopatric to island groups rather than to a particular island. Despite the apparent high site fidelity of females, coalescence-based models of gene flow suggest that asymmetrical western dispersal occurs between island groups and is likely mediated by Mikkelsen Bay females stopping early on spring migration at Simpson Lagoon to breed. Alternatively, late-arriving females may be predisposed to nest in Simpson Lagoon because of the greater availability and wider distribution of nesting habitat. Our results indicate that genetic discontinuities, mediated by female philopatry, can exist at microgeographic scales along established migratory corridors. Received 31 October 2008, accepted 3 May 2009.

Schizothorax o'connori is endemic to the Yarlung Tsangpo River on the Tibetan Plateau. We assessed the relative impacts of historical and contemporary factors in organizing genetic variation in S. o'connori populations using mitochondrial cytochrome b sequences. We analyzed 191 samples from 11 populations and identified 78 haplotypes. The phylogenetic analyses and analysis of molecular variance all supported the same conclusions of two well-differentiated east-west phylogroups, separated by the Tsangpo Great Gorge. The split between the two clades accounted for 58% of the genetic variance observed among the examined samples. Waterfalls as effective barriers played an important role in shaping the phylogeographical structure of this species. Analyses of migration rates revealed that upstream dispersal was limited crossing waterfalls. Our study revealed substantial spatial and temporal variation in the influence of landscape features on contemporary patterns of genetic structure in S. o'connori. Interglacial range expansions clearly left their mark on contemporary populations above the Tsangpo Great Gorge.

Using Pectinaria koreni as a biological model of larval dispersal, we coupled the analysis of differently evolving genetic markers (mitochondrial cytochrome oxidase I and four microsatellite loci) to hydrodynamic modeling of larval transport in the English Channel. To determine the influence of historical and contemporary processes on the genetic structure of our study populations, genetic relationships between English Channel, Irish Sea, and southern North Sea populations were assessed in relation to the long-term pattern of marine currents and to postglacial colonization pathways. Although significant, low level of overall nuclear genetic differentiation was best explained by the recent origin of populations within the study area and the retention of ancestral polymorphism. Both genetic data sets suggest that two ancestral gene pools contributed to the origin of our study populations, and secondary contacts occurred in the English Channel and southern North Sea as a result of two migration routes around the British Isles. Although Irish Sea and Belgium populations appeared more recently connected, populations of the eastern English Channel were more isolated. English Channel patterns of connectivity indicated high dispersal and gene flow along the French coast, from Normandy to the southern North Sea. Despite significant genetic differentiation between both coasts, migration model selection favored cross-channel gene flow and long-distance migration following the coastlines. Our results highlight the influence of postglacial colonization on genetic patterns in the English Channel, and indicate that contemporary mesoscale connectivity inferred by hydrodynamic modeling cannot, alone, explain the present genetic structure of populations in this area.

Background: The population mutation rate (theta) remains one of the most fundamental parameters in genetics, ecology, and evolutionary biology. However, its accurate estimation can be seriously compromised when working with error prone data such as expressed sequence tags, low coverage draft sequences, and other such unfinished products. This study is premised on the simple idea that a random sequence error due to a chance accident during data collection or recording will be distributed within a population dataset as a singleton (i.e., as a polymorphic site where one sampled sequence exhibits a unique base relative to the common nucleotide of the others). Thus, one can avoid these random errors by ignoring the singletons within a dataset. Results: This strategy is implemented under an infinite sites model that focuses on only the internal branches of the sample genealogy where a shared polymorphism can arise (i.e., a variable site where each alternative base is represented by at least two sequences). This approach is first used to derive independently the same new Watterson and Tajima estimators of theta, as recently reported by Achaz [1] for error prone sequences. It is then used to modify the recent, full, maximum-likelihood model of Knudsen and Miyamoto [2], which incorporates various factors for experimental error and design with those for coalescence and mutation. These new methods are all accurate and fast according to evolutionary simulations and analyses of a real complex population dataset for the California seahare. Conclusion: In light of these results, we recommend the use of these three new methods for the determination of theta from error prone sequences. In particular, we advocate the new maximum likelihood model as a starting point for the further development of more complex coalescent/mutation models that also account for experimental error and design.

Wildlife on isolated oceanic islands is highly susceptible to the introduction of pathogens. The recent establishment in the Galapagos Islands of the mosquito Culex quinquefasciatus, a vector for diseases such as avian malaria and West Nile fever, is considered a serious risk factor for the archipelago's endemic fauna. Here we present evidence from the monitoring of aeroplanes and genetic analysis that C. quinquefasciatus is regularly introduced via aircraft into the Galapagos Archipelago. Genetic population structure and admixture analysis demonstrates that these mosquitoes breed with, and integrate successfully into, already-established populations of C. quinquefasciatus in the Galapagos, and that there is ongoing movement of mosquitoes between islands. Tourist cruise boats and inter-island boat services are the most likely mechanism for transporting Culex mosquitoes between islands. Such anthropogenic mosquito movements increase the risk of the introduction of mosquito-borne diseases novel to Galapagos and their subsequent widespread dissemination across the archipelago. Failure to implement and maintain measures to prevent the human-assisted transport of mosquitoes to and among the islands could have catastrophic consequences for the endemic wildlife of Galapagos.

A major goal in evolutionary biology is to understand how and why populations differentiate, both genetically and phenotypically, as they invade a novel habitat. A classical example of adaptation is the pale colour of beach mice, relative to their dark mainland ancestors, which colonized the isolated sandy dunes and barrier islands on Florida's Gulf Coast. However, much less is known about differentiation among the Gulf Coast beach mice, which comprise five subspecies linearly arrayed on Florida's shoreline. Here, we test the role of selection in maintaining variation among these beach mouse subspecies at multiple levels-phenotype, genotype and the environments they inhabit. While all beach subspecies have light pelage, they differ significantly in colour pattern. These subspecies are also genetically distinct: pair-wise F-ST-values range from 0.23 to 0.63 and levels of gene flow are low. However, we did not find a correlation between phenotypic and genetic distance. Instead, we find a significant association between the average `lightness' of each subspecies and the brightness of the substrate it inhabits: the two most genetically divergent subspecies occupy the most similar habitats and have converged on phenotype, whereas the most genetically similar subspecies occupy the most different environments and have divergent phenotypes. Moreover, allelic variation at the pigmentation gene, Mc1r, is statistically correlated with these colour differences but not with variation at other genetic loci. Together, these results suggest that natural selection for camouflage-via changes in Mc1r allele frequency-contributes to pigment differentiation among beach mouse subspecies.

One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to determine if phylogeographical breaks in this species were congruent with previously defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we might find four clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographical regions. We generated DNA sequence data (mitochondrial cytochrome b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analysed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow and effective population size. Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographical community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not predicted by community province boundaries.

After migrant chromosomes enter a population, they are progressively sliced into smaller pieces by recombination. Therefore, the length distribution of “migrant tracts” (chromosome segments with recent migrant ancestry) contains information about historical patterns of migration. Here we introduce a theoretical framework describing the migrant tract length distribution and propose a likelihood inference method to test demographic hypotheses and estimate parameters related to a historical change in migration rate. Applying this method to data from the hybridizing subspecies Mus musculus domesticus and M. m. musculus, we find evidence for an increase in the rate of hybridization. Our findings could indicate all evolutionary trajectory toward fusion rather than speciation in these taxa.

In recentyears approximate Bayesian computation (ABC) methods have become popular in population genetics as an alternative to full-likelihood methods to make inferences under complex demographic models. Most ABC methods rely on the choice of a set of summary statistics to extract information from the data. In this article we tested the use of the full allelic distribution directly in an ABC framework. Although the ABC techniques are becoming more widely used, there is still uncertainty over how they perform in comparison with full-likelihood methods. We thus conducted a simulation Study and provide a detailed examination of ABC in comparison with kill likelihood in the case of a model of admixture. This model assumes that two parental populations mixed at a certain time in the past, creating a hybrid population, and that the three populations then evolve under pure drift. Several aspects of ABC methodology, were investigated, such as the effect of the distance metric chosen to measure the similarity between simulated and observed data sets. Results show that in general ABC provides good approximations to the posterior distributions obtained with the full-likelihood method. This suggests that it is possible to apply ABC using allele frequencies to make inferences in cases where it is difficult to select a set of suitable summary statistics and when the complexity of the model or the size of the data set makes it computationally prohibitive to use full-likelihood methods.

In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu-speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu-speaking populations. Moreover, by comparing our data with those from other Niger-Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub-Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu-speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu-speaking populations, but also between Bantu and non-Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu-speakers, with strong interactions between the different lines of Bantu-speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages. Am J Phys Anthropol 140:302-311, 2009. (C) 2009 Wiley-Liss, Inc.

Environmental variables can strongly influence a variety of intra- and inter-population processes, including demography, population structure and gene flow. When environmental conditions are particularly harsh for a certain species, investigating these effects is important to understanding how populations persist under difficult conditions. Furthermore, species inhabiting challenging environments present excellent opportunities to examine the effects of complex landscapes on population processes because these effects will often be more pronounced. In this study, I use 16 microsatellite loci to examine population structure, gene flow and demographic history in the black toad, Bufo exsul, which has one of the most restricted natural ranges of any amphibian. Bufo exsul inhabits four springs in the Deep Springs Valley high desert basin and has never been observed more than several meters from any source of water. My results reveal limited gene flow and moderately high levels of population structure (F-ST = 0.051-0.063) between all but the two closest springs. I found that the geographic distance across the arid scrub habitat between springs is significantly correlated with genetic structure when distance accounts for topography and barriers to dispersal. I also found very low effective population sizes (N-e = 7-30) and substantial evidence for historical population bottlenecks in all four populations. Together, these results suggest that the desert landscape and B. exsul's high habitat specificity contribute significantly to population structure and demography in this species and emphasize the importance of considering behavioural and landscape data in conservation genetic studies of natural systems.

The use of sequence polymorphism from individual mitochondrial genes to infer past demography has recently proved controversial because of the recurrence of selective sweeps acting over genes and the need for unlinked multilocus data sets. However, comparative analyses using several species for one gene and/or multiple genes for one species can serve as a test for potential selective effects and clarify our understanding of historical demographic effects. This study compares nucleotide polymorphisms in mitochondrial cytochrome oxidase I across seven deep-sea hydrothermal vent species that live along the volcanically active East Pacific Rise. Approximate Bayesian Computation (ABC) method, developed to trace shared vicariant events across species pairs, indicates the occurrence of two across species divergence times, and suggests that the present geographical patterns of genetic differentiation may be explained by two periods of significant population isolation. The oldest period dates back 11.6 Ma and is associated with the vent limpet Lepetodrilus elevatus, while the most recent period of isolation is 1.3 Ma, which apparently affected all species examined and coincides with a transition zone across the equator. Moreover, significant negative Tajima's D and star-like networks were observed for all southern lineages, suggesting that these lineages experienced a concomitant demographic and geographical expansion about 100 000-300 000 generations ago. This expansion may have initiated from a wave of range expansions during the secondary colonization of new sites along the Southern East Pacific Rise (founder effects below the equator) or recurrent bottleneck events because of the increase of eruptive phases associated with the higher spreading rates of the ridge in this region.

Analysis of the mitochondrial DNA control region resolved two stocks of whitemouth croaker Micropogonias furnieri in Uruguayan waters, one in the Rio de la Plata and the other on the Uruguayan shelf. The whitemouth croaker is the most important coastal fishery resource along the coast and has the greatest commercial importance in the Rio de la Plata and its oceanic front. The number of pair-wise differences (pi) and haplotype diversity (h) showed significant differences between the two regions. Frequencies of mtDNA haplotypes did not differ between Rio de la Plata from Bahia Blanca M. furnieri. Samples from the oceanic front showed greater genetic variability and a larger effective number of females that were an order of magnitude larger than that in Rio de la Plata. Mismatch distributions showed evidence of a recent population expansion in the oceanic region, beginning c. 40 000 b.p. The presence of two stocks of the M. furnieri in the study area should be considered in the management of this species' fishery.

In the present study, we compare the genetic structure of a flooded forest tree Caryocar microcarpum and a terra firme forest tree Caryocar villosum in the lower Rio Negro region and test the hypothesis that the Rio Negro, the largest tributary on the left bank of the Amazon River, has been acting as a geographical barrier to gene flow between populations from the left and right banks. Seventeen adult individuals on the left bank and 27 on the right bank of Rio Negro were sampled for C. microcarpum, whereas 27 on the left and 20 on the right bank were sampled for C. villosum. Two chloroplast DNA regions were sequenced: the intron of trnL gene and the intergenic region between psbA and trnH genes; and all individuals were genotyped using ten microsatellite loci. The trnL intron and psbA-trnH intergenic spacer generated fragments of 459 bp and 424 bp, respectively. For C. microcarpum, six haplotypes were identified for trnL and seven for psbA-trnH. By contrast, only one haplotype was found for C. villosum for both sequences. The results obtained showed that the Rio Negro has not been a barrier to gene flow by pollen and seeds for either species. No genetic differentiation and a high migration rate between populations from the left and right banks of the Rio Negro were detected for the chloroplast sequences and nuclear microsatellites, for both C. villosum and C. microcarpum. Although the two analysed sequences showed a sharp topology difference, both indicated that multiple lineages may have contributed to the origin of C. microcarpum populations in the Rio Negro basin. Nevertheless, for C. villosum, from terra firme, the results obtained may provide evidence of a recent expansion of one maternal lineage from an ancient relic population surviving in one of the few moist forest refuges of the Guiana Shield during extended droughts of the glacial periods. We hypothesize that the contrasting environments colonized by this congener pair may have played an important role in shaping the genetic structure of both species. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 278-290.

Wright's F-statistics, and especially F-ST, provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. Estimates of F-ST can identify regions of the genome that have been the target of selection, and comparisons of F-ST from different parts of the genome can provide insights into the demographic history of populations. For these reasons and others, F-ST has a central role in population and evolutionary genetics and has wide applications in fields that range from disease association mapping to forensic science. This Review clarifies how F-ST is defined, how it should be estimated, how it is related to similar statistics and how estimates of F-ST should be interpreted.

Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of > 600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underestimated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recovered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America. (C) 2009 Elsevier Inc. All rights reserved.

In organisms with haploid-dominant life cycles, natural selection is expected to be especially effective because genetic variation is exposed directly to selection. However, in spore-producing plants with high dispersal abilities, among-population migration may counteract local adaptation by continuously redistributing genetic variability. In this study, we tested for adaptation at the molecular level by comparing nucleotide polymorphism in two genes (GapC and Rpb2) in 10 European populations of the peatmoss species, Sphagnum fimbriatum with variability at nine microsatellite loci assumed to be selectively neutral. in line with previous results, the GapC and Rpb2 genes showed strikingly different patterns of nucleotide polymorphism. Neutrality tests and comparison of population differentiation based on the GapC and Rpb2 genes with neutrally evolving microsatellites using coalescent simulations supported non-neutral evolution in GapC, but neutral evolution in the Rpb2 gene. These observations and the positions of the replacement mutations in the GAPDH enzyme (coded by GapC) indicate a significant impact of replacement mutations on enzyme function. Furthermore, the geographic distribution of alternate GapC alleles and/or linked genomic regions suggests that they have had differential success in the recolonization of Europe following the Last Glacial Maximum. (C) 2009 Elsevier Inc. All rights reserved.

Conventionally, Lepus capensis is considered to range across large parts of Africa, the Middle East., Central and Far East Asia. However, a recent morphological study restricts cape hares tentatively to a small range in the Western Cape Region of South Africa and groups all other L. capensis- type hares from South Africa into a new species: L. centralis. Here, we studied molecular relationships among L. capensis-type hares from South Africa. Phenotypically and morphologically the individuals matched either the newly described L. capensis or L. centralis. We examined 66 hares for allelic variation at 13 microsatellite loci and for sequence variation of the hypervariable domain I of the mitochondrial control region. All tree-generating analyses of the currently obtained sequences and all South African cape hare sequences downloaded from GenBank revealed monophyly when compared to sequences of various other Lepus species. A network analysis indicated close evolutionary relationships between hares of the “L. capensis-phenotype” and the “L. centralis-phenotype” (according to Palacios et al. 2008) from the southwest of the Western Cape, relative to their pronounced evolutionary divergence from all other more central, northern, and north-eastern L. capensis-type hares. F-statistics, a Bayesian admixture STRUCTURE model, as well as a principal coordinate of microsatellite data indicated close genetic relationships among all South African L. capensis-type hares analysis I presently. A coalescence model-based migration analysis for microsatellite alleles indicated gene flow between most of the considered subspecies of cape hare, including L. capensis capensis and L. capensis centralis, theoretically sufficient to balance stochastic drift effects. Concordantly, AMOVA models revealed only little effects of partitioning microsatellite variation into the two suggested morpho-species “L. capensis” and “L. centralis”. Under an “Interbreeding Species Concept” (e.g. a strict or relaxed Biological Species Concept), the current molecular data demonstrate conspecificity of the two proposed morpho-species “L. capensis” and “L. centralis”. Based on the present molecular data the differentiation of subspecies of cape hares from southern Africa is discussed. (C) 2009 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.

Sheath blight disease (SBD) on rice, caused by Rhizoctonia solani AG-1 IA, is one of the most devastating rice diseases on a global basis, including China (in Eastern Asia), the world's largest rice-growing country. We analyzed the population genetics of nine rice-infecting populations from China using nine microsatellite loci. One allopatric population from India (Southern Asia) was included in the analyses. In total, 300 different multilocus genotypes were found among 572 fungal isolates. Clonal fractions within rice fields were 16 to 95%, suggesting that sclerotia were a major source of primary inoculum in some fields. Global Phi(ST) statistics (Phi(ST) = 42.49; P <= 0.001) were consistent with a relatively high level of differentiation among populations overall; however, pairwise comparisons gave nonsignificant R-ST values, consistent with contemporary gene flow among five of the populations. Four of these populations were located along the Yangtze River tributary network. Gene flow followed an isolation-by-distance model consistent with restricted long-distance migration. Historical migration rates were reconstructed and yielded values that explained the current levels of population subdivision. Except for one population which appeared to be strictly clonal, all populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction. One population had a strictly recombining structure (all loci were in Hardy-Weinberg equilibrium) but the remaining populations from China and the one from India exhibited varying degrees of sexual reproduction. Six populations showed significant F-IS values consistent with inbreeding.

We re-sequenced 815 bp of the mtDNA of loggerhead turtles from a population nesting in Calabria (southern Italy), which was found recently. Non-invasive sampling was applied and information on deposition date and place was used to avoid possible resampling of nesting females. Among 38 nests laid by independent females, we found the common haplotype CC-A2.1 (57.9%) and two other haplotypes which have never been described in Mediterranean nesting grounds, CC-A20.1 (36.8%) and CC-A31.1 (5.3%). Calabria harbors the highest intra-population diversity among 11 Mediterranean nesting populations. Our findings narrow the gap between haplotypes recorded in feeding grounds and those found in nesting grounds. Analyses of population structure show a strong maternal isolation, with Calabria and east Turkey displaying far more diversity than expected considering their census size. These observations suggest that recurrent female founder effects from sources yet to be identified in the Atlantic or in the Mediterranean may have shaped the pattern of mtDNA diversity in this latter basin. Our results provide evidence that the Ionian Calabrian sites should be protected because of the high diversity found there.

The Yellow Sea, located between the Korean Peninsula and mainland China, was completely exposed during the last glacial maximum of the Pleistocene when the sea level was 120-130 m below the present level. We studied patterns of genetic variation in a marine red alga to examine whether the recent recolonization of algal populations occurred on the west coast of Korea after the end of the last glacial maximum. In total, 53 specimens of the red alga Ceramium japonicum were collected in Korea and Japan. We examined the geographic distribution of haplotypes and patterns of migration using mitochondrial cox1 and plastid rbcL. From the specimens collected, 22 cox1 haplotypes and eight rbcL haplotypes were identified. The network and neutrality tests for cox1 support three clusters (which are geographically grouped into east, south, and west coast populations) and provide evidence for population expansion on the west coast. The levels of gene flow were high in the south coast T west coast direction. Analysis of molecular variation in two protein-coding genes revealed significant genetic structure among the three coasts. The results support the concept that C. japonicum populations recolonized the west coast from the south coast following sea level rise in the northern hemisphere after the last glacial maximum during the late Pleistocene.

Despite only limited Pleistocene glacial activity in the southern hemisphere, temperate forest species experienced complex distributional changes resulting from the combined effects of glaciation, sea level change and increased aridity. The effects of these historical processes on population genetic structure are now overlain by the effects of contemporary habitat modification. In this study, 10 microsatellites and 629 bp of the mitochondrial control region were used to assess the effects of historical forest fragmentation and recent anthropogenic habitat change on the broad-scale population genetic structuring of a southern temperate marsupial, the Tasmanian pademelon. A total of 200 individuals were sampled from seven sites across Tasmania and two islands in Bass Strait. High mitochondrial and nuclear genetic diversity indicated the maintenance of large historical population sizes. There was weak phylogeographical structuring of haplotypes, although all King Island haplotypes and three Tasmanian haplotypes formed a divergent clade implying the mid-Pleistocene isolation of a far northwestern population. Both the mitochondrial and nuclear data indicated a division of Tasmanian populations into eastern and western regions. This was consistent with a historical barrier resulting from increased aridity in the lowland `midlands' region during glacial periods, and with a contemporary barrier resulting from recent habitat modification in that region. In Tasmania, gene flow appears to have been relatively unrestricted during glacial maxima in the west, while in the east there was evidence for historical expansion from at least one large glacial refuge and recolonization of Flinders Island.

While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct.

Computer programs for the statistical analysis of microsatellite data use allele length variation to infer, e. g. population genetic parameters, to detect quantitative trait loci or selective sweeps. However, observed allele lengths are usually inaccurate and may deviate from the expected periodicity of repeats. The common practice of rounding to the nearest whole number frequently results in miscalls and underestimations of allelic richness. Manual sorting of allele lengths into discrete classes, a process called binning, is tedious and error-prone. Here, we present a new program for the automated binning of microsatellite allele lengths to overcome these problems and to facilitate high-throughput allele binning.

Lane snappers (Lutjanus synagris), sampled from eight localities in the northern Gulf of Mexico (Gulf) and one locality along the Atlantic coast of Florida, were assayed for allelic variation at 14 nuclear-encoded microsatellites and for sequence variation in a 590 base-pair fragment of the mitochondrially encoded ND-4 gene (mtDNA). Significant heterogeneity among the nine localities in both microsatellite allele and genotype distributions and mtDNA haplotype distributions was indicated by exact tests and by analysis of molecular variance (AMOVA). Exact tests between pairs of localities and spatial analysis of molecular variance (SAMOVA) for both microsatellites and mtDNA revealed two genetically distinct groups: a Western Group that included six localities from the northwestern and northcentral Gulf and an Eastern Group that included three localities, one from the west coast of Florida, one from the Florida Keys, and one from the east (Atlantic) coast of Florida. The between-groups component of molecular variance was significant for both microsatellites (I broken vertical bar (CT) = 0.016, P = 0.009) and mtDNA (I broken vertical bar (CT) = 0.208, P = 0.010). Exact tests between pairs of localities within each group and spatial autocorrelation analysis did not reveal genetic heterogeneity or an isolation-by-distance effect among localities within either group. MtDNA haplotype diversity was significantly less (P < 0.0001) in the Western Group than in the Eastern Group; microsatellite allelic richness and gene diversity also were significantly less in the Western Group (P = 0.015 and 0.013, respectively). The difference in genetic variability between the two groups may reflect reduced effective population size in the Western Group and/or asymmetric rates of genetic migration. The relative difference in variability between the two groups was substantially greater in mtDNA and may reflect one or more mtDNA selective sweeps; tests of neutrality of the mtDNA data were consistent with this possibility. Bayesian analysis of genetic demography indicated that both groups have experienced a historical decline in effective population size, with the decline being greater in the Western Group. Maximum-likelihood analysis of microsatellite data indicated significant asymmetry in average, long-term migration rates between the two groups, with roughly twofold greater migration from the Western Group to the Eastern Group. The difference in mtDNA variability and the order-of-magnitude difference in genetic divergence between mtDNA and microsatellites may reflect different demographic events affecting mtDNA disproportionately and/or a sexual and/or spatial bias in gene flow and dispersal. The spatial discontinuity among lane snappers in the region corresponds to a known zone of vicariance in other marine species. The evidence of two genetically distinct groupings (stocks) has implications for management of lane snapper resources in the northern Gulf.

Landscape genetics is an important framework for investigating the influence of spatial pattern on ecological process. Nevertheless, the standard analytic frameworks in landscape genetics have difficulty evaluating hypotheses about spatial processes in dynamic landscapes. We use a predictive hypothesis-driven approach to quantify the relative contribution of historic and contemporary processes to genetic connectivity. By confronting genetic data with models of historic and contemporary landscapes, we identify dispersal processes operating in naturally heterogeneous and human-altered systems. We demonstrate the approach using a case study of microsatellite polymorphism and indirect estimates of gene flow for a rainforest bird, the logrunner (Orthonyx temminckii). Of particular interest was how much information in the genetic data was attributable to processes occurring in the reconstructed historic landscape and contemporary human-modified landscape. A linear mixed model was used to estimate appropriate sampling variance from nonindependent data and information-theoretic model selection provided strength of evidence for alternative hypotheses. The contemporary landscape explained slightly more information in the genetic differentiation data than the historic landscape, and there was considerable evidence for a temporal shift in dispersal pattern. In contrast, migration rates estimated from genealogical information were primarily influenced by contemporary landscape change. We discovered that landscape heterogeneity facilitated gene flow before European settlement, but contemporary deforestation is rapidly becoming the most important barrier to logrunner dispersal.

To date, little is still known about how alpine species occurring in the Qinghai-Tibetan Plateau (QTP) responded to past climatic oscillations. Here, by using variations of the chloroplast trnT-L, we examined the genetic distribution pattern of 101 individuals of Potentilla glabra, comprising both the interior QTP and the plateau edge. Phylogenetic and network analyses of 31 recovered haplotypes identified three tentative clades (A, B and C). Analysis of molecular variance (amova) revealed that most of the genetic variability was found within populations (0.693), while differentiations between populations were obviously distinct (F-st = 0.307). Two independent range expansions within clades A and B occurring at approximately 316 and 201 thousand years ago (kya) were recovered from the hierarchical mismatch analysis, and these two expansions were also confirmed by Fu's F-S values and `g' tests. However, distant distributions of clade C and private haplotypes from clades A and B suggest that they had survived the Last Glacial Maximum (LGM) and previous glaciers in situ since their origins. Our findings based on available limited samples support that multiple refugia of a few cold-enduring species had been maintained in the QTP platform during LGM and/or previous glacial stages.

The spread of highly pathogenic avian influenza virus (AIV) (H5N1) underlines the potential for global AIV movement through birds. The phylogenies of AN genes from avian hosts usually separate into Eurasian and North American clades, reflecting limited bird migration between the hemispheres. However, mounting evidence that some H6 sequences from North America cluster with Eurasian subtype H6 sequences calls the strict hemispheric divide into question. We conducted a comprehensive phylogenetic analysis of the extent and timing of cross-hemisphere movements by the H6 gene. Results suggested that Eurasian H6 subtype has invaded North America several times, with the first invasions occurring 10 years before the first detection of invading isolates. The members of the North American clade decreased from 100% in the 1980s to 20% in the 2000s among H6 isolates from North America. Unraveling the reasons for this large-scale gene movement between hemispheres might identify drivers of global AN circulation.

The objective of this study was to estimate the dispersal rate in an organism assumed to be confined to tree stands with unbroken continuity. We used the lichen-forming ascomycete Cliostomum corrugatum, which is largely confined to old oak stands. Five populations, with pairwise distances ranging from 6.5 to 83 km, were sampled in Ostergotland, south-eastern Sweden. DNA sequence data from an intron in the small subunit nuclear ribosomal RNA gene was obtained from 85 samples. Nearly all molecular variance (99.6%) was found within populations and there were no signs of isolation-by-distance. The absolute number of immigrants per population per generation (estimated to 30 years), inferred by Bayesian MCMC, was found to be between 1 and 5. Altogether, evidence suggests abundant gene flow in the history of our sample. A simulation procedure demonstrated that we cannot know whether effective dispersal is ongoing or if it ceased at the time when oaks started to decrease dramatically around 400 years BP. However, a scenario where effective dispersal ceased already at the time when the postglacial reinvasion of oak had reached the region around 6000 years BP is unlikely. Vegetation history suggests that the habitat of C. corrugatum was patchily distributed in the landscape since the early Holocene. Combined with the high dispersal rate estimate, this suggests that the species has been successful at frequently crossing distances of at least several kilometres and possibly that it has primarily been limited by the availability of habitat rather than by dispersal. (C) 2009 Elsevier Ltd. All rights reserved.

Connectivity, or the exchange of individuals among marine populations, is a central topic in marine ecology. For most benthic marine species with complex life cycles, this exchange occurs primarily during the pelagic larval stage. The small size of larvae coupled with the vast and complex fluid environment they Occupy hamper Our ability to quantify dispersal and connectivity. Evidence from direct and indirect approaches using geochemical and genetic techniques suggests that populations range front fully open to hilly closed. Understanding the biophysical processes that contribute to observed dispersal patterns requires integrated interdisciplinary approaches that incorporate high-resolution biophysical modeling and empirical data. Further, differential postsettlement survival of larvae may add complexity to measurements of connectivity. The degree to which populations self recruit or receive subsidy from other populations has consequences for a number of fundamental ecological processes that affect population regulation and persistence. Finally, a full understanding of population connectivity has important applications for management and conservation.

The extent and evolutionary significance of hybridization is difficult to evaluate because of the difficulty in distinguishing hybridization from incomplete lineage sorting. Here we present a novel parametric approach for statistically distinguishing hybridization from incomplete lineage sorting based on minimum genetic distances of a nonrecombining locus. It is based on the idea that the expected minimum genetic distance between sequences from two species is smaller for some hybridization events than for incomplete lineage sorting scenarios. When applied to empirical data sets, distributions can be generated for the minimum interspecies distances expected under incomplete lineage sorting using coalescent simulations. If the observed distance between sequences from two species is smaller than its predicted distribution, incomplete lineage sorting can be rejected and hybridization inferred. We demonstrate the power of the method using simulations and illustrate its application on New Zealand alpine buttercups (Ranunculus). The method is robust and complements existing approaches. Thus it should allow biologists to assess with greater accuracy the importance of hybridization in evolution.

It is commonly found that effective population sizes of natural populations are much smaller than census sizes of plants and animals. However, theoretical studies have shown that factors rarely investigated empirically, like seed banks in plants and diapause in animals, may have profound influence on effective sizes. Here we investigate whether the presence of seed banks can explain the relatively high genetic variability observed in northern European Arabidopsis thaliana populations with small census sizes. We have genotyped three above- and below- ground cohorts in 27 Norwegian populations using single nucleotide polymorphism markers. Although the populations varied extensively in levels of variability within and between cohorts, standard genetic population measures were comparable to those obtained in previous studies on above-ground cohorts using microsatellite markers. Estimated effective population sizes are larger for total populations (containing both seed bank and above-ground cohorts for 1 year) compared to each of the cohorts considered separately. Using a conservative approach, we find that the effective sizes are larger than census sizes of local populations, and that the effective generation time is higher than 1 year (3-4 years, on average), making A. thaliana a perennial semelparous plant at many northern European localities.

In historical biogeography, phylogenetic trees have long been used as tools for addressing a wide range of inference problems, from explaining common distribution patterns of species to reconstructing ancestral geographic ranges on branches of the tree of life. However, the potential utility of phylogenies for this purpose has yet to be fully realized, due in part to a lack of explicit conceptual links between processes underlying the evolution of geographic ranges and processes of phylogenetic tree growth. We suggest that statistical approaches that use parametric models to forge such links will stimulate integration and propel hypothesis-driven biogeographical inquiry in new directions. We highlight here two such approaches and describe how they represent early steps towards a more general framework for model-based historical biogeography that is based on likelihood as an optimality criterion, rather than having the traditional reliance on parsimony. The development of this framework will not be without significant challenges, particularly in balancing model complexity with statistical power, and these will be most apparent in studies of regions with many component areas and complex geological histories, such as the Mediterranean Basin.

Adaptive population divergence is often driven by divergent natural selection, but can be constrained by the homogenizing effect of gene flow between populations. Indeed, a common pattern in nature is an inverse correlation between the degree of adaptive phenotypic divergence between populations and levels of gene flow between populations. However, there is essentially no experimental data on whether this correlation arises because gene flow constrains adaptation or, conversely, because adaptive divergence causes barriers to gene flow (ecological speciation). Here, I report increased adaptive divergence in cryptic color pattern between a pair of Timema insect populations following an experimental reduction in between-population gene flow. The reduction in gene flow arose due to a natural experiment, and thus was not replicated at a second site. However, temporal replication of the trends among six generations of data, coupled with a lack of increased adaptive divergence for two other population pairs where gene flow was not manipulated (i.e., control sites), argues that the results did not arise by chance. Estimates of dispersal ability and population size further support reduced gene flow, rather than increased genetic drift, as the cause of divergence. Thus, the findings provide experimental evidence that gene flow constrains adaptation in nature.

The Chinese mitten crab Eriocheir sinensis is an indigenous and economically important species in China, but can also be found as invasive species in Europe and America. Mitten crabs have been exploited extensively as a food resource since the 1990s. Despite its ecological and economic importance, the genetic structure of native mitten crab populations is not well understood. In this paper, we investigated the genetic structure of mitten crab populations in China by screening samples from ten locations covering six river systems at six microsatellite loci. Our results provide further evidence that mitten crabs from the River Nanliujiang in Southern China are a genetically differentiated population within the native range of Eriocheir, and should be recognized as a separate taxonomic unit. In contrast, extremely low levels of genetic differentiation and no significant geographic population structure were found among the samples located north of the River Nanliujiang. Based on the reproductive biology of mitten crabs and the geography of their habitat we argue that both natural and human-mediated gene flow are unlikely to fully account for the similar allele frequency distributions at microsatellite loci. Large population sizes of mitten crabs suggest instead that a virtual absence of genetic drift and significant homoplasy of microsatellite alleles have contributed to the observed pattern. Furthermore, a coalescent-based maximum likelihood method indicated a more than two-fold lower effective population size of the Southern population compared to the Northern Group and low but significant levels of gene flow between both areas.

Here the population genetic structure of an ecologically and economically important coral reef fish, the coral trout Plectropomus leopardus, is investigated in the context of contemporary and historical events. Coral trout were sampled from four regions (six locations) and partial mtDNA D-loop sequences identified six populations (Fst = 0.89209, P < 0.0001): Scott Reef and the Abrolhos Islands in west Australia; the Great Barrier Reef (GBR), represented by northern and southern GBR samples; New Caledonia and Taiwan, with Taiwan containing two genetic lineages. Furthermore, this study identified source and sink populations within and among regions. Specifically, the northern population in west Australia (Scott Reef) was identified, as the source for replenishment of the Abrolhos population, whilst New Caledonia was a source for recruitment to the GBR. Based on these insights from a single mtDNA marker, this study will facilitate the development of rational management plans for the conservation of P. leopardus populations and therefore mitigate the risk of population declines from anthropogenic influences.

Harbor seals (Phoca vitulina richardii (Gray, 1864)) in Alaska are currently treated as three distinct management stocks. Previous genetic analyses using mitochondrial DNA suggested that these stocks are differentiated genetically. We studied populations in Glacier Bay (GB; Southeast Alaska Stock), where harbor seals are declining, and Prince William Sound (PWS; Gulf of Alaska Stock), where the population has recently stabilized. Using six pairs of hypervariable microsatellite primers, we determined that these populations are a single panmictic unit with estimated migration rates of 22 animals/generation (PWS to GB) and 63 animals/generation (GB to PWS). The asymmetrical gene flow between GB and PWS is likely driven in part by a recent increase in competitors and predators of seals in GB. In contrast with males, emigration of females from PWS to GB (8.3 seals/generation) is higher than emigration of females from GB to PWS (3.3 seals/generation), likely because females use glacial ice as pupping habitat. Despite the high gene flow, the number of migrants per year (0.02% of the Gulf of Alaska population) is likely too low to influence the demographics of harbor seals in PWS, and the two populations may best be managed as separate stocks.

Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyse 21 microsatellite loci in historical (archived scales from 1927 to 1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with nonlocal strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation by distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation by distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analysing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.

The survival of threatened species its the European tree frog (Hyla arborea) is strongly dependent on the genetic variability within populations. its well as gene flow between them,. In Switzerland. only two sectors in its western part still harbour metapopulations. The first is characterised by a very heterogeneous and Urbanized landscape. while the second is characterised by it uninterrupted array Of suitable habitats. In this study, six microsatellite loci were used it) establish levels of genetic differentiation among the populations from the two different location,,. The results, show that the metapopulations have (i) weak levels of genetic differentiation (F-ST within metapopulation approximate to 0.04) (ii) no difference in levels of genetic structuring between them, (iii) significant (p = 0.019) differences in terms of genetic diversity (Hs) and observed heterozygozity (Ho), the metapopulation located in it disturbed landscape showing lower values. Our results suggest that even if the dispersal of H. arborea among contiguous ponds seems to be efficient in areas of heterogeneous landscape, a loss of genetic diversity call occur.

The Gulf of California endemic reef fish, Acanthemblemaria crockeri (Blennioidei, Chaenopsidae), reportedly has two colour morphs, one with melanic lateral spots ('Gulf' morph) and one with orange spots ('Cape' morph). In this study, we recorded colour morph in both males and females and collected mitochondrial DNA sequence data for cytochrome c oxidase I (COI) and tRNA-Pro/D-loop of specimens from throughout the Gulf to explore the genetic basis of the colour morphs. Two highly divergent (HKY + I distance = 11.9% for COI), reciprocally monophyletic lineages were identified, consistent with the presence of two parapatric species. A 30-km gap between the distributions of mitochondrial lineages roughly corresponds to a hypothesized former seaway across the Baja California peninsula north of La Paz, although the estimated divergence time (1.84 million years ago) is more recent than the hypothetical seaway (3-4 million years ago). Surprisingly, the distribution of mitochondrial species is not congruent with the distribution of either male or female colour morphs. Our analysis also revealed significant population differentiation within both species and no shared haplotypes among populations. The northern Gulf species includes four populations (NB, CB, NM and CM) corresponding to northern and central Baja and northern and central mainland sites, while the Cape species includes two populations (SB and SM) corresponding to the Baja and mainland sides of the southern Gulf. The NB/CB division corresponds to a hypothesized Plio-Pleistocene mid-peninsular seaway. The level of genetic divergence documented in this lineage is extraordinary for a marine fish with a pelagic larval stage within a semi-enclosed basin.

Comparative phylogeographical studies in island archipelagos can reveal lineage-specific differential responses to the geological and climatic history. We analysed patterns of genetic diversity in six codistributed lineages of darkling beetles (Tenebrionidae) in the central Aegean archipelago which differ in wing development and habitat preferences. A total of 600 specimens from 30 islands and eight adjacent mainland regions were sequenced for mitochondrial cytochrome oxidase I and nuclear Muscular protein 20. Individual gene genealogies were assessed for the presence of groups that obey an independent coalescent process using a mixed Yule coalescent model. The six focal taxa differed greatly in the number of coalescent groups and depth of lineage subdivision, which was closely mirrored by the degree of geographical structuring. The most severe subdivision at both mitochondrial DNA and nuclear DNA level was found in flightless lineages associated with presumed stable compact-soil habitats (phrygana, maquis), in contrast to sand-obligate lineages inhabiting ephemeral coastal areas that displayed greater homogeneity across the archipelago. A winged lineage, although associated with stable habitats, showed no significant phylogenetic or geographical structuring. Patterns of nucleotide diversity and local genetic differentiation, as measured using Phi(ST) and hierarchical amova, were consistent with high levels of ongoing gene flow in the winged taxon; frequent local extinction and island recolonisation for flightless sand-obligate taxa; and very low gene flow and geographical structure largely defined by the palaeogeographical history of the region in flightless compact-soil taxa. These results show that differences in dispersal rate, mediated by habitat persistence, greatly influence the levels of phylogeographical subdivision in lineages that are otherwise subjected to the same geological events and palaeoclimatic changes.

Blue (Scomber australasicus) and chub mackerel (Scomber japonicus) occur sympatrically in the western North Pacific. Blue mackerel were previously classified as a subspecies of S. japonicus based on morphological similarities. The practical management unit for blue mackerel is contentious owing to incomplete resolution by biological analyses. We used rapidly evolving microsatellites and slow-changing mitochondrial cytochrome b (mtCyt-b) markers to examine the phylogeographic relationships of the two species across four major hydrographic regions of the western North Pacific. Genetic variability was high in each hydrographic region and in the putative species unit, and Hardy-Weinberg equilibrium tests confirmed that blue and chub mackerel are separate genetic components. Population genetic and multiple-dimensional scaling analyses of the genotypes indicated clear genetic differences, and phylogenetic analyses of the mtCyt-b haplotypes showed a level of genetic divergence (F-ST = 0.038, p < 0.001) consistent with separation of the two species. Based on the coalescence theory, the difference in mtCyt-b genes was small, indicating incipient speciation between blue and chub mackerel, with a diversification time of 1.9 million years ago (mya) during the Pleistocene when the East China Sea (ECS) and the South China Sea (SCS) were separated physically. Significant differences between populations of blue mackerel in the ECS and SCS were also found. Our findings confirm that blue mackerel is a valid biological species and that its populations in the ECS and SCS should be considered separate fishery stocks and conservation units for management.

Phytophthora ramorum (oomycetes) is the causal agent of sudden oak death and ramorum blight on trees, shrubs, and woody ornamentals in the forests of coastal California and southwestern Oregon and in nurseries of California, Oregon, and Washington. In this study, we investigated the genetic structure of P. ramorum on the West Coast of the United States, focusing particularly on population differentiation potentially indicative of gene flow. In total, 576 isolates recovered from 2001 to 2005 were genotyped at 10 microsatellite loci. Our analyses of genetic diversity and inferences of reproductive mode confirm previous results for the Oregon and California populations, with the strong majority of the genotypes belonging to the NA1 clonal lineage and showing no evidence for sexual reproduction. The high incidence of genotypes shared among populations and the lack of genetic structure among populations show that important large-scale, interpopulation genetic exchanges have occurred. This emphasizes the importance of human activity in shaping the current structure of the P. ramorum population on the West Coast of the United States.

Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.

This study focuses on a pair of fungal species, Moelleriella libera and M. raciborskii (Ascomycota: Clavicipitaceae) from the neotropics and paleotropics, respectively, that are phenotypically nearly indistinguishable. Molecular analyses based on DNA sequences from RNA polymerase II subunit 2 (RPB2), translation elongation factor 1-alpha (EF1-alpha) and beta-tubulin genes confirm that they are recently derived sister species. Speciation appears to have followed an historical transoceanic dispersal event. Models of population structure and migration from TCS, IM, and coalescent-based analyses suggest there is little gene flow between the two species. The direction of dispersal, investigated using the progression rule and coalescent-based gene genealogies, was likely from the New World to the Old World. (C) 2009 Elsevier Inc. All rights reserved.

An evaluation of genetic structuring and morphometric variation within tusked king crickets, Libanasidus vittatus (Kirby, 1899), from South Africa suggests two main population assemblages. Maximum likelihood (ML), Parsimony, Bayesian and phenetic analyses of mitochondrial cytochrome oxidase I (COI) sequence data recovered two well-supported clades corresponding to two biogeographically distinct populations. Canonical variates (discriminant) analysis (CVA) also showed evidence of two phenetic assemblages that correspond to the genetically delineated groups. Libanasidus vittatus is the recognized species occurring within an eastern population in South Africa (Mpumalanga and Eastern Cape Provinces), while a possible novel species occurs within a north-western population in South Africa (Limpopo and Gauteng Provinces). Using a molecular clock estimate of 2.0% divergence per million years, suggests isolation of the two populations at approx. 1.65 million years ago, possibly due to the formation of isolating forest pockets during the dry Pleistocene Epoch. The average genetic divergence of 3.3% between the two populations, and low migration rate estimates corresponding to less than one female migration per generation further support the presence of two cryptic tusked king cricket species in South Africa.

Postglacial colonization has created the main phylogeographical structures in the endemic species of the Tibetan plateau; however, patterns of diversification are species idiosyncratic and indicative of variations in geographic divergence. Here we compare the phylogeographical structures of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume's ground tit (Pseudopodoces humilis), both of which are commonly associated with alpine meadow habitats. our results suggested that these two species experienced rapid population expansion at times estimated as 0.05-0.16 million years ago (Ma). These expansion periods were congruent with the retreat of the last extensive glacial period (0.5-0.175 Ma). Whereas O. taczanowskii populations were derived from a single more widely distributed refugium that existed along the east margin of the Tibetan plateau, P. humilis expanded from independent refugia that were located within both the northeast and southeast margin of the Tibetan plateau. While both birds experienced similar colonization events, their phylogeographical structures are quite contrasting. No trace of geographical divergence is found in O. taczanowskii, suggesting that considerable gene flow occurred after the postglacial colonization. in contrast, a geographic separation can be detected between two refugia populations of P. humilis, specifically the higher altitude platform and lower altitude edge regional groups. The gene flow between these two regions is restricted (M = 0.43). We estimate the divergence time as approximately 0.361 Ma, dating to the extensive glacial period. Potential explanations for the different phylogeographical structures of these two sympatric birds may include variance in dispersal ability, altitude specific and independent or semicontinuous refugia. While a combination of high flight ability and semicontinuous refugium may have promoted gene flow in O. taczanowskii populations, weak dispersal coupled with separated refugia may have sufficiently isolated populations such to facilitate genetic divergence in P. humilis. (C) 2009 Elsevier Inc. All Fights reserved.

Fishery genetics has a history of half a century, applying Molecular biological and genetic techniques to answer fisheries-related questions in taxonomy and ecology of fishes and invertebrates. This review aims to provide an overview of the developments in fishery genetics of the last decade, focussing on DNA-based species and stock identification. Microsatellites became the `gold standard' ill genetic stock identification, but accumulating sequence information for commercially important species opens the door for genome-wide SNP (Single Nucleotide Polymorphism) analysis, which will support or even displace microsatellites in file future. Recent advancements in DNA analytics, such as DNA microarrays and pyrosequencing, are highlighted and their possible applications ill Fishery genetics are discussed. Emphasis is also given to DNA barcoding, a recently advocated concept using a fragment of the mitochondrial cytochrome oxidase I (COI) gene as a standard marker for the identification of animals. DNA barcoding becomes more and more accepted in the scientific community and the international initiative Fish-BOL (Fish Barcoding or Life) aims to barcode all fish species. These novel technologies and concepts will enable a tremendous progress in fishery genetics,.

Geomorphological changes have been demonstrated to have had profound impacts on biodiversity, often leading to demographic expansions and contractions and allopatric divergence of taxa. We examined DNA sequence variation at two nuclear and one maternally inherited plastid locus among 10 populations of Schiedea globosa on the Hawaiian Islands to assess the Primary factors shaping genetic structure, phylogeographic patterns, and the importance of geogaphic isolation to population divergence. Schiedea globosa has characteristics that may promote gene flow, including wind pollination and rafting of plants in ocean currents. However we detected significant differentiation among populations on all islands except Hawaii, with the maternally inherited plastid locus having the the greatest genetic structure (F-ST = 0.81). Migration rates across all loci are less than ine migrant pergeneration. We found evidence of growth in several populations and on the islands of Molokai and Maui, which supports population expansion associated with the formation of Maui Nui during the last glacial maximum. Similar to data for many other Hawaiian taxa, these data suggest S. globosa originated on Oahu and subsequently colonized Molokai, Maui, and Hawaii in progression. Given the high level of genetic structure, allopatric divergence will likely contribute to further diverence of populations.

We investigated the effect of development mode on the spatial and temporal population genetic structure of four littorinid gastropod species. Snails were collected from the same three sites on the west coast of Vancouver Island, Canada in 1997 and again in 2007. DNA sequences were obtained for one mitochondrial gene, cytochrome b (Cyt b), and for up to two nuclear genes, heat shock cognate 70 (HSC70) and aminopeptidase N intron (APN54). We found that the mean level of genetic diversity and long-term effective population sizes (N-e) were significantly greater for two species, Littorina scutulata and L. plena, that had a planktotrophic larval stage than for two species, Littorina sitkana and L. subrotundata, that laid benthic egg masses which hatched directly into crawl-away juveniles. Predictably, two poorly dispersing species, L. sitkana and L. subrotundata, showed significant spatial genetic structure at an 11- to 65-km geographical scale that was not observed in the two planktotrophic species. Conversely, the two planktotrophic species had more temporal genetic structure over a 10-year interval than did the two direct-developing species and showed highly significant temporal structure for spatially pooled samples. The greater temporal genetic variation of the two planktotrophic species may have been caused by their high fecundity, high larval dispersal, and low but spatially correlated early survivorship. The sweepstakes-like reproductive success of the planktotrophic species could allow a few related females to populate hundreds of kilometres of coastline and may explain their substantially larger temporal genetic variance but lower spatial genetic variance relative to the direct-developing species.

Comparing the patterns of population differentiation among genetic markers with different modes of inheritance call provide insights into patterns of sex-biased dispersal and gene flow. The blue-and-yellow Macaw (Ara ararauna) is a Neotropical parrot with a broad geographic distribution ill South America. However, little is known about the natural history and current status Of remaining wild populations, including levels of genetic variability. The progressive decline and possible fragmentation of populations may endanger this species in the near future. We analyzed mitochondrial DNA (mtDNA) control-region sequences and six microsatellite 106 Of Blue-and-yellow Macaws sampled throughout their geographic range ill Brazil to describe population genetic Structure, to make inferences about historical demography and dispersal behavior, and to provide insight for conservation efforts. Analyses of population genetic structure based on mtDNA showed evidence of two major populations ill western and eastern Brazil that share a few low-frequency haplotypes. This phylogeographic pattern seems to have originated by the historical isolation of Blue-and-yellow Macaw populations similar to 374,000 years ago and has been maintained by restricted gene flow and female philopatry. By contrast, variation ill biparentally inherited microsatellites was not structured geographically, Male-biased dispersal and female philopatry best explain the different patterns observed in these two markers. Because females disperse less than males, the two regional populations with well-differentiated mtDNA haplogroups should be considered two different management units for conservation purposes. Received 4 November 2007 accepted 10 December 2008.

The genetic composition of a population reflects several aspects of the organism and its environment. The Icelandic Arctic fox population exceeds 8000 individuals and is comprised of both coastal and inland foxes. Several factors may affect within-population movement and subsequent genetic population structure. A narrow isthmus and sheep-proof fences may prevent movement between the north-western and central part and glacial rivers may reduce movement between the eastern and central part of Iceland. Moreover, population density and habitat characteristics can influence movement behaviour further. Here, we investigate the genetic structure in the Icelandic Arctic fox population (n = 108) using 10 microsatellite loci. Despite large glacial rivers, we found low divergence between the central and eastern part, suggesting extensive movement between these areas. However, both model- and frequency-based analyses suggest that the north-western part is genetically differentiated from the rest of Iceland (F-ST = 0.04, D-S = 0.094), corresponding to 100-200 generations of complete isolation. This suggests that the fences cannot be the sole cause of divergence. Rather, the isthmus causes limited movement between the regions, implying that protection in the Hornstrandir Nature Reserve has a minimal impact on Arctic fox population size in the rest of Iceland. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 18-26.

As interest and efforts in ecological restoration of native bivalve populations grow, the genetic implications of various restoration strategies Lire often unclear to resource managers and restoration practitioners, even though genetic considerations are vital to the ultimate success or failure of restoration endeavors. in an effort to fill this void, we present an overview of the underlying genetic concepts, a brief review of documented examples of native mollusc populations impacted by hatchery production, and a summary of the potential genetic impacts of restoration activities ranging from eliminating ongoing negative impacts with minimal genetic effects to intentional genetic manipulations Of extant Populations. We emphasize throughout the importance of understanding how adaptive, quantitative genetic variation is distributed within and among populations and the limitations of Studies that address only selectively neutral molecular genetic variation. We also describe a conceptual framework for making genetically sound management and restoration decisions based on historical and current ecological and genetic considerations. Finally, because fully-informed decisions require a great deal of difficult-to-obtain data, we make suggestions on how to prioritize future research and Outline practical measures that can be implemented in the absence of rigorous genetic data to prevent inadvertent negative genetic impacts by well-intended restoration efforts.

Northern South America presents a diverse array of nonforest or savanna-like ecosystems that are patchily distributed. The distribution of these open habitats has been quite dynamic during Quaternary glacial-interglacial cycles; yet, the relevance of climatically driven vicariance events to the diversification of nonforest Amazonian vertebrates remains poorly known. We analyzed karyologic and mitochondrial DNA sequence data of the genus Zygodontomys, a small cricetid rodent distributed throughout nonforest habitats of northern Amazonia. Samples analyzed represented 4 Brazilian Amazonian localities and 2 French Guiana localities. Karyologic variation among Amazonian Brazilian Zygodontomys populations is high, with, at least, 3 karyomorphotypes. Molecular phylogenetic analyses recovered 3 major clades congruent with known karyotypes, a finding that suggests the existence of 3 species, 2 of which currently undescribed. The French Guiana and Suruma clade, identified as Zygodontomys brevicauda microtinus, is characterized by 2n = 86 and is sister to the clade formed by the 2 nondescribed forms. The Rio Negro-Rio Branco form is characterized by 2n = 82, and the Ferreira Gomes-Itapoa form is characterized by 2n = 84. The distribution of the 3 Zygodontomys lineages identified is in accordance with the geography of the open vegetation patches in Northern Amazonia, and divergence time estimates relate speciation events to the middle-upper Pleistocene, supporting the prominent role of Quaternary climatically driven vicariance events in the diversification of the genus.

Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well-constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled Differential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally Superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to Complex, multi-modal search problems.

Several evolutionary hypotheses help explain why only some species adapt readily to new conditions and expand distributions beyond borders, but there is limited evidence testing these hypotheses. In this study, we consider patterns of neutral (microsatellite) and quantitative genetic variation in traits in three species of Drosophila from the montium species group in eastern Australia. We found little support for restricted or asymmetrical gene flow in any species. In rainforest-restricted Drosophila birchii, there was evidence of selection for increased desiccation and starvation resistance towards the southern border, and a reduction in genetic diversity in desiccation resistance at this border. No such patterns existed for Drosophila bunnanda, which has an even more restricted distribution. In the habitat generalist Drosophila serrata, there was evidence for geographic selection for wing size and development time, although clinal patterns for increased cold and starvation resistance towards the southern border could not be differentiated from neutral expectations. These findings suggest that borders in these species are not limited by low overall genetic variation but instead in two of the species reflect patterns of selection and genetic variability in key traits limiting borders.

The persistence of plants inhabiting restricted alpine areas under climate change will depend upon many factors including levels of genetic variation in adaptive traits, population structure, and breeding system. Using microsatellite markers, the genetic structure of populations of a relatively common alpine grass, Poa hiemata, is examined across three altitudinal gradients within the restricted Australian alpine zone where this species has previously been shown to exhibit local adaptation across a narrow altitudinal gradient. Genetic variation across six microsatellite markers revealed genetic structuring along altitudinal transects, and a reduction in genetic variation at high and low altitude extremes relative to sites central within transects. There was less genetic variation among transect sites compared with altitudinal gradients within transects, even though distances among transects were relatively larger. Central sites within transects were less differentiated than those at extremes. These patterns suggest higher rates of gene flow among sites at similar altitudes than along transects, a process that could assist altitudinal adaptation. Patterns of spatial autocorrelation and isolation by distance changed with altitude and may reflect altered patterns of dispersal via pollen and/or seed. There was evidence for selfing and clonality in neighbouring plants. Levels of gene flow along transects were insufficient to prevent adaptive changes in morphological traits, given previously measured levels of selection.

We investigated potential microgeographical population structure among spatial and temporal samples of cod Gadus morhua L., collected in the northern North Sea and around Scotland, using microsatellite genetic markers. Results were highly dependent on the samples and microsatellite loci included. Analysis of molecular variance (AMOVA) revealed significant spatial (p = 0.04) and temporal (p = 0.02) variance when including samples of juveniles and the microsatellite Gmo 132, which is known to be subject to selection. However, neither spatial nor temporal variance components were significant (p = 0.15 and 0.23, respectively) after exclusion of juvenile samples and Gmo 132. Patterns of genetic differentiation showed a similar sensitivity to the sampling of loci. No apparent pattern was identified when only using suspected neutral microsatellites. In contrast, analysis of Gmo132 alone revealed a clear isolation of 2 samples collected at Viking and pairwise grouping of temporal adult samples from the same location. On a northeast Atlantic regional scale, inferences on local populations and patterns of population structuring were more robust to the inclusion of the microsatellite under selection. Our results demonstrate that, without cautious consideration of biased samples of individuals and loci, apparent microgeographical patterns of spatial genetic differentiation could be caused by sampling non-randomly distributed individuals of hitch-hiking selection at presumed neutral marker loci. However, while loci subject to selection may provide biased results in relation to identifying populations based on an evolutionary paradigm, they may prove valuable for separating populations on ecological time scales,

The black-fin icefish Chaenocephalus aceratus is among the most abundant fish species on the Antarctic continental shelves of the Scotia Arc, and Bouvet Island. We genotyped 11 microsatellite loci in C. aceratus population samples from South Orkney, southern South Shetlands, and Elephant Island (northern South Shetlands) collected in 2002 and 2006. This investigation further develops a previous study on the species reporting the presence of one panmittic population in southern South Shetlands and Elephant Island, with genetic differentiation between year classes. Our results reveal a more complex pattern of differentiation than shown previously, as genetic differences occur both at the temporal level at Elephant Island and at the geographic scale between southern South Shetland-Elephant Islands and South Orkney population samples. In particular, the magnitude of genetic differentiation at the temporal scale, the relatively high effective population size (N-e) and high gene flow indicate that genetic differentiation is not only driven by geographic distance. At present, our results should be taken into account when defining conservation measures and management boundaries in regions where fishery is still open or where other Antarctic fish species are still exploited.

Alien species have profound ecological and evolutionary impacts on native species. In this study, we used microsatellite loci to evaluate the impact of grazing on Crossosoma californicum on the California Channel Islands to predict future threats to this species and to assess the origin of a mainland population. San Clemente Island supports populations of one to seven individuals, whereas Santa Catalina Island supports populations of 30 - 50 individuals. We hypothesize that these demographic differences are due to variable grazing pressures, and as a result, the islands will differ in genetic structure. We found a strong correlation between population size and genetic variation, with Santa Catalina populations more variable (p = 85.9, A = 3.2) than San Clemente populations (p = 49.7, A = 1.7). We also found evidence for ancient but not recent bottlenecks, indicating that C. californicum may have historically maintained small populations. The islands are similar in total genetic variation, suggesting that while grazing reduced the number of plants, it did not deplete genetic variation. Simulation studies predict substantial declines in allelic diversity within the next 50 yr. Thus, conservation measures should seek to establish sustainable populations, especially on San Clemente. The mainland population of C. californicum was equally divergent from island populations and likely represents insular colonization to the mainland.

In conventional phylogeographic studies, historical demographic processes are elucidated from the geographical distribution of individuals represented on an inferred gene tree. However, the interpretation of gene trees in this context can be difficult as the same demographic/geographical process can randomly lead to multiple different genealogies. Likewise, the same gene trees can arise under different demographic models. This problem has led to the emergence of many statistical methods for making phylogeographic inferences. A popular phylogeographic approach based on nested clade analysis is challenged by the fact that a certain amount of the interpretation of the data is left to the subjective choices of the user, and it has been argued that the method performs poorly in simulation studies. More rigorous statistical methods based on coalescence theory have been developed. However, these methods may also be challenged by computational problems or poor model choice. In this review, we will describe the development of statistical methods in phylogeographic analysis, and discuss some of the challenges facing these methods.

We present a novel and straightforward method for estimating recent migration rates between discrete populations using multilocus genotype data. The approach builds upon a two-step sampling design, where individual genotypes are sampled before and after dispersal. We develop a model that estimates all pairwise backwards migration rates (m(ij), the probability that an individual sampled in population i is a migrant from population j) between a set of populations. The method is validated with simulated data and compared with the methods of BayesAss and Structure. First, we use data for an island model and then we consider more realistic data simulations for a metapopulation of the greater white-toothed shrew (Crocidura russula). We show that the precision and bias of estimates primarily depend upon the proportion of individuals sampled in each population. Weak sampling designs may particularly affect the quality of the coverage provided by 95% highest posterior density intervals. We further show that it is relatively insensitive to the number of loci sampled and the overall strength of genetic structure. The method can easily be extended and makes fewer assumptions about the underlying demographic and genetic processes than currently available methods. It allows backwards migration rates to be estimated across a wide range of realistic conditions.

Genetic variation within and among stone loach, Barbatula barbatula L., populations inhabiting anthropogenically degraded watercourses in Flanders (northern part of Belgium) was assessed using five microsatellite markers. High levels of genetic diversity were observed at all sampling sites, (MNA: 6.2-11.2; H-O: 0.64-0.75; H-E: 0.67-0.85). Estimates of the effective population size varied between 1535 and 3021 individuals and there were no indications of recent severe bottlenecks. Significant genetic differentiation was observed among sites belonging to different river systems and drainage basins. These results suggest human activities, such as pollution and river engineering, have not impacted significantly on genetic variability in the stone loach populations investigated. It is possible that this lack of genetic erosion may be attributed to species-specific characteristics such as pollution tolerance and ecological flexibility.

Japanese goshawk was classified as a vulnerable species in the Red Data Book. There have been possibilities of a decrease of genetic diversity accompanied by habitat loss and genetic pollution due to hybridization with escaping imported goshawks. In this paper, genetic diversity, gene flow and conservation of Northern Goshawk (Accipiter gentilis) in Japan are discussed and compared with that in Central Asia. We used 11 newly developed microsatellite markers and also adopted six previously published markers. Genetic diversity was shown to be maintained with 0.58 as mean heterozygosity and 3.95 as mean allelic richness. The degree of genetic differentiation across all populations was low (Nei's genetic differentiation index = 0.036, Wright's genetic differentiation index = 0.039), possibly due to gene flow via adjacent regions (average number of migrants = 4.26; 0.68-20.30). However, it is possible that slight differentiation resulted from the short divergence time and/or inflow of escaping imported individuals. We recommend that goshawks in eastern Japan should be managed as a single unit. They do not appear to be under threat genetically at present, but there is the potential for rapid loss of genetic diversity. For future conservation, investigations of dispersal routes and actual conditions of gene flow are also recommended. To prevent further inflow of escaping goshawks into natural populations, it is desirable to reduce importation of goshawks and to enact a regulation obliging purchasers to register imported goshawks.

In recent years, genetic studies have been used to investigate mating systems of marine turtles, but to date no such research has been conducted on the flatback turtle (Natator depressus). This study investigates paternity of flatback turtle clutches at two rookeries in Queensland, Australia; Peak Island (Keppel Bay), and Mon Repos (Bundaberg). In the 2004-2005 nesting season, tissue samples were taken from either single or multiple clutches (n = 16) of nesting females (n = 8) representing a sampling effort ranging from 25% to 50% offspring per nest. Determination of the extent of multiple paternity was done using a comparative approach that included initial inferences based on observed alleles, Chi-square tests for deviations from Mendelian expectations, and three software programs (PARENTAGE1.0, GERUD2.0 and MER3.0). Results varied depending on the approach, but by calculating a consensus value of the output from these different methods, the null hypothesis of single paternity could be rejected in at least 11 of the 16 clutches (69%). Multiple paternity was thus observed in the clutches of six of nine females (67%), with two or three fathers being the most likely outcome. Analyses of successive clutches illustrated that paternal contribution to clutch fertilization can vary through time, as observed for two females. This first evidence regarding the mating system of flatback turtles indicates that multiple paternity is common in this species and that the observed frequency of multiple paternity is among the higher values reported in marine turtle species. Application of these results to estimates of effective population size (N (e)) suggests that population size may have been relatively stable over long periods. Continued monitoring of population dynamics is recommended to ensure that future changes in the east coast can be detected.

The estimation and maintenance of connectivity among local populations is an important conservation goal for many species at risk. We used Bayesian statistics and coalescent theory to estimate short- and long-term directional gene flow among subpopulations for two reptiles that occur in Canada as peripheral populations that are geographically disjunct from the core of their respective species' ranges: the black ratsnake and the Blanding's turtle. Estimates of directional gene flow were used to examine population connectivity and potential genetic source-sink dynamics. For both species, our estimates of directional short- and long-term gene flow were consistently lower than estimates inferred previously from F (ST) measures. Short- and long-term gene flow estimates were discordant in both species, suggesting that population dynamics have varied temporally in both species. These estimates of directional gene flow were used to identify specific subpopulations in both species that may be of high conservation value because they are net exporters of individuals to other subpopulations. Overall, our results show that the use of more sophisticated methods to evaluate population genetic data can provide valuable information for the conservation of species at risk, including bidirectional estimates of subpopulation connectivity that rely on fewer assumptions than more traditional analyses. Such information can be used by conservation practitioners to better understand the geographic scope required to maintain a functional metapopulation, determine which habitat corridors within a working landscape may be most important to maintain connectivity among subpopulations, and to prioritize subpopulations with respect to their potential to act as genetic sources within the metapopulation.

Due to lack of an adequate statistical framework, biologists studying phylogeography are abandoning traditional methods of estimating phylogeographic history in favor of statistical methods designed to test a priori hypotheses. These new methods may, however, have limited descriptive utility. Here, we develop a new statistical framework that can be used to both test a priori hypotheses and estimate phylogeographic history of a gene (and the statistical confidence in that history) in the absence of such hypotheses. The statistical approach concentrates on estimation of geographic locations of the ancestors of a set of sampled organisms. Assuming a spatially explicit random walk model of migration, we derive an equation describing the likelihood of the geographic coordinates of the individuals represented by internal nodes on a tree (the parameters of interest) and the mean per-generation dispersal distance (which can be estimated as a nuisance parameter), given the geographic coordinates of the individuals represented by tips on the tree (topology and branch lengths are assumed to be known). Using a maximum likelihood approach, which is implemented in the new program PhyloMapper, we apply this statistical framework to a 246-taxon mitochondrial genealogy of North American chorus frogs, focusing in detail on one of these species. We demonstrate three lines of evidence for recent northward expansion of the mitochondrion of the coastal clade of Pseudacris feriarum: higher per-generation dispersal distance in the recently colonized region, a noncentral ancestral location, and directional migration. After illustrating one method of accommodating phylogenetic uncertainty, we conclude by discussing how extensions of this framework could function to incorporate a priori ecological and geological information into phylogeographic analyses.

We review recent trends in phylogeography and phylogenetics and argue that these two fields stand to be reunited by the common yardstick provided by sequence and SNP data and by new multilocus methods for phylogenetic analysis. Whereas the modern incarnation of both fields was spawned by PCR approaches applied to mitochondrial DNA in the late 1980s, the two fields diverged during the 1990s largely due to the adoption by phylogeographers of microsatellites, in contrast to the adoption of nuclear sequence data by phylogeneticists. Sequence-based markers possess a number of advantages over microsatellites, even on the recent time scales that are the purview of phylogeography. Using examples primarily from vertebrates, we trace the maturation of nuclear gene phylogeography and phylogenetics and suggest that the abundant instances of gene tree heterogeneity beckon a new generation of phylogenetic methods that focus on estimating species trees as distinct from gene trees. Whole genomes provide a powerful common yardstick on which both phylogeography and phylogenetics can assume their proper place as ends of a continuum.

Comparative phylogeography is a powerful method for testing hypotheses of evolutionary diversification in ecological communities. Caribbean lizards of the genus Anolis are a species-rich group and a well-known example of adaptive radiation. In 1983, Ernest Williams suggested that species of Anolis that belong to the same `climate type' (taxa that occur sympatrically in either xeric, mesic or very wet habitats) probably evolved under similar ecological conditions, and thus have experienced a parallel evolutionary history. This hypothesis implies that the phylogeographical patterns of such species can be expected to be concordant, a prediction that has not been tested. We conducted a comparative phylogeographical and population genetic study of Anolis poncensis and Anolis cooki, two sympatric lizards restricted to the aridlands of southwestern Puerto Rico, to determine whether there are similarities in the genetic architecture of the two anoles that may have resulted from a parallel response to the same historical events, or whether each taxon displays a distinct pattern of geographical distribution of intraspecific genealogical lineages. Our dataset consisted of approximately 2120 base pairs of the ND2 and cytochrome b genes from specimens from the known extant populations of the two species. The average haplotype diversity in A. poncensis (0.36) was considerably lower than that in A. cooki (0.62), whereas the average nucleotide diversity in A. cooki was ten times higher than that in A. poncensis. Both anoles showed pronounced phylogeographical structure, with no shared haplotypes among populations. The gene genealogy of A. poncensis recovered three strongly supported clades: the westernmost population, the easternmost deme and the three intermediate populations. In A. cooki, the populations from the western part of the species' range formed a well-supported group, to the exclusion of the eastern demes. Pairwise F-ST values revealed significant genetic differentiation among all conspecific populations of both anoles. Coalescent simulations indicated that A. poncensis could have evolved under a scenario of simple population fragmentation during the Pleistocene, but that A. cooki did not. The estimate of the effective population size of A. cooki was an order of magnitude larger than that of A. poncensis. Because time to the most recent common ancestor is dependent on effective population size, this tenfold difference implies that the time to the most recent common ancestor of A. cooki is much longer than that of A. poncensis, which indicates that A. cooki diversified earlier than A. poncensis. Collectively, these findings suggest that, although A. poncensis and A. cooki are syntopic throughout much of their current distribution, intraspecific diversification in the two species has not proceeded in parallel, which does not support the hypothesis that Anolis lizards that occupy the same climate-type region possess spatially and temporally congruent genetic architectures. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96, 617-634.

Rhizoctonia solani anastomosis group (AG)-1 IA causes soybean foliar blighting (aerial blight) and rice sheath blight diseases. Although taxonomically related within the AG-1 complex, sister populations of R. solani AG-1 IA infecting Poaceae (rice) and Fabaceae (soybean) are genetically distinct based on internal transcribed spacer rDNA. However, there is Currently no information available regarding the extent of genetic differentiation and host specialization between rice- and soybean-infecting populations of R. solani AG-1 IA. We used 10 microsatellite loci to compare sympatric R. solani AG-1 IA populations infecting rice and soybeans in Louisiana and one allopatric rice-infecting population from Texas. None of the 154 multilocus genotypes found among the 223 isolates were shared among the three populations. Partitioning of genetic diversity showed significant differentiation among sympatric populations from different host Species (Phi(ST) = 0.39 to 0.41). Historical migration patterns between sympatric rice- and soybean-infecting populations from Louisiana were asymmetrical. Rice- and soybean-derived isolates of R. solani AG-1 IA were able to infect both rice and soybean, but were significantly more aggressive on their host of on-in, consistent with host specialization. The soybean-infecting Population from Louisiana was more clonal than the sympatric rice-infecting population. Most of the loci in the soybean-infecting populations were Out of Hardy-Weinberg equilibrium (HWE.), but the sympatric rice-infecting population from Louisiana was mainly in HWE. All populations presented evidence for a mixed reproductive system.

The potential effect of population outbreaks on within and between genetic variation of populations in pest species has rarely been assessed. In this study, we compare patterns of genetic variation in different sets of historically frequently outbreaking and rarely outbreaking populations of an agricultural pest of major importance, the migratory locust, Locusta migratoria. We analyse genetic variation within and between 24 populations at 14 microsatellites in Western Europe, where only ancient and low-intensity outbreaks have been reported (non-outbreaking populations), and in Madagascar and Northern China, where frequent and intense outbreak events have been recorded over the last century (outbreaking populations). Our comparative survey shows that (i) the long-term effective population size is similar in outbreaking and non-outbreaking populations, as evidenced by similar estimates of genetic diversity, and (ii) gene flow is substantially larger among outbreaking populations than among non-outbreaking populations, as evidenced by a fourfold to 30-fold difference in F-ST values. We discuss the implications for population dynamics and the consequences for management strategies of the observed patterns of genetic variation in L. migratoria populations with contrasting historical outbreak frequency and extent.

Previous studies on Pleistocene phylogeography of European taxa are biased towards (i) vertebrates, (ii) terrestrial taxa, (iii) single species, and (iv) taxa that survived the Pleistocene in southern refugia. Relatively little is known about whether evolutionary patterns of vertebrate and terrestrial taxa are also applicable to freshwater invertebrates, whether cold-adapted freshwater species could survive in extensive permafrost areas without retreating into refugia, and whether Pleistocene phylogeographical patterns are influenced by phylogeny. Here, the widespread and species-rich European spring snail genus Bythinella Moquin-Tandon, 1856 is utilized in an attempt to mitigate this bias. These strongly cold-adapted freshwater animals mostly occur in springs - highly isolated habitats that are relatively unaffected by anthropogenic influences. Phylogenetic and phylogeographical analyses based on mitochondrial DNA and nuclear DNA sequence data were conducted in 458 specimens from 142 populations occurring throughout Europe. The study provides evidence that most Bythinella spp. survived the Pleistocene in restricted northern glacial refugia that largely correspond to refugia previously recognized for other European biota. However, survival of Bythinella spp. in extensive permafrost areas outside of refugia can likely be rejected. Low dispersal ability and the isolation and fragmentation of spring habitats, as well as the distribution of perennial springs within permafrost regions, may account for this result. Tests involving a total of 29 nominal species showed that phylogenetically closely related Bythinella species did not occupy similar refugia. This lack of phylogenetic concordance could possibly be explained by the stochasticity of survival and dispersal in spring snails.

Pseudoautosomal regions (PARs) shared by avian Z and W sex chromosomes are typically small homologous regions within which recombination still occurs and are hypothesized to share the properties of autosomes. We capitalized on the unusual structure of the sex chromosomes of emus, Dromaius novaehollandiae, which consist almost entirely of PAR shared by both sex chromosomes, to test this hypothesis. We compared recombination, linkage disequilibrium (LD), GC content, and nucleotide diversity between pseudoautosomal and autosomal loci derived from 11 emu bacterial artificial chromosome (BAC) clones that were mapped to chromosomes by fluorescent in situ hybridization. Nucleotide diversity (pi = 4N(e)mu) was not significantly lower in pseudoautosomal loci (14 loci, 1.9 +/- 2.4 x 10(-3)) than autosomal loci (8 loci, 4.2 +/- 6.1 x 10(-3)). By contrast, recombination per site within BAC-end sequences (rho = 4Nc) (pseudoautosomal, 3.9 +/- 6.9 x 10(-2); autosomal, 2.3 +/- 3.7 x 10(-2)) was higher and average LD (D') (pseudoautosomal, 4.2 +/- 0.2 x 10(-1); autosomal, 4.7 +/- 0.5 x 10(-1)) slightly lower in pseudoautosomal sequences. We also report evidence of deviation from a simple neutral model in the PAR and in autosomal loci, possibly caused by departures from demographic equilibrium, such as population growth. This study provides a snapshot of the population genetics of avian sex chromosomes at an early stage of differentiation.

Rhesus macaque (Macaca mulatta) and long-tailed macaque (Macaca fascicularis) are the 2 most commonly used primate model species in biomedical sciences. Although morphological studies have revealed a weak hybridization at the interspecific contact zone, in the north of Indochina, a molecular study has suggested an ancient introgression from rhesus to long-tailed macaque into the Indo-Chinese peninsula. However, the gene flow between these 2 taxa has never been quantified using genetic data and theoretical models. In this study, we have examined genetic variation within and between the parapatric Chinese rhesus macaque and Indo-Chinese long-tailed macaque populations, using 13 autosomal, 5 sex-linked microsatellite loci and mitochondrial DNA sequence data. From these data, we assessed genetic structure and estimated gene flow using a Bayesian clustering approach and the “Isolation with Migration” model. Our results reveal a weak interspecific genetic differentiation at both autosomal and sex-linked loci, suggesting large population sizes and/or gene flow between populations. According to the Bayesian clustering, Chinese rhesus macaque is a highly homogeneous gene pool that contributes strongly to the current Indo-Chinese long-tailed macaque genetic makeup, whether or not current admixture is assumed. Coalescent simulations, which integrated the characteristics of the loci, pointed out 1) a higher effective population size in rhesus macaque, 2) no mitochondrial gene flow, and 3) unilateral and male-mediated nuclear gene flow of similar to 10 migrants per generation from rhesus to long-tailed macaque. These patterns of genetic structure and gene flow suggest extensive ancient introgression from Chinese rhesus macaque into the Indo-Chinese long-tailed macaque population.

Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H-E = 0.483-0.612), and private alleles ranged from 0 to 6. Both F-ST and R-ST indicated significant population structure (P < 0.001) with F-ST < 0.109 and R-ST < 0.125. Results of analyses from STRUCTURE indicated 2 prominent population groups, a mix of moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R-2 = 0.45, P < 0.01). Finally, there was no evidence of bottlenecks either at the population level or overall. We conclude that weak population structure occurs among moose in Alaska with population expansion from interior Alaska westward toward the coast.

Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation-drift equilibrium. Dominant downstream migration over both short- and long-time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source-sink metapopulation, with the tributary furthest downstream representing a `super sink', receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.

To understand mechanisms structuring diversity in young adaptive radiations, quantitative and unbiased information about genetic and phenotypic diversity is much needed. Here, we present the first in-depth investigation of whitefish diversity in a Swiss lake, with continuous spawning habitat sampling in both time and space. Our results show a clear cline like pattern in genetics and morphology of populations sampled along an ecological depth gradient in Lake Neuchatel. Divergent natural selection appears to be involved in shaping this cline given that trait specific P-ST-values are significantly higher than F-ST-values when comparing populations caught at different depths. These differences also tend to increase with increasing differences in depth, indicating adaptive divergence along a depth gradient, which persists despite considerable gene flow between adjacent demes. It however remains unclear, whether the observed pattern is a result of currently stable selection-gene flow balance, incipient speciation, or reverse speciation due to anthropogenic habitat alteration causing two formerly divergent species to collapse into a single gene pool.

Coalescent genealogy samplers attempt to estimate past qualities of a population, such as its size, growth rate, patterns of gene flow or time of divergence from another population, based on samples of molecular data. Genealogy samplers are increasingly popular because of their potential to disentangle complex population histories. In the last decade they have been widely applied to systems ranging from humans to viruses. Findings include detection of unexpected reproductive inequality in fish, new estimates of historical whale abundance, exoneration of humans for the prehistoric decline of bison and inference of a selective sweep on the human Y chromosome. This review summarizes available genealogy-sampler software, including data requirements and limitations on the use of each program.

Two types of demographic analyses, perturbation analysis and uncertainty analysis, can be conducted to gain insights about matrix population models and guide population management. Perturbation analysis studies how the perturbation of demographic parameters (survival, growth, and reproduction parameters) may affect the population projection, while uncertainty analysis evaluates how much uncertainty there is in population dynamic predictions and where the uncertainty comes from. Previously, both perturbation analysis and uncertainty analysis were conducted on the long-term population growth rate. However, the population may not reach its equilibrium state, especially when there is management by harvesting or hunting. Recently, there has been an increased interest in short-term transient dynamics, which can differ from asymptotic long-term dynamics. There are currently techniques to conduct perturbation analyses of short-term transient dynamics, but no techniques have been proposed for uncertainty analysis of such dynamics. In this study, we introduced an uncertainty analysis technique, the general Fourier Amplitude Sensitivity Test (FAST), to study uncertainties in transient population dynamics. The general FAST is able to identify the amount of uncertainty in transient dynamics and contributions by different demographic parameters. We applied the general FAST to a mountain goat (Oreamnos americanus) matrix population model to give a clear illustration of how uncertainty analysis can be conducted for transient dynamics arising from matrix population models. (C) 2008 Elsevier B.V All rights reserved.

To describe and analyse phylogeographical patterns in the endangered endemic lizard Podarcis lilfordi from across its remaining range and thereby establish baseline information on genetic diversity that will help determine conservation priorities and assist future reintroduction programs. Balearic Islands, Spain. We analysed mitochondrial DNA (2382 bp sequence from eight genes) from 118 individuals and characterized the relationships among haplotypes using parsimony networks, as well as phylogenetic inference. Analyses of historical gene flow and population growth were used to provide further insights into population histories. Four unconnected parsimony networks were obtained that mirrored the main clades in the phylogenetic tree: (I) all Menorcan populations, (II) Dragonera, Malgrats and Toro islands (Western Mallorca) (III and IV) and the remaining populations from Cabrera and Mallorca. Two major haplotype groups were detected in Menorca (I) and these provided signatures of a demographic expansion and asymmetrical historical gene flow, respectively, concordant with the expected direction of colonization from south to north of the island. Populations from western Mallorca (II) showed evidence of historical allopatric fragmentation events following isolation around the start of the Pleistocene. In networks III and IV, Cabreran populations appear to have become isolated from north and south Mallorca quite recently, with asymmetric gene flow indicating a northwards dispersal direction. P. lilfordi is a genetically diverse species that shows substantial mtDNA structuring both between regions and, at a finer scale, between some islet populations within regions. The precarious state of some islet populations shown here to be quite divergent (e.g. Toro island in western Mallorca) means that conservation of this intraspecific biodiversity requires urgent action.

Pleistocene climate fluctuations shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Late Pleistocene for East Asia, a region of great topographical complexity and presumably milder historical climate, remains poorly understood. We analysed 3.86 kb of the mitochondrial genome of 186 Chinese Hwamei birds, Leucodioptron canorum canorum, and found that contrary to the conventional expectation of population decline during cold periods (stadials), the demographic history of this species shows continuous population growth since the penultimate glacial period (about 170 000 years ago). Refugia were identified in the south, coastal regions, and northern inland areas, implying that topographic complexity played a substantial role in providing suitable habitats for the Chinese Hwamei during cold periods. Intermittent gene flow between these refugia during the warmer periods (interstadials) might have resulted in a large effective population of this bird through the last glacial period.

IBDSim is a package for the simulation of genotypic data under isolation by distance. It is based on a backward `generation by generation' coalescent algorithm allowing the consideration of various isolation by distance models with discrete subpopulations as well as continuous populations. Many dispersal distributions can be considered as well as heterogeneities in space and time of the demographic parameters. Typical applications of our program include (i) the study of the effect of various sampling, mutational and demographic factors on the pattern of genetic variation; and (ii) the production of test data sets to assess the influence of these factors on inferential methods available to analyse genotypic data.

Cold-adapted species in the Northern Hemisphere frequently show arctic-alpine discontinuous ranges at high latitudes and on mountains farther south, but area connectivity through current and historical gene flow remains unclear. We used the coalescent-based program IMa (Isolation with Migration-analytic) to test for migration among disjunct European areas of arctic-alpine wolf spiders of the Pardosa saltuaria group. Mitochondrial (ND1) and nuclear (ITS1, 5.8S rDNA, ITS2) markers were analyzed simultaneously. Gene flow was unidirectional from Scandinavia to the Alps and the Carpathians, complex with respect to intermediate relict areas in central Europe, and very limited in outlying areas in the Balkans and Pyrenees. Population connectivity may have been greater during glacial events that might alternatively account for the inferred arctic-alpine links. A simulation study under various demographic histories (using a new module in the Mesquite package, which models episodic migration) showed that the empirical results are equally consistent with moderate levels of ongoing (continuous) migration or, alternatively, with strong migration bursts at the last glacial maximum but not at earlier times. Habitat connectivity was probably maximal during glacial events, illustrating the potential influence of ecology and life history on organismal responses to past climatic change.

Disease ecologists strive to understand the causes and consequences of parasite infection, including the emergence, spread, persistence and evolution of infectious disease. These processes can be illuminated by parasite genetic markers, which can be used to track parasite spread and infer population history. Recently, a growing number of studies have used molecular tools to examine questions on the ecology of infectious diseases. We review this burgeoning area of research by focusing on three topics where genetic tools will increasingly make major contributions: inferring parasite transmission, reconstructing epidemiological history and identifying physical and environmental drivers of disease spread. We also discuss areas for future research and highlight the promise of multidisciplinary collaborations among geneticists, ecologists and epidemiologists.

BACKGROUND: QoI fungicides or quinone outside inhibitors (also called strobilurins) have been widely used to control agriculturally important fungal pathogens since their introduction in 1996. Strobilurins block the respiration pathway by inhibiting the cytochrome bc1 complex in mitochondria. Several plant pathogenic fungi have developed field resistance. The first QoI resistance in Mycosphaerella graminicola (Fuckel) Schroter was detected retrospectively in UK in 2001 at a low frequency in QoI-treated plots. During the following seasons, resistance reached high frequencies across northern Europe. The aim of this study was to identify the main evolutionary forces driving the rapid emergence and spread of QoI resistance in M. graminicola populations. RESULTS: The G143A mutation causing QoI resistance was first detected during 2002 in all tested populations and in eight distinct mtDNA sequence haplotypes. By 2004, 24 different mtDNA haplotypes contained the G143A mutation. Phylogenetic analysis showed that strobilurin resistance was acquired independently through at least four recurrent mutations at the same site of cytochrome b. Estimates of directional migration rates showed that the majority of gene flow in Europe had occurred in a west-to-east direction. CONCLUSION: This study demonstrated that recurring mutations independently introduced the QoI resistance allele into different genetic and geographic backgrounds. The resistant haplotypes then increased in frequency owing to the strong fungicide selection and spread eastward through wind dispersal of ascospores. (C) 2008 Society of Chemical Industry

A phylogeographical analysis of the scald pathogen Rhynchosporium secalis was conducted using nuclear DNA sequences from two neutral restriction fragment length polymorphism loci and the mating-type idiomorphs. Approximately 500 isolates sampled from more than 60 field populations from five continents were analysed to infer migration patterns and the demographic history of the fungus. Migration rates among continents were generally low, consistent with earlier reports of significant population subdivision among continents. Northern Europe was mainly a source population for global migration. We hypothesize that the pathogen only recently moved out of its centre of origin, resulting in founder populations that are reproductively isolated due to the contemporary absence of long-distance gene flow.

We fit a molecular data set, consisting of the rpL16 cpDNA marker and eight microsatellite loci, to the isolation-with-migration model as implemented in IMa to test a well-supported phylogenetic hypothesis of relationships within the Carex macrocephala species complex (Cyperaceae). The phylogenetic hypothesis suggests C. macrocephala from North America is reciprocally monophyletic and is sister to a reciprocally monophyletic clade of C. kobomugi. The North American C. macrocephala and C. kobomugi clade form a sister clade with a lineage of Asian C. macrocephala, thereby forming a paraphyletic C. macrocephala species. Not only does the phylogenetic hypothesis suggest C. macrocephala is paraphyletic, but it also suggests that the two lineages which share a partially overlapping distribution, Asian C. macrocephala and C. kobomugi, are not the most closely related. To test these relationships, we used coalescent-based population genetic models to infer divergence time for each lineage pair within the species complex. The coalescent-based models account for the stochastic forces which drive population divergence, and can account for the lineage sorting that occurs prior to lineage divergence. A drawback to phylogenetic-based phylogeographical analyses is that they do not account for stochastic lineage sorting that occurs between gene divergence and lineage divergence. By comparing the relative divergence time of the three main lineages within this group, Asian C. macrocephala, North American C. macrocephala, and C. kobomugi, we concluded that the phylogenetic hypothesis is incorrect, and the divergence between these lineages occurred during the Late Pleistocene epoch.

Understanding the impact of past climatic events on species may facilitate predictions of how species will respond to future climate change. To this end, we sampled populations of the common pond snail Radix balthica over the entire species range (northwestern Europe). Using a recently developed analytical framework that employs ecological niche modelling to obtain hypotheses that are subsequently tested with statistical phylogeography, we inferred the range dynamics of R. balthica over time. A Maxent modelling for present-day conditions was performed to infer the climate envelope for the species, and the modelled niche was used to hindcast climatically suitable range at the last glacial maximum (LGM) c. 21 000 years ago. Ecological niche modelling predicted two suitable areas at the LGM within the present species range. Phylogeographic model selection on a COI mitochondrial DNA data set confirmed that R. balthica most likely spread from these two disjunct refuges after the LGM. The match observed between the potential range of the species at the LGM given its present climatic requirements and the phylogeographically inferred refugial areas was a clear argument in favour of niche conservatism in R. balthica, thus allowing to predict the future range. The subsequent projection of the potential range under a global change scenario predicts a moderate pole-ward shift of the northern range limits, but a dramatic loss of areas currently occupied in France, western Great Britain and southern Germany.

We examine the genetic structure of a fungal polypore, Datronia caperata (Berk.) Ryvarden (Polyporaceae), colonizing white mangrove, Laguncularia racemosa (L.) Gaertn. f. (Combretaceae), of Central America. Mangrove forests of Costa Rica and Panama. Sequences of elongation factor alpha (EFA), beta tubulin (BTUB) and nuclear ribosomal internal transcribed spacer (ITS) regions were obtained from 54 collections of D. caperata collected from Caribbean and Pacific L. racemosa forests in Central America. Measures of haplotype and nucleotide diversity, nested clade analyses and coalescent analyses were used to estimate the direction and extent of migration of the fungus, and the factors promoting population divergence. We also conducted phylogenetic analyses using Bayesian estimation to test whether putative D. caperata collected from L. racemosa was conspecific with D. caperata colonizing other hosts from diverse Neotropical forests. Our results demonstrate that there is genetic isolation between D. caperata populations from Caribbean mangroves and those from Pacific mangroves. Our data suggest that the best explanation for the observed haplotype distribution is a recent range expansion from the Caribbean to the Pacific coasts, with subsequent isolation. This is supported by the infrequent overlap of haplotypes, unidirectional migration estimates from the Caribbean to the Pacific and the older estimated age of mutations in the Caribbean low-copy BTUB and EFA loci. In addition, our data suggest that D. caperata from mangroves are not conspecific with collections from other hosts found in diverse Neotropical forests. The low frequency of shared haplotypes between coasts, coupled with the incomplete lineage sorting after cessation of gene flow, is consistent with isolation during the last Pleistocene glaciation. We hypothesize that the greater haplotype and nucleotide diversity in the Pacific occurs either because larger effective population sizes of D. caperata are maintained in Pacific mangroves or because D. caperata populations underwent a significant bottleneck as a result of local extinction followed by recolonization. In addition, we found that D. caperata found on L. racemosa was not conspecific with D. caperata from non-mangrove hosts and suggest that D. caperata found on L. racemosa may be a host specialist.

The advent and maturation of algorithms for estimating species trees-phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes-represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for themolecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a “local optimum” for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term “phylogeny” for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.

Beginning in the 1930s, eelgrass meadows declined throughout the Wadden Sea, leaving populations susceptible to extinction through patchiness, low density and isolation. Additional anthropogenic impacts have altered current regimes, nutrients and turbidity-all of which affect eelgrass. Recent abiotic modeling studies suggest that poor recovery is the result of a regime shift caused by the loss of positive feedbacks between seagrass meadows and their capacity to mediate turbidity. Additionally, it is hypothesized that genetic and demographic factors-in particular, the loss of genetic diversity and patch connectivity-have contributed to lower fitness of eelgrass, thereby further diminishing recovery potential. We assessed genetic diversity and connectivity of Zostera marina among 19 locations, covering some 950 km of coastline between Zeeland, Netherlands and Langholmen, Sweden. Both allelic and genotypic diversity were high. A Bayesian analysis of population structure revealed 6 significant clusters of subpopulations that are connected by varying degrees of dispersal. Although population divergence was significant at as little as 5 km, isolation by distance was very weak, indicating high connectivity at scales of 1.50 km. A demographic interpretation of these data suggests that realized gene flow is strong and predominantly northward, leaving the western Wadden Sea relatively isolated. The failure of eelgrass to recover in the western Wadden Sea is, therefore, due to both unsuitable physical conditions and low incoming gene flow, Nonetheless, the greater Wadden Sea can be considered a seed transfer zone providing source material for restoration efforts in any areas where abiotic conditions are more favorable.

The study of population genetics of invasive species offers opportunities to investigate rapid evolutionary processes at work, and while the ecology of biological invasions has enjoyed extensive attention in the past, the recentness of molecular techniques makes their application in invasion ecology a fairly new approach. Despite this, molecular biology has already proved powerful in inferring aspects not only relevant to the evolutionary biologist but also to those concerned with invasive species management. Here, we review the different molecular markers routinely used in such studies and their application(s) in addressing different questions in invasion ecology. We then review the current literature on molecular genetic studies aimed at improving management and the understanding of invasive species by resolving of taxonomic issues, elucidating geographical sources of invaders, detecting hybridisation and introgression, tracking dispersal and spread and assessing the importance of genetic diversity in invasion success. Finally, we make some suggestions for future research efforts in molecular ecology of biological invasions.

Background: Oceanography and life-history characteristics are known to influence the genetic structure of marine species, however the relative role that these factors play in shaping phylogeographic patterns remains unresolved. The population genetic structure of the endemic, rocky shore dwelling Caffrogobius caffer was investigated across a known major oceanographic barrier, Cape Agulhas, which has previously been shown to strongly influence genetic structuring of South African rocky shore and intertidal marine organisms. Given the variable and dynamic oceanographical features of the region, we further sought to test how the pattern of gene flow between C. caffer populations is affected by the dominant Agulhas and Benguela current systems of the southern oceans. Results: The variable 5' region of the mtDNA control region was amplified for 242 individuals from ten localities spanning the distributional range of C. caffer. Fifty-five haplotypes were recovered and in stark contrast to previous phylogeographic studies of South African marine species, C. caffer showed no significant population genetic structuring along 1300 km of coastline. The parsimony haplotype network, AMOVA and SAMOVA analyses revealed panmixia. Coalescent analyses reveal that gene flow in C. caffer is strongly asymmetrical and predominantly affected by the Agulhas Current. Notably, there was no gene flow between the east coast and all other populations, although all other analyses detect no significant population structure, suggesting a recent divergence. The mismatch distribution suggests that C. caffer underwent a population expansion at least 14 500 years ago. Conclusion: We propose several possible life-history adaptations that could have enabled C. caffer to maintain gene flow across its distributional range, including a long pelagic larval stage. We have shown that life-history characteristics can be an important contributing factor to the phylogeography of marine species and that the effects of oceanography do not necessarily suppress its influence on effective dispersal.

Background: Evolutionary genetics provides a rich theoretical framework for empirical studies of phylogeography. Investigations of intraspecific genetic variation can uncover new putative species while allowing inference into the evolutionary origin and history of extant populations. With a distribution on four continents ranging throughout most of the Old World, Lampides boeticus ( Lepidoptera: Lycaenidae) is one of the most widely distributed species of butterfly. It is placed in a monotypic genus with no commonly accepted subspecies. Here, we investigate the demographic history and taxonomic status of this widespread species, and screen for the presence or absence of the bacterial endosymbiont Wolbachia. Results: We performed phylogenetic, population genetic, and phylogeographic analyses using 1799 bp of mitochondrial sequence data from 57 specimens collected throughout the species' range. Most of the samples(> 90%) were nearly genetically identical, with uncorrected pairwise sequence differences of 0 0.5% across geographic distances > 9,000 km. However, five samples from central Thailand, Madagascar, northern Australia and the Moluccas formed two divergent clades differing from the majority of samples by uncorrected pairwise distances ranging from 1.79-2.21%. Phylogenetic analyses suggest that L. boeticus is almost certainly monophyletic, with all sampled genes coalescing well after the divergence from three closely related taxa included for outgroup comparisons. Analyses of molecular diversity indicate that most L. boeticus individuals in extant populations are descended from one or two relatively recent population bottlenecks. Conclusion: The combined analyses suggest a scenario in which the most recent common ancestor of L. boeticus and its sister taxon lived in the African region approximately 7 Mya; extant lineages of L. boeticus began spreading throughout the Old World at least 1.5 Mya. More recently, expansion after population bottlenecks approximately 1.4 Mya seem to have displaced most of the ancestral polymorphism throughout its range, though at least two early-branching lineages still persist. One of these lineages, in northern Australia and the Moluccas, may have experienced accelerated differentiation due to infection with the bacterial endosymbiont Wolbachia, which affects reproduction. Examination of a haplotype network suggests that Australia has been colonized by the species several times. While there is little evidence for the existence of morphologically cryptic species, these results suggest a complex history affected by repeated dispersal events.

Previous genetic studies suggest Cape Cod, MA, as a phylogenetic break for benthic marine invertebrates; however, diffuse sampling in this area has hindered fine-scale determination of the break's location and underlying causes. Furthermore, some species exhibit breaks in different places, and others exhibit no breaks in this region. We analyze the phylogeographic patterns of 2 mitochondrial genes from 10 populations of the bamboo worm Clymenella torquata (Annelida: Maldanidae) focused around Cape Cod but extending from the Bay of Fundy, Canada, to New Jersey. A common invertebrate along the US coast, C. torquata, possesses life-history characteristics that should make it sensitive to factors such as dispersal barriers, bottlenecks, and founder events. As an inhabitant of soft sediments, C. torquata offers a unique contrast to existing research dominated by organisms dwelling on hard substrates. Our genetic data show a clear phylogenetic break and a cline of haplotype frequencies from north to south. Fine-scale sampling of populations on Cape Cod, combined with other sampled populations, confirm that this distinct break is not on the Cape Cod peninsula itself but to the south near a boundary of oceanic water masses. Low levels of gene flow occur in these populations, in an asymmetric manner congruent with coastal current patterns. No significant effect of Pleistocene glaciation was seen in the pattern of genetic diversity over the sampled range.

Incomplete lineage sorting has been documented across a diverse set of taxa ranging from song birds to conifers. Such patterns are expected theoretically for species characterized by certain life history characteristics (e.g. long generation times) and those influenced by certain historical demographic events (e.g. recent divergences). A number of methods to estimate the underlying species phylogeny from a set of gene trees have been proposed and shown to be effective when incomplete lineage sorting has occurred. The further effects of gene flow on those methods, however, remain to be investigated. Here, we focus on the performance of three methods of species tree inference, ESP-COAL, minimizing deep coalescence (MDC), and concatenation, when incomplete lineage sorting and gene flow jointly confound the relationship between gene and species trees. Performance was investigated using Monte Carlo coalescent simulations under four models (n-island, stepping stone, parapatric, and allopatric) and three magnitudes of gene flow (N(e)m = 0.01, 0.10, 1.00). Although results varied by the model and magnitude of gene flow, methods incorporating aspects of the coalescent process (ESP-COAL and MDC) performed well, with probabilities of identifying the correct species tree topology typically increasing to greater than 0.75 when five more loci are sampled. The only exceptions to that pattern included gene flow at moderate to high magnitudes under the n-island and stepping stone models. Concatenation performs poorly relative to the other methods. We extend these results to a discussion of the importance of species and population phylogenies to the fields of molecular systematics and phylogeography using an empirical example from Rhododendron. (C) 2008 Elsevier Inc. All rights reserved.

The endemic fauna of the Comoro Archipelago is composed of a mixture of taxa originating from Africa and Madagascar. Bats are the only native land dwelling mammals on this archipelago, but the biogeographical origins for the vast majority of species within this group are ambiguous. We report here genetic analyses based on two mitochondrial DNA markers to infer the origin of Comorian bats belonging to a reputed species complex of Miniopterus that is further distributed across Africa and Madagascar. Phylogenetic reconstructions show that east African M. minor are not closely related to the insular Miniopterus of Madagascar and the Comoros (Grande Comore and Anjouan). The latter cluster into two distinct, monophyletic clades (Clade 1 and Clade 2). Representatives of these clades occur sympatrically both on the Comoros and on Madagascar, and are distinguished by a large genetic distance (K2P: 9.9% for cytochrome b). No haplotypes are shared between any islands, suggesting the absence of contemporary gene flow. Populations of the widespread Clade 1 are furthermore characterized by a significant inter-island structure (Phi(CT) = 0.249), and by high haplotype and nucleotide diversities (h = 0.90-0.98, pi = 0.04-0.06). Demographic analyses of Clade 1 suggest secondary contact between two distinct phylogroups (Subclade 1 A and 1B) that reached Grande Comore and Anjouan, and a large, stable population with a long evolutionary history on Madagascar. These results and the current distribution of related lineages suggest that the Comoros were colonized independently at least two or three times by ancestors from Madagascar.

Ploidy level is an important aspect of the genetic makeup of a plant, and can strongly influence ecological characteristics such as invasiveness. We used a phylogeographical approach to elucidate the history of polyploidization and colonization success of diploid and tetraploid Solidago gigantea Aiton (Asteraceae) within its native range in North America. We were also able to identify the probable source material of the haplotype lineages invasive in Europe and Asia, where only tetraploid plants occur. To do this, we sequenced 1275 bp of chloroplast intergenic spacer DNA in 268 individuals from 57 populations. In addition, we performed a crossing experiment, which supported the hypothesis that chloroplast inheritance in this species is maternal. The phylogeographical analysis showed a complex pattern of 20 haplotypes of diploid and tetraploid plants. In North America, we found significant differentiation among regions, private haplotypes, and isolation by distance. Ploidy levels were more differentiated in the northern regions than in the South. The haplotype network was shallow and included one tetraploid-only, star-shaped cluster of haplotypes that were particularly successful colonizers. Post-glacial migration of diploid S. gigantea occurred mainly northwards east of the Appalachian Mountains, and to a lesser degree also southward. Our data suggest that tetraploids have formed several times in North America. Haplotype number and diversity were lower in European populations than in the native range, and we found evidence that four haplotypes were introduced to Europe from two source areas, New England and the Southern Appalachian Mountains.

Several lines of evidence suggest that recent long-distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi-Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (im and migrate) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F-ST = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long-range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000-289 000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi-Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.

Mitochondrial DNA (mtDNA) is a pivotal tool in molecular ecology, evolutionary and population genetics. The power of mtDNA analyses derives from a relatively high mutation rate and the apparent simplicity of mitochondrial inheritance (maternal, without recombination), which has simplified modelling population history compared to the analysis of nuclear DNA. However, in biology things are seldom simple, and advances in DNA sequencing and polymorphism detection technology have documented a growing list of exceptions to the central tenets of mitochondrial inheritance, with paternal leakage, heteroplasmy and recombination now all documented in multiple systems. The presence of paternal leakage, recombination and heteroplasmy can have substantial impact on analyses based on mtDNA, affecting phylogenetic and population genetic analyses, estimates of the coalescent and the myriad of other parameters that are dependent on such estimates. Here, we review our understanding of mtDNA inheritance, discuss how recent findings mean that established ideas may need to be re-evaluated, and we assess the implications of these new-found complications for molecular ecologists who have relied for decades on the assumption of a simpler mode of inheritance. We show how it is possible to account for recombination and heteroplasmy in evolutionary and population analyses, but that accurate estimates of the frequencies of biparental inheritance and recombination are needed. We also suggest how nonclonal inheritance of mtDNA could be exploited, to increase the ways in which mtDNA can be used in analyses.

A suite of 10 microsatellite loci was used to examine genetic divergence between two sympatric morphs of Arctic charr Salvelinus alpinus ('dark' and `pale') inhabiting Gander Lake, Newfoundland. Results can be summarized as follows: (1) the morphs are strongly reproductively isolated - gene flow-migration estimates were consistently low in long and short-term evolutionary timescales of analysis; (2) intermorph divergence based on allele size (R-ST) was significantly larger than those based on allele state (theta) implying a cumulative effect of stepwise-like mutations; (3) historical (coalescent) and current (linkage disequilibrium) point estimates of effective population size (N-e) were consistently higher for dark than for pale S. alpinus. The first and second findings lend support to the hypothesis that divergence between forms may have preceded the last glacial period (ending c. 12 000 years bp). The third finding argues for significant differences in habitat quantity and quality between morphs, which were emphasized in a previous study. Overall, these analyses underscore the importance of genetic assessment and monitoring in the conservation of fish diversity, with emphasis on `rare' or under-represented forms among temperate species pairs.

Understanding patterns of genetic structure is fundamental for developing successful management programmes for deme-structured organisms, such as amphibians. We used five microsatellite loci and DNA sequences of the mitochondrial control region to assess the relative influences of landscape (geographic distance, altitude and rivers as corridors for dispersal) and historical factors on patterns of gene flow in populations of the toad Bufo bufo in Central Spain. We sampled 175 individuals from eight populations distributed along two major river drainages and used maximum-likelihood and Bayesian approaches to infer patterns of gene flow and population structure. The mitochondrial DNA data show closely-related haplotypes distributed across the Iberian Peninsula with no geographic structuring, suggesting recent differentiation of haplotypes and extensive gene flow between populations. On the other hand, microsatellites provide finer resolution, showing that high altitude populations (> 2000 m) exchange lower numbers of migrants with other populations. The results of Bayesian estimates for recent migration rates in high altitude populations suggest source-sink dynamics between ponds that are consistent with independent data from monitoring over the past 20 years. (C) 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 824-839.

By providing new approaches to the investigation of demographic and evolutionary dynamics of wild populations, molecular genetics has led to fundamental changes in our understanding of marine ecology. In particular, genetic approaches have revolutionized our understanding in three areas: (i) most importantly, they have contributed to the discovery of extensive genetic population structure in many marine species, overturning the notion of large, essentially homogenous marine populations limiting local adaptation and speciation. (ii) Concomitant differences in ecologically important traits now indicate extensive adaptive differentiation and biocomplexity, potentially increasing the resilience to exploitation and disturbance. Evidence for rapid adaptive change in many populations underlies recent concerns about fisheries-induced evolution affecting life-history traits. (iii) A compilation of recent published research shows estimated effective population sizes that are 2-6 orders of magnitude smaller than census sizes, suggesting more complex recruitment dynamics in marine species than previously assumed. Studies on Atlantic cod are used to illustrate these paradigm shifts. In our synthesis, we emphasize the implications of these discoveries for marine ecology and evolution as well as the management and conservation of exploited marine fish populations. An important implication of genetic structuring and the potential for adaptive divergence is that locally adapted populations are unlikely to be replaced through immigration, with potentially detrimental consequences for the resilience to environmental change - a key consideration for sustainable fisheries management.

Clinus cottoides is a fish endemic to the coast of South Africa, predominantly inhabiting rock pools. All South African clinids are viviparous, but probably breed throughout the year; as such, their dispersal may be limited, unlike species with pelagic larval stages. We analysed 343 fish from 14 localities on the west, south and east coasts using two mitochondrial genes and the second intron of the S7 ribosomal gene. Mitochondrial DNA analyses recovered significant genetic differentiation between fish populations from the east coast and other sampling locations, with a second break found between Gansbaai and Cape Agulhas on the south coast. Nuclear DNA recovered shallower, but significant, levels of population structure. Coalescent analyses suggested remarkably asymmetrical gene flow between sampling locations, suggesting that the cold Atlantic Benguela Current and Indian Ocean Agulhas counter-current play important roles in facilitating dispersal. There was no gene flow between the east coast and the other sites, suggesting that these populations are effectively isolated. Divergence times between them were estimated to at least 68 000 years. Neutrality tests and mismatch distributions suggest recent population expansions, with the exception of peripheral western and eastern populations (possibly a consequence of environmental extremes at the edge of the species distribution). Analyses of the current South African marine protected areas network show that it is not connected and that De Hoop, one of South Africa's largest marine reserves, appears to be an important source population of recruits to both the south and southwest coasts.

Mountain Plover (Charadrius montanus) is a species of conservation concern that has experienced significant habitat loss and population decline. This, coupled with previous observations that the species exhibits strong fidelity to breeding grounds, suggests that breeding populations may be genetically differentiated and possibly suffer from reduced genetic variation associated with relatively small population sizes. A previous genetic study comparing mitochondrial DNA sequences of plovers in Montana and Colorado found high levels of genetic variability and very little genetic differentiation among breeding locales. Because mitochondrial DNA can track only female movements and is sampled from only one locus, we used 14 nuclear microsatellite loci to further examine population structure, thereby both documenting male movements and providing a more comprehensive view of genetic structure. We found no significant differences among breeding populations. The most likely number of unique genetic clusters was one, suggesting that all sampled breeding locations comprise a single relatively homogenous gene pool. Levels of genetic diversity were similar across all four populations, with the greatest diversity in the southern plains population. We speculate that the lack of detectable genetic differentiation among populations is due to sufficient gene flow among breeding populations that might ensue if at least some pair bonds are formed when birds form mixed flocks on wintering grounds. This study corroborates and expands upon the findings of a previous mitochondrial DNA study providing a more comprehensive view of Mountain Plover population structure.

Sequence variation of control region mitochondrial DNA, phylogenetic reconstruction, and analysis of molecular variance (AMOVA) were used to determine the degree of genetic structure of Yellow Warblers (Dendroica petechia) in the Galapagos Archipelago. When the Galapagos population was partitioned into subpopulations (by island), AMOVA indicated a nonsignificant level of genetic structure. The presence of the same haplotype on more than one island also indicated low genetic divergence among subpopulations. Using these sequences and those available in Genbank, we also determined the degree of divergence between the Galapagos Yellow Warbler population and other New World populations. Mean sequence divergence between the Galapagos population and Latin American populations was 3.7%, and between the Galapagos population and North American populations was 6.7%.

Background: The early radiation of the Cetartiodactyla is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (Cetacea and Ruminantia). There is also a need for informative genealogic markers for Y-chromosome population genetics as well as a sexing method applicable to all species from this group. We therefore studied the sequence variation of a partial sequence of the evolutionary conserved amelogenin gene to assess its potential use in each of these fields. Results and discussion: We report a large interstitial insertion in the Y amelogenin locus in most of the Cetartiodactyla lineages (cetaceans and ruminants). This sex-linked size polymorphism is the result of a 460-465 bp inserted element in intron 4 of the amelogenin gene of Ruminants and Cetaceans. Therefore, this polymorphism can easily be used in a sexing assay for these species. When taking into account this shared character in addition to nucleotide sequence, gene genealogy follows sex-chromosome divergence in Cetartiodactyla whereas it is more congruent with zoological history when ignoring these characters. This could be related to a loss of homology between chromosomal copies given the old age of the insertion. The 1 kbp Amel-Y amplified fragment is also characterized by high nucleotide diversity (64 polymorphic sites spanning over 1 kbp in seven haplotypes) which is greater than for other Y-chromosome sequence markers studied so far but less than the mitochondrial control region. Conclusion: The gender-dependent polymorphism we have identified is relevant not only for phylogenic inference within the Cetartiodactyla but also for Y-chromosome based population genetics and gender determination in cetaceans and ruminants. One single protocol can therefore be used for studies in population and evolutionary genetics, reproductive biotechnologies, and forensic science.

In the last two decades, mitochondrial DNA (mtDNA) and the non-recombining portion of the Y chromosome (NRY) have been extensively used in order to measure the maternally and paternally inherited genetic structure of human populations, and to infer sex-specific demography and history. Most studies converge towards the notion that among populations, women are genetically less structured than men. This has been mainly explained by a higher migration rate of women, due to patrilocality, a tendency for men to stay in their birthplace while women move to their husband's house. Yet, since population differentiation depends upon the product of the effective number of individuals within each deme and the migration rate among demes, differences in male and female effective numbers and sex-biased dispersal have confounding effects on the comparison of genetic structure as measured by uniparentally inherited markers. In this study, we develop a new multi-locus approach to analyze jointly autosomal and X-linked markers in order to aid the understanding of sex-specific contributions to population differentiation. We show that in patrilineal herder groups of Central Asia, in contrast to bilineal agriculturalists, the effective number of women is higher than that of men. We interpret this result, which could not be obtained by the analysis of mtDNA and NRY alone, as the consequence of the social organization of patrilineal populations, in which genetically related men (but not women) tend to cluster together. This study suggests that differences in sex-specific migration rates may not be the only cause of contrasting male and female differentiation in humans, and that differences in effective numbers do matter.

Although the power of multi-locus data in estimating species trees is apparent, it is also clear that the analytical methodologies for doing so are still maturing. For example, of the methods currently available for estimating species trees from multiocus data, the Bayesian method introduced by Liu and Pearl (2007; BEST) is the only one that provides nodal support values. Using gene sequences from five nuclear loci, we explored two analytical methods (deep coalescence and BEST) to reconstruct the species tree of the five primary Manacus OTUs: M. aurantiacus, M. candei, M. vitellinus, populations of M. manacus from west of the Andes (M. manacus (w)), and populations of M. manacus from east of the Andes (M. manacus (e)). Both BEST and deep coalescence supported a sister relationship between M. vitellinus and M. manacus (w). A lower probability tree from the BEST analysis and one of the most parsimonious deep coalescence trees also supported a sister relationship between M. candei and M. aurantiacus. Because hybrid zones connect the distributions of most Manacus species, we examined the potential influence of post-divergence gene flow on the sister relationship of parapatrically distributed M. vitellinus and M. manacus (w). An isolation-with-migration (IM) analysis found relatively high levels of gene flow between M. vitellinus and M. manacus (w). Whether the gene flow is obscuring a true sister relationship between M. manacus (w) and M. manacus (e) remained unclear, pointing to the need for more detailed models accommodating multispecies, multilocus DNA sequence data.

Source-sink dynamics have been suggested to characterize the population structure of many species, but the prevalence of source-sink systems in nature is uncertain because of inherent challenges in estimating migration rates among populations. Migration rates are often difficult to estimate directly with demographic methods, and indirect genetic methods are subject to a variety of assumptions that are difficult to meet or to apply to evolutionary timescales. Furthermore, such methods cannot be rigorously applied to high-gene-flow species. Here, we employ genetic parentage assignments in conjunction with demographic simulations to infer the level of immigration into a putative sink population. We use individual-based demographic models to estimate expected distributions of parent offspring dyads under competing sink and closed-population models. By comparing the actual number of parent-offspring dyads (identified from multilocus genetic profiles) in a random sample of individuals taken from a population to expectations under these two contrasting demographic models, it is possible to estimate the rate of immigration and test hypotheses related to the role of immigration on population processes on an ecological timescale. The difference in the expected number of parent-offspring dyads between the two population models was greatest when immigration into the sink population was high, indicating that unlike traditional population genetic inference models, the highest degree of statistical power is achieved for the approach presented here when migration rates are high. We used the proposed genetic parentage approach to demonstrate that a threatened population of Marbled Murrelets (Brachyramphus marmotus) appears to be supplemented by a low level of immigration (similar to 2-6% annually) from other populations.

To better understand the evolutionary and ecological effects of dispersal, there is growing emphasis on the need to integrate direct data on movement behaviour into landscape-scale analyses. However, little is known about the general link between movement behaviour and large-scale patterns of dispersal and gene flow. Likewise, although recent studies suggest that nonrandom, directionally biased movement and dispersal can promote evolutionary divergence, the generality of this mechanism is unknown. We test the hypothesis that directionally biased movement and dispersal by plethodontid salamanders interact with the topography of headwater areas to affect genetic and phenotypic divergence. Movements by Gyrinophilus porphyriticus and Eurycea bislineata show contrasting directional biases: upstream bias in G. porphyriticus and downstream bias in E. bislineata. Consistent with predictions of how these biases interact with slope to affect dispersal and gene flow, genetic distance increased with slope in G. porphyriticus and decreased with slope in E. bislineata over a standardized distance of 1 km along six headwater streams. In both species, phenotypic divergence in relative trunk length was positively related to genetic divergence. These results indicate that landscape-scale patterns of dispersal and gene flow are closely related to movement behaviour in G. porphyriticus and E. bislineata, and underscore the value of information on movement behaviour for predicting and interpreting patterns of dispersal and gene flow in complex landscapes. This study also provides new evidence that directionally biased movement and dispersal can be important sources of intra- and interspecific variation in population divergence, and highlights the value of explicit, a priori predictions in landscape genetic studies.

Background: Management strategies for coral reefs are dependant on information about the spatial population structure and connectivity of reef organisms. Genetic tools can reveal important information about population structure, however, this information is lacking for many reef species. We used a mitochondrial molecular marker to examine the population genetic structure and the potential for meta-population dynamics in a direct developing coral reef fish using 283 individuals from 15 reefs on the Great Barrier Reef, Australia. We employed a hierarchical sampling design to test genetic models of population structure at multiple geographical scales including among regions, among shelf position and reefs within regions. Predictions from island, isolation-by-distance and meta-population models, including the potential for asymmetric migration, local extinction and patterns of re-colonisation were examined. Results: Acanthochromis polyacanthus displayed strong genetic structure among regions (Phi(ST) = 0.81, P < 0.0001) that supported an equilibrium isolation-by-distance model (r = 0.77, P = 0.001). Significant structuring across the continental shelf was only evident in the northern region (Phi(ST) = 0.31, P < 0.001) and no evidence of isolation-by-distance was found within any region. Pairwise Phi(ST) values indicated overall strong but variable genetic structure (mean Phi(ST) among reefs within regions = 0.28, 0.38, 0.41), and asymmetric migration rates among reefs with low genetic structure. Genetic differentiation among younger reefs was greater than among older reefs supporting a meta-population propagule-pool colonisation model. Variation in genetic diversities, demographic expansion and population growth estimates indicated more frequent genetic bottlenecks/founder effects and subsequent population expansion in the central and southern regions compared to the northern one. Conclusion: Our findings provide genetic evidence for meta-population dynamics in a direct developing coral reef fish and we reject the equilibrium island and isolation-by distance models at local spatial scales. Instead, strong non-equilibrium genetic structure appears to be generated by genetic bottlenecks/founder effects associated with population reductions/extinctions and asymmetric migration/(re)-colonisation of such populations. These meta-population dynamics varied across the geographical range examined with edge populations exhibiting lower genetic diversities and higher rates of population expansion than more central populations. Therefore, coral reef species may experience local population reductions/extinctions that promote overall meta-population genetic differentiation.

Background: Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e. g. homing behaviour) and physical (e. g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. Results: We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, R-ST pairwise comparisons, isolation by distance (Mantel) tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. Conclusion: Lack of congruence between mt and nuclear evidences, which is also found in other species, most likely reflects past events of isolation and secondary contact. Given the inferred relatively low number of immigrants per generation around the Cape of Good Hope, the proportions of the mitochondrial clades in the different oceans may keep stable, and it seems plausible that the presence of individuals belonging to the mt Clade I in the Atlantic Ocean may be due to extensive migrations that predated the last glaciation.

Disentangling the relative contributions of selective and neutral processes underlying phenotypic and genetic variation under natural, environmental conditions remains a central challenge in evolutionary ecology. However, much of the variation that could be informative in this area of research is likely to be cryptic in nature; thus, the identification of wild populations suitable for study may be problematic. We use a landscape genetics approach to identify such populations of three-spined stickleback inhabiting the Saint Lawrence River estuary. We sampled 1865 adult fish over multiple years. Individuals were genotyped for nine microsatellite loci, and georeferenced multilocus data were used to infer population groupings, as well as locations of genetic discontinuities, under a Bayesian model framework (GENELAND). We modelled environmental data using nonparametric multiple regression to explain genetic differentiation as a function of spatio-ecological effects. Additionally, we used genotype data to estimate dispersal and gene flow to parameterize a simple model predicting adaptive vs. plastic divergence between demes. We demonstrate a bipartite division of the genetic landscape into freshwater and maritime zones, independent of geographical distance. Moreover, we show that the greatest proportion of genetic variation (31.5%) is explained by environmental differences. However, the potential for either adaptive or plastic divergence between demes is highly dependent upon the strength of migration and selection. Consequently, we highlight the utility of landscape genetics as a tool for hypothesis generation and experimental design, to identify focal populations and putative selection gradients, in order to distinguish between phenotypic plasticity and local adaptation.

The evolutionary viability of an endangered species depends upon gene flow among subpopulations and the degree of habitat patch connectivity. Contrasting population connectivity over ecological and evolutionary timescales may provide novel insight into what maintains genetic diversity within threatened species. We employed this integrative approach to evaluating dispersal in the critically endangered Coahuilan box turtle (Terrapene coahuila) that inhabits isolated wetlands in the desert-spring ecosystem of Cuatro Cienegas, Mexico. Recent wetland habitat loss has altered the spatial distribution and connectivity of habitat patches; and we therefore predicted that T. coahuila would exhibit limited movement relative to estimates of historic gene flow. To evaluate contemporary dispersal patterns, we employed mark-recapture techniques at both local (wetland complex) and regional (intercomplex) spatial scales. Gene flow estimates were obtained by surveying genetic variation at nine microsatellite loci in seven subpopulations located across the species' geographical range. The mark-recapture results at the local spatial scale reveal frequent movement among wetlands that was unaffected by interwetland distance. At the regional spatial scale, dispersal events were relatively less frequent between wetland complexes. The complementary analysis of population genetic substructure indicates strong historic gene flow (global F-ST = 0.01). However, a relationship of genetic isolation by distance across the geographical range suggests that dispersal limitation exists at the regional scale. Our approach of contrasting direct and indirect estimates of dispersal at multiple spatial scales in T. coahuila conveys a sustainable evolutionary trajectory of the species pending preservation of threatened wetland habitats and a range-wide network of corridors.

Mayr's best recognized scientific contributions include the biological species concept and the theory of geographic speciation. In the latter, reproductive isolation evolves as an incidental by-product of genetic divergence between allopatric populations. Mayr noted that divergent natural selection could accelerate speciation, but also argued that gene flow so strongly retards divergence that, even with selection, non-allopatric speciation is unlikely. However, current theory and data demonstrate that substantial divergence, and even speciation, in the face of gene flow is possible. Here, I attempt to connect some opposing views about speciation by integrating Mayr's ideas about the roles of ecology and geography in speciation with current data and theory. My central premise is that the speciation process (i.e. divergence) is often continuous, and that the opposing processes of selection and gene flow interact to determine the degree of divergence (i.e. the degree of progress towards the completion of speciation). I first establish that, in the absence of gene flow, divergent selection often promotes speciation. I then discuss how population differentiation in the face of gene flow is common when divergent selection occurs. However, such population differentiation does not always lead to the evolution of discontinuities, strong reproductive isolation, and thus speciation per se. I therefore explore the genetic and ecological circumstances that facilitate speciation in the face of gene flow. For example, particular genetic architectures or ecological niches may tip the balance between selection and gene flow strongly in favour of selection. The circumstances allowing selection to overcome gene flow to the extent that a discontinuity develops, and how often these circumstances occur, are major remaining questions in speciation research. (C) 2008 The Linnean Society of London.

The harpacticoid copepod Macrosetella gracilis uses colonies of the nitrogen-fixing cyanobacterium Trichodesmium spp. as a floating substrate and nursery. This association enables the copepod to lead a pelagic existence, Molecular and morphological data both indicate that M. gracilis is maintained as a single, circumglobal species across the tropical and subtropical Atlantic and Pacific. Mitochondrial DNA sequence data from cytochrome c oxidase subunit I (COI) showed moderate to high levels of diversity and limited phylogeographic structure in M. gracilis. Thirty-six different haplotypes were found among the 149 M. gracilis individuals sequenced; 4 haplotypes were shared between the Atlantic and Pacific. Samples from Japan showed the highest haplotypic and nucleotide diversity levels, suggesting that the Indo-West Pacific may be the center of diversity for M. gracilis. Wide distribution and large population size in M, gracilis may limit divergence through increased gene flow or slowing of the loss of ancestral diversity through lineage sorting. The pelagic existence of M. gracilis has led to less phylogenetic structuring than found in other species of harpacticoid copepods, illustrating the evolutionary significance of specialization on a floating substrate in this copepod.

Speciation, despite ongoing gene flow can be studied directly in nature in ring species that comprise two reproductively isolated populations connected by a chain or ring of intergrading populations. We applied three tiers of spatio-temporal analysis (phylogeny/historical biogeography, phylogeography and landscape/population genetics) to the data from mitochondrial and nuclear genomes of eastern Australian parrots of the Crimson Rosella Platycercus elegans complex to understand the history and present genetic structure of the ring they have long been considered to form. A ring speciation hypothesis does not explain the patterns we have observed in our data (e.g. multiple genetic discontinuities, discordance in genotypic and phenotypic assignments where terminal differentiates meet). However, we cannot reject that a continuous circular distribution has been involved in the group's history or indeed that one was formed through secondary contact at the `ring's' east and west; however, we reject a simple ring-species hypothesis as traditionally applied, with secondary contact only at its east. We discuss alternative models involving historical allopatry of populations. We suggest that population expansion shown by population genetics parameters in one of these isolates was accompanied by geographical range expansion, secondary contact and hybridization on the eastern and western sides of the ring. Pleistocene landscape and sea-level and habitat changes then established the birds' current distributions and range disjunctions. Populations now show idiosyncratic patterns of selection and drift. We suggest that selection and drift now drive evolution in different populations within what has been considered the ring.

Swainson's Warbler (Limnothlypis swainsonii) is a species of conservation concern because of its small wintering range in the Caribbean Basin. relatively low population densities, and habitat fragmentation in its core breeding range in the southeastern United States. We investigated microsatellite DNA variation among I I breeding, populations from eastern Texas to Virginia and two populations from wintering areas in Jamaica and Mexico. Analyses of six polymorphic loci indicated a moderate level of gene flow among breeding populations. relatively small effective population sizes (< 200 individuals in each sampled population), and subtle population variation. We detected no evidence of population bottlenecks in breeding or wintering populations. Bayesian assignment tests suggested that substantial mixing of breeding populations may Occur in wintering areas. Genetic differences between the Mexican and Jamaican populations indicate they may be drawn from different subsets of breeding Populations. Patterns of genetic variation among breeding and wintering Populations Suggest a network of local and regional conservation programs may be necessary to maintain genetic diversity in Swainson's Warbler.

The majority of reported multilocus heterozygosity-fitness correlations (HFCs) are from large, outbred populations, and their relevance to studies on inbreeding depression in threatened populations is often stressed. The results of such HFC studies conducted on outbred populations may be of limited application to threatened population management, however, as bottlenecked populations exhibit increased incidence of inbreeding, increased linkage disequilibrium, reduced genetic diversity and possible effects of historical inbreeding such as purging. These differences may affect both our ability to detect inbreeding depression in threatened species, and our interpretation of the underlying mechanisms for observed heterozygosity-fitness relationships. The study of HFCs in outbred populations is of interest in itself, but the results may not translate directly to threatened populations that have undergone severe bottlenecks.

Using one male-inherited, one female-inherited and eight biparentally inherited markers, we investigate the population genetic structure of the Valais shrew (Sorex antinorii) in the Swiss Alps. Bayesian analysis on autosomal microsatellites suggests a clear genetic differentiation between two groups of populations. This geographically based structure is consistent with two separate postglacial recolonization routes of the species into Switzerland from Italian refugia after the last Pleistocene glaciations. Sex-specific markers also confirm genetic structuring among western and eastern areas, since very few haplotypes for either Y chromosome or mtDNA genome are shared between the two regions. Overall, these results suggest that two already well-differentiated genetic lineages colonized the Swiss Alps and came into secondary contact in the Rhone Valley. Low level of admixture between the two lineages is likely explained by the mountainous landscape structure of lateral valleys orthogonal to the main Rhone valley.

New statistical techniques and software have improved our ability to quantify fine-scale population structure. We isolated 11 microsatellite markers for eastern foxsnakes (Elaphe gloydi) and surveyed the variability of each using 115-136 individuals from one population in southwestern Ontario. We determined that all loci were variable and conformed to Hardy-Weinberg expectations and that no locus demonstrated linkage disequilibrium. We are using these markers to quantify the scale of gene flow, and to assess the effect of variable landscapes on connectivity and genetic diversity of three disjunct regional populations in the northern portion of the species' range.

Arctic warbler Phylloscopus borealis is one of several high-latitude Passerines which are widely distributed across one northern continent but restricted to the Beringian part of the other. Most species with such asymmetric intercontinental ranges are monomorphic across Beringia, suggesting either recent colonization of the second continent or considerable gene flow across the Bering Strait. Arctic warbler is the only migratory species in this group that has three different subspecies in Beringia: Ph. b. borealis (Scandinavia to western Beringia, south to Mongolia), Ph. b. xanthodryas (Japan, Sakhalin, Kamchatka, western Beringia), and Ph. b. kennicotti (Alaska). This polymorphism may indicate that Arctic warbler has a unique and complex phylogeographic history that differs significantly from other species with similar ranges. Our analyses of complete mtDNA ND2 sequences of 88 Arctic warblers collected across the species range showed that the clade comprised of birds breeding on Sakhalin Island and Kamchatka Peninsula diverged from the Palearctic/Beringian clade by 3.8% in ND2 sequence. Beringian birds formed a recently derived clade embedded within the Palearctic clade. Nucleotide diversity declined sharply eastward from Palearctic to western Beringia and then to eastern Beringia. Our data provided no support for currently recognized subspecies. They suggested that the barrier at the western edge of Beringia was crossed by Arctic warbler earlier than the Bering Strait resulting in a stepping-stone colonization of Beringia by this species. Gene flow appears to be restricted across the western border of Beringia but not the Bering Strait.

We review the expanding role of molecular genetics in the emergence of a vibrant and vital integrative biogeography. The enormous growth over the past several decades in the number and variety of molecular-based phylogenetic and population genetics studies has become the core information used by biogeographers to reconstruct the causal connections between historical evolutionary and ecological attributes of taxa and biotas, and the landscapes and seascapes that contain them. A proliferation of different approaches, sequences, and genomes have provided for the integration of a `biogeography of the Late Neogene' with other Earth and biological sciences under the rubrics of phylogeography, landscape genetics, and phylochronology. Approaches designed explicitly to take advantage of unique properties of molecular genetic information have led to the re-emergence of dispersal as an analytically tractable process that historical biogeographers can now use, along with vicariance, to reconstruct the geographical context of diversification. Concomitant with the expanding amount of information available, molecular data sets often provide for estimates of lineage divergence dates, and analytical tools for doing so continue to improve. The comparability of molecular-based estimates of phylogenetic and population genetic histories across non-related taxa has stimulated deployment of new methods to test for spatial and temporal congruence across co-distributed taxa and ecosystems, and thus increased rigour in hypothesis-testing. We illustrate how a molecular genetics framework has provided robust and novel reconstructions of historical biogeographical pattern and process in three different systems, and finish with some thoughts on the role a molecular genetic-based biogeography will play in predicting alternative futures of biodiversity.

Subspecific affinites, determination of population boundaries, and levels of population connectedness are of critical importance for the development of management and conservation planning. We used variation at a mitochondrial locus and 5 biparentally inherited nuclear loci to determine partitioning of genetic variation of western big-cared bats (Corynorhinus townsendii) within and among caves occurring in a fragmented landscape of gypsum deposits in western Oklahoma. To accomplish this objective, we first performed a phylogenetic analysis based on the mitochondrial locus of western big-eared bats from a large portion of their range. This analysis indicated that western big-eared bats at the periphery of the distribution in western Oklahoma share phylogenetic affinites with the most geographically restricted subspecies, C. t. pallescens. Because C, townsendii is rare in Oklahoma and is listed as a species of special in Oklahoma. Within western Oklahoma, we failed to detect significant differentiation among any caves for the biparentally inherited microsatellite data. However, the mitochondrial locus exhibited significant levels of genetic differentiation among caves, with the highest level of differentiation occurring between caves within the disjunct distributions of gypsum (Phi(ST) = 38.76%). Although a significant amount of genetic differentiation was detected between populations on the 2 disjunct distributions of gypsum deposits, Analysis with the program Migrate suggested high levels of asymmetric gene flow among some populations. Our results provide a greater understanding of the population dynamics of western big-cared bats on the periphery of their range and highlight the importance of continued monitoring and study of this taxon.

Spalacopus cyanus is a subterranean rodent inhabiting coastal and mountain habitats. Individuals from mountain populations are larger than individuals from the coast, and mountain populations have a more limited geographic range. To investigate the genetic structure and biogeography of this species, we analyzed mitochondrial DNA control region sequences. We found low levels of nucleotide diversity in comparison with other subterranean rodents. Coastal populations had higher nucleotide diversity and effective population size than mountain populations. Phylogenetic analysis using maximum parsimony and a haplotype network generated using statistical parsimony recognized 3 groups of haplotypes: northern coastal and mountain populations, central coastal populations, and southern coastal population. Consistent with the presence of unshared haplotypes, migration rates were practically 0, except from Valparaiso to Ventanas and from La Parva to Huentelauquen. We observed asymmetric migration rates from mountain to coastal populations, suggesting that this species originated in the Andean mountains. A likelihood ration test could not reject the null hypothesis of a stable population when all sequences were grouped into a single population and when coastal populations were analyzed separately. However, a negative exponential growth parameter was estimated for mountain populations,suggesting that these populations have undergone recent demographic changes.

Genealogy based methods were used to estimate phylogeographic history for a Tasmanian endemic conifer. Huon pine (Lagarostrobos franklinii (Hook. f.) Quinn). DNA from trees in eight populations was sequenced using three chloroplast primers (trnS-trnT, trnD-trnT, and psbC-trnS). Mean nucleotide diversity was low (pi = 0.00093 +/- 0.00006) from 892 base pairs of sequence, but varied in stands from 0.0 to 0.001 15. Two of the five haplotypes were widely distributed, but the most frequently occurring haplotype Was found only in the western portion of the range. Population Structure was highly significant among populations overall (G(ST) = 0.261, where G(ST) is the coefficient of gene differentiation, and p <= 0.0001), and there were indications of significant isolation by distance (p <= 0.022). Populations exhibited the highest levels of differentiation between the Southeastern and northwestern watersheds. Estimates of migration between Populations obtained using both parametric and nonparametric methods indicated levels of gene flow consistent with an isolation by distance model. Nested clade analysis demonstrated a pattern of genetic diversity in Huon pine that is consistent with a history of range expansion. The exceptionally low level of nucleotide diversity, haplotype distribution. and paleoecological data are congruent with a history of long-term range reduction, population bottlenecks, and subsequent colonization events from refugial areas.

Aim contractions of species ranges, with accompanying fragmentation and population bottlenecks, which are evidenced by spatial variation in genetic structure of populations. We examine here hypotheses concerning dispersal and vicariance in response to historical geoclimatic change and potential isolation produced by mountains and water barriers. Location The temperate rain forest of southern South America, which is distributed from coastal Chile, including the large continental island of Chiloe, across the Andes into Argentina. Methods We investigated our hypotheses in the phylogenetically and biogeographically relictual marsupial Dromiciops gliroides. We examined 56 specimens, which resulted from field samples and museum study skins from 21 localities. We evaluated the influence of two major barriers, the Andean cordillera and the waterway between the mainland and the large island of Chiloe, by performing Bayesian and maximum-likelihood phylogenetic analyses on sequences of 877 base pairs of mitochondrial DNA. We further tested the contribution of the proposed geographical barriers using analysis of molecular variance (AMOVA). We also evaluated the responses of populations to historical north-south shifts of habitat associated with glacial history and sea-level change. Results Our analyses revealed a phylogeny with three clades, two of which are widespread and contain nearly all the haplotypes: a northern clade (36-39 degrees S) and a southern clade (40-43 degrees S). These two clades contain forms from both sides of the Andes. Within the southern clade, island and mainland forms were not significantly differentiated. Tests of recent demographic change revealed that southern populations have experienced recent expansion, whereas northern populations exhibit long-term stability. The direction of recent gene flow and range expansion is predominantly from Chile to Argentina, with a modest reciprocal exchange across the Andes. Recent gene flow from the island of Chiloe to the mainland is also supported. Main conclusions The genetic structure of contemporary D. gliroides populations suggests recent gene flow across the Andes and between the mainland and the island of Chiloe. Differences in demographic history that we detected between northern and southern populations have resulted from historical southward shifts of habitat associated with glacial recession in South America. Our results add to a growing literature that demonstrates the value of genetic data to illuminate how environmental history shapes species range and population structure.

Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multipleallele, multilocus sequence data, building on a recently proposed method for estimating species trees from single allele multilocus data. A two-step Markov Chain Monte Carlo (MCMC) algorithm is adopted to estimate the posterior distribution of the species tree. The model is applied to estimate the posterior distribution of species trees for two multiple-allele datasets-yeast (Saccharomyces) and birds (Manacus-manakins). The estimates of the species trees using our method are consistent with those inferred from other methods and genetic markers, but in contrast to other species tree methods, it provides credible regions for the species tree. The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics.

The Basidiomycete fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen of soybean in Brazil, where the average yield losses have reached 30 to 60% in some states in Northern Brazil. No information is currently available concerning levels of genetic diversity and population structure for this pathogen in Brazil. A total of 232 isolates of R. solani AG1 IA were collected from five soybean fields in the most important soybean production areas in central-western, northern, and northeastern Brazil. These isolates were genotyped using 10 microsatellite loci. Most of the multilocus genotypes (MLGTs) were site-specific, with few MLGTs shared among populations. Significant population subdivision was evident. High levels of admixture were observed for populations from Mato Grosso and Tocantins. After removing admixed genotypes, three out of five field populations (Maranhao, Mato Grosso, and Tocantins), were in Hardy-Weinberg (HW) equilibrium, consistent with sexual recombination. HW and gametic disequilibrium were found for the remaining soybean-infecting populations. The findings of low genotypic diversity, departures from HW equilibrium, gametic disequilibrium, and high degree of population subdivision in these R. solani AG-1 IA populations from Brazil are consistent with predominantly asexual reproduction, short-distance dispersal of vegetative propagules (mycelium or sclerotia), and limited long-distance dispersal, possibly via contaminated seed. None of the soybean-infecting populations showed a reduction in population size (bottleneck effect). We detected asymmetric historical migration among the soybean-infecting populations, which could explain the observed levels of subdivision.

Sex-based differences in dispersal distances can affect critical population parameters such as inbreeding rates and the spatial scale of local adaptation. Males tend to disperse further than females in mammals, whereas the reverse is true for birds; too few reptiles have been studied to reveal generalities for that group. Although reptiles are most diverse and abundant in the tropics, few tropical reptiles have been studied in this respect. We combine data from a long-term (10-year) mark-recapture study with genetic information (based on nine microsatellite markers) on slatey-grey snakes (Stegonotus cucullatus, Colubridae) in the Australian wet-dry tropics. Males attain larger body sizes than females, and both genetic and mark-recapture data show that males also disperse further than females. Recapture records show that hatchling males dispersed away from their release points whereas hatchling females did not, and adult males moved further than adult females. In the genetic analysis, males contributed less to overall F-ST and relatedness than did females (F-STm = 0.0025, F-STf = 0.0275, P < 0.001; r(m) = 0.0053; r(f) = 0.0550; P < 0.001). Spatial autocorrelation analyses within the largest population revealed a similar pattern, with spatial structuring stronger for females than males. Overall, our genetic analyses not only supported the mark-recapture data, but also extended our insights by revealing occasional long-distance dispersal not detected by the mark-recapture study.

Genetic variation was surveyed at five microsatellite loci and the mitochondrial control region (819 bp) to test for the presence of genetic stock structure in striped marlin (Kajikia audax) collections taken from seven locations throughout the Pacific Ocean. Temporal replicates separated by 9 years were taken off Japan, and three temporal samples spanning 11 years were collected off the coast of eastern Australia. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences showed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for microsatellite markers (F-ST = 0.013, P < 0.001). Mitochondrial control region sequences were not different across all samples (Phi(ST) = -0.01, P = 0.642). Analyses of molecular variance (AMOVA) revealed significant genetic differentiation between geographic regions for both microsatellite and mitochondrial markers. These results suggest the presence of genetically discrete populations within the Pacific Ocean and are supported by both the results of tagging studies, which show limited dispersal, and the presence of geographically separated spawning grounds.

Neotricula aperta is the only known intermediate host of Schistosoma mekongi which infects humans in Cambodia and the southern tip of Lao PDR. DNA-sequence data (partial rrnL, i.e., mitochondrial 16S large ribosomal-RNA gene) were obtained for 359 N. aperta snails sampled at 31 localities in Cambodia, Lao PDR and Thailand. A nested clade analysis was performed to detect and evaluate any geographical patterns in the observed variation and to identify genetic subpopulations or clades. Coalescent simulations were used to compare different historical biogeographical hypotheses for N. aperta and S. mekongi. A coalescent based method was also used to provide maximum likelihood estimates (MLEs) for effective populations sizes and historical growth and migration rates. Dates were also estimated for phylogenetic events on the gene tree reconstructed for the sampled haplotypes (e.g. the time to most recent common ancestor). N. aperta was found to be divided into two monophyletic clades, a spring-dwelling form of northern Lao PDR and a more widespread larger-river dwelling form of southern Lao PDR and Cambodia: this divergence was dated at 9.3 Ma. The populations with the largest estimated population sizes were found in the Mekong River of Lao PDR and Cambodia; these, together with those of the rivers of eastern Cambodia, appeared to have been the fastest growing populations. Dominant levels of gene-flow (migration) were apparent in a South to North direction, particularly out of seeder populations in the Cambodian Mekong River. The radiation of N. aperta into sub-clades across Cambodia and Lao PDR is dated at around 5 Ma. The findings suggest that historical events, rather than ecology, might best explain the absence of S. mekongi from most of Lao PDR. The public health implications of these findings are discussed, as are pointers for future studies and surveillance. (C) 2008 Elsevier Ireland Ltd. All rights reserved.

Question: How do post-glacial colonization history and current watershed geomorphology affect population genetic structure in lacustrine fish populations? Study system: Eleven populations of lacustrine threespine sticklebacks (Gasterosteus aculeatus) from a single watershed, and two adjacent marine populations of G. aculeatus as outgroups. Methods: Individuals were genotyped using six microsatellite loci and several population genetic parameters were calculated (including genetic differentiation, genetic diversity, migration, and divergence time). We regressed population genetic parameters against environmental variables such as stream gradient and length, distance from the mouth of the watershed, and lake area. Results: Genetic differentiation was highest between lakes separated by high-gradient streams, but was unaffected by stream length. Estimated divergence times between adjoining populations declined from >10,000 years ago for lake pairs close to the ocean to less than 5000 years for lake pairs near the top of the watershed. Genetic diversity declined as a function of geographic distance from the mouth of the watershed but was positively correlated with lake area, Conclusions: Our findings confirm expectations that landscape features such as stream gradient and stream branching structure strongly influence patterns of genetic divergence. However, in contrast to previous studies, we found no significant relationship between geographic distance and genetic divergence among lake pairs. We present novel evidence that post-glacial colonization occurred gradually over a significant period of time, rather than a single rapid invasion into all lakes.

We revisited a classic study of morphological variation in the oldfield mouse (Peromyscus polionotus) to estimate the strength of selection acting on pigmentation patterns and to identify the underlying genes. We measured 215 specimens collected by Francis Sumner in the 1920s from eight populations across a 155-km, environmentally variable transect from the white sands of Florida's Gulf coast to the dark, loamy soil of southeastern Alabama. Like Sumner, we found significant variation among populations: mice inhabiting coastal sand dunes had larger feet, longer tails, and lighter pigmentation than inland populations. Most striking, all seven pigmentation traits examined showed a sharp decrease in reflectance about 55 km from the coast, with most of the phenotypic change occurring over less than 10 km. The largest change in soil reflectance occurred just south of this break in pigmentation. Geographic analysis of microsatellite markers shows little interpopulation differentiation, so the abrupt change in pigmentation is not associated with recent secondary contact or reduced gene flow between adjacent populations. Using these genetic data, we estimated that the strength of selection needed to maintain the observed distribution of pigment traits ranged from 0.0004 to 21%, depending on the trait and model used. We also examined changes in allele frequency of SNPs in two pigmentation genes, Mc1r and Agouti, and show that mutations in the cis-regulatory region of Agouti may contribute to this cline in pigmentation. The concordance between environmental variation and pigmentation in the face of high levels of interpopulation gene flow strongly implies that natural selection is maintaining a steep cline in pigmentation and the genes underlying it.

Human head lice (Anoplura: Pediculidae: Pediculus) are pandemic, parasitizing countless school children worldwide due to the evolution of insecticide resistance, and human body (clothing) lice are responsible for the deaths of millions as a result of vectoring several deadly bacterial pathogens. Despite the obvious impact these lice have had on their human hosts, it is unclear whether head and body lice represent two morphological forms of a single species or two distinct species. To assess the taxonomic status of head and body lice, we provide a synthesis of publicly available molecular data in GenBank, and we compare phylogenetic and population genetic methods using the most diverse geographic and molecular sampling presently available. Our analyses find reticulated networks, gene flow, and a lack of reciprocal monophyly, all of which indicate that head and body lice do not represent genetically distinct evolutionary units. Based on these findings, as well as inconsistencies of morphological, behavioral, and ecological variability between head and body lice, we contend that no known species concept would recognize these louse morphotypes as separate species. We recommend recognizing head and body lice as morphotypes of a single species, Pediculus humanus, until compelling new data and analyses (preferably analyses of fast evolving nuclear markers in a coalescent framework) indicate otherwise. (C) 2008 Elsevier Inc. All rights reserved.

Chilo suppressalis (Walker) displays significant geographical differences in ecological preference that may be congruent with patterns of molecular variation. To test this, we collected and analysed 381 individuals of this species from cultivated rice at 18 localities in China during the rice-growing season of 2005-2006. We used four microsatellite DNA markers and four mitochondrial DNA gene fragments. We found that this species is highly differentiated, coupled with an estimated population expansion date of at least 60 000 BP. Phylogenetic analyses, Bayesian clustering, and phylogeographical analyses of statistical parsimony haplotype network consistently divided the populations into three clades: a central China (CC) clade, a northern plus northeastern China (NN) clade and a southwestern China (SW) clade. Analysis of molecular variance indicated a high level of geographical differentiation at different hierarchical levels [F-ST for microsatellite markers, COI, COII, 16S and ND1 is 0.06004 (P < 0.0001), 0.27607 (P < 0.0001), 0.22949 (P < 0.0001), 0.19485 (P < 0.0001) and 0.29285 (P < 0.0001), respectively]. Isolation by distance appeared among the samples from within China (r = 0.404, P = 0.0002); N(e)m values estimated using a coalescent-based method were small (< 2 migrants per generation), suggesting that the observed levels of differentiation are a result of migration-drift equilibrium. Our results imply that the genetic differentiation of this borer, which is approximately in accordance with its observed number of generations per year in different Chinese geographical regions, is probably attributed to climatic and/or geological events (e.g. the last glacial maximum) and subsequently strengthened by the domestication of rice.

Background: Two processes may contribute to the formation of global centers of biodiversity: elevated local speciation rates (the center of origin hypothesis), and greater accumulation of species formed elsewhere (the center of accumulation hypothesis). The relative importance of these processes has long intrigued marine biogeographers but rarely has been tested. Results: To examine how origin and accumulation affected the Greater Caribbean center of diversity, we conducted a range-wide survey of mtDNA cytochrome b in the widespread Atlantic reef damselfish Chromis multilineata (N = 183) that included 10 locations in all four tropical Atlantic biogeographic provinces: the Greater Caribbean, Brazil, the mid-Atlantic ridge, and the tropical eastern Atlantic. We analyzed this data and re-evaluated published genetic data from other reef fish taxa (wrasses and parrotfishes) to resolve the origin and dispersal of mtDNA lineages. Parsimony networks, mismatch distributions and phylogenetic analyses identify the Caribbean population of C. multilineata as the oldest, consistent with the center of origin model for the circum-Atlantic radiation of this species. However, some Caribbean haplotypes in this species were derived from Brazilian lineages, indicating that mtDNA diversity has not only originated but also accumulated in the Greater Caribbean. Data from the wrasses and parrotfishes indicate an origin in the Greater Caribbean in one case, Caribbean origin plus accumulation in another, and accumulation in the remaining two. Conclusion: Our analyses indicate that the Greater Caribbean marine biodiversity hotspot did not arise through the action of a single mode of evolutionary change. Reef fish distributions at the boundaries between Caribbean and Brazilian provinces (the SE Caribbean and NE Brazil, respectively) indicate that the microevolutionary patterns we detected in C. multilineata and other reef fishes translate into macroevolutionary processes and that origin and accumulation have acted in concert to form the Greater Caribbean biodiversity hotspot.

Background: Adaptive radiation within fishes of the Coregonus lavaretus complex has created numerous morphs, posing significant challenges for taxonomy and conservation priorities. The highly endangered North Sea houting (C. oxyrhynchus; abbreviated NSH) has been considered a separate species from European lake whitefish (C. lavaretus; abbreviated ELW) due to morphological divergence and adaptation to oceanic salinities. However, its evolutionary and taxonomic status is controversial. We analysed microsatellite DNA polymorphism in nine populations from the Jutland Peninsula and the Baltic Sea, representing NSH (three populations, two of which are reintroduced) and ELW (six populations). The objectives were to: 1) analyse postglacial recolonization of whitefish in the region; 2) assess the evolutionary distinctiveness of NSH, and 3) apply several approaches for defining conservation units towards setting conservation priorities for NSH. Results: Bayesian cluster analyses of genetic differentiation identified four major groups, corresponding to NSH and three groups of ELW (Western Jutland, Central Jutland, Baltic Sea). Estimates of historical migration rates indicated recolonization in a north-eastern direction, suggesting that all except the Baltic Sea population predominantly represent postglacial recolonization via the ancient Elbe River. Contemporary gene flow has not occurred between NSH and ELW, with a divergence time within the last 4,000 years suggested from coalescence methods. NSH showed interbreeding with ELW when brought into contact by stocking. Thus, reproductive isolation of NSH was not absolute, although possible interbreeding beyond the F1 level could not be resolved. Conclusion: Fishes of the C. lavaretus complex in the Jutland Peninsula originate from the same recolonization event. NSH has evolved recently and its species status may be questioned due to incomplete reproductive isolation from ELW, but it was shown to merit consideration as an independent conservation unit. Yet, application of several approaches for defining conservation units generated mixed outcomes regarding its conservation priority. Within the total species complex, it remains one among many recently evolved unique forms. Its uniqueness and high conservation priority is more evident at a local geographical scale, where conservation efforts will also benefit populations of a number of other endangered species.

Most studies of the genetic structure of Atlantic cod have focused on small geographical scales. In the present study, the genetic structure of cod sampled on spawning grounds in the North Atlantic was examined using eight microsatellite loci and the Pan I locus. A total of 954 cod was collected from nine different regions: the Baltic Sea, the North Sea, the Celtic Sea, the Irish Sea and Icelandic waters during spring 2002 and spring 2003, from Norwegian waters and the Faroe Islands (North and West spawning grounds) in spring 2003, and from Canadian waters in 1998. Temporal stability among spawning grounds was observed in Icelandic waters and the Celtic Sea, and no significant difference was observed between the samples from the Baltic Sea and between the samples from Faroese waters. F-statistics showed significant differences between most populations and a pattern of isolation-by-distance was described with microsatellite loci. The Pan I locus revealed the presence of two genetically distinguishable basins, the North-west Atlantic composed of the Icelandic and Canadian samples and the North-east Atlantic composed of all other samples. Permutation of allele sizes at each microsatellite locus among allelic states supported a mutational component to the genetic differentiation, indicating a historical origin of the observed variation. Estimation of the time of divergence was approximately 3000 generations, which places the origin of current genetic pattern of cod in the North Atlantic in the late Weichselian (Wisconsinian period), at last glacial maximum. (C) 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 315-329.

Many recent studies have sought to quantify the degree to which viral phenotypic characters (such as epidemiological risk group, geographic location, cell tropism, drug resistance state, etc.) are correlated with shared ancestry, as represented by a viral phylogenetic tree. Here, we present a new Bayesian Markov-Chain Monte Carlo approach to the investigation of such phylogeny-trait correlations. This method accounts for uncertainty arising from phylogenetic error and provides a statistical significance test of the null hypothesis that traits are associated randomly with phylogeny tips. We perform extensive simulations to explore and compare the behaviour of three statistics of phylogeny-trait correlation. Finally, we re-analyse two existing published data sets as case studies. Our framework aims to provide an improvement over existing methods for this problem. (c) 2007 Elsevier B.V. All rights reserved.

Agriculture played a significant role in increasing the number of pathogen species and in expanding their geographic range during the last 10,000 years. We tested the hypothesis that a fungal pathogen of cereals and grasses emerged at the time of domestication of cereals in the Fertile Crescent and subsequently speciated after adaptation to its hosts. Rhynchosporium secalis, originally described from rye, causes an important disease on barley called scald, although it also infects other species of Hordeum and Agropyron. Phylogenetic analyses based on four DNA sequence loci identified three host-associated lineages that were confirmed by cross-pathogenicity tests. Bayesian analyses of divergence time suggested that the three lineages emerged between similar to 1200 to 3600 years before present (B.P.) with a 95% highest posterior density ranging from 100 to 12,000 years B.P. depending on the implemented clock models. The coalescent inference of demographic history revealed a very recent population expansion for all three pathogens. We propose that Rhynchosporium on barley, rye, and Agropyron host species represent three cryptic pathogen species that underwent independent evolution and ecological divergence by host-specialization. We postulate that the recent emergence of these pathogens followed host shifts. The subsequent population expansions followed the expansion of the cultivated host populations and accompanying expansion of the weedy Agropyron spp. found in fields of cultivated cereals. Hence, agriculture played a major role in the emergence of the scald diseases, the adaptation of the pathogens to new hosts and their worldwide dissemination.

The genetic structure of a broad hybrid zone involving three hybridizing Aesculus species, Aesculus flava, Aesculus pavia, and Aesculus sylvatica, was examined. The objectives were to assess genetic variability, to test previously reported hypotheses on patterns of gene flow, and to infer the genetic structure and evolutionary processes in the hybrid zone. Samples from 24 populations within parental ranges and the hybrid zone were analyzed for variation at microsatellite and intersimple sequence repeat loci. The results indicated that genetic variability was similar among parental and hybrid populations, indicating no evident increased diversity in the hybrid zone. Most hybrid individuals were genetically more similar to A. sylvatica than to the other two species, and the overall genetic structure of the hybrid zone is asymmetrically biased toward A. sylvatica. Our analyses supported occasional recurrent long-distant gene flow from A. pavia and frequent gene flow from A. sylvatica into the hybrid zone, agreeing with results of a previous allozyme study. Collectively, the data from our study and previous allozyme and chloroplast DNA studies indicate that both historical localized gene flow and recurrent long-distant gene flow have contributed to the existence of the hybrid zone, that is, its origin via historical localized gene flow, while its maintenance involves ongoing long-distance pollen dispersal.

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of “reverse evolution,” [9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime.

Background: There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary genetic models can be undertaken using backward or forward strategies. Backward simulations, also called coalescent-based simulations, are computationally efficient. The reason is that they are based on the history of lineages with surviving offspring in the current population. On the contrary, forward simulations are less efficient because the entire population is simulated from past to present. However, the coalescent framework imposes some limitations that forward simulation does not. Hence, there is an increasing interest in forward population genetic simulation and efficient new tools have been developed recently. Software tools that allow efficient simulation of large DNA fragments under complex evolutionary models will be very helpful when trying to better understand the trace left on the DNA by the different interacting evolutionary forces. Here I will introduce GenomePop, a forward simulation program that fulfills the above requirements. The use of the program is demonstrated by studying the impact of intracodon recombination on global and site-specific dN/dS estimation. Results: I have developed algorithms and written software to efficiently simulate, forward in time, different Markovian nucleotide or codon models of DNA mutation. Such models can be combined with recombination, at inter and intra codon levels, fitness-based selection and complex demographic scenarios. Conclusion: GenomePop has many interesting characteristics for simulating SNPs or DNA sequences under complex evolutionary and demographic models. These features make it unique with respect to other simulation tools. Namely, the possibility of forward simulation under General Time Reversible (GTR) mutation or GTR x MG94 codon models with intra-codon recombination, arbitrary, user-defined, migration patterns, diploid or haploid models, constant or variable population sizes, etc. It also allows simulation of fitness-based selection under different distributions of mutational effects. Under the 2-allele model it allows the simulation of recombination hot-spots, the definition of different frequencies in different populations, etc. GenomePop can also manage large DNA fragments. In addition, it has a scaling option to save computation time when simulating large sequences and population sizes under complex demographic and evolutionary situations. These and many other features are detailed in its web page [1].

Evolutionary trajectories of codistributed taxa with comparable ecological preferences and dispersal abilities may be similarly impacted by historical landscape-level processes. Species' responses to changes in a shared biogeographic landscape may be purely concerted, completely independent, or classified as falling within an intermediate part of the continuum bounded by these two extremes. With sufficient molecular data, temporal contrasts of congruence among taxa with respect to these responses can be made. Such contrasts provide insights into the relative influence of ancient versus more recent climatic (and other) impacts on genetic structuring. Using phylogenetic, allele frequency, and genotypic data from two low-mobility, rotting-log-adapted (saproxylic) springtail species (Collembola) from an isolated 100-km-long section of the Great Dividing Range in southeastern Australia, we tested the concerted-response hypothesis over three timescales. Tests of phylogeographic, demographic, and contemporary population-genetic congruence were performed using an integrative approach that draws on both direct (pattern-based) and indirect (scenario-based) analyses. Our data revealed a general pattern of broad-scale similarities in species' responses to the interaction between Pleistocene climatic cycles and landscape setting, overlaid with some species-specific differences on local geographic and more recent temporal scales. This general pattern of phylogeographic congruence was accompanied by evidence for contemporaneous demographic incongruence indicating that, even at relatively small spatial scales, biogeographic context can exert an overarching influence on genetic structuring.

Adaptive diversification is driven by selection in ecologically different environments. In absence of geographical barriers to dispersal, this adaptive divergence (AD) may be constrained by gene flow (GF). And yet the reverse may also be true, with AD constraining GF (i.e. `ecological speciation'). Both of these causal effects have frequently been inferred from the presence of negative correlations between AD and GF in nature - yet the bi-directional causality warrants caution in such inferences. We discuss how the ability of correlative studies to infer causation might be improved through the simultaneous measurement of multiple ecological and evolutionary variables. On the one hand, inferences about the causal role of GF can be made by examining correlations between AD and the potential for dispersal. On the other hand, inferences about the causal role of AD can be made by examining correlations between GF and environmental differences. Experimental manipulations of dispersal and environmental differences are a particularly promising approach for inferring causation. At present, the best studies find strong evidence that GF constrains AD and some studies also find the reverse. Improvements in empirical approaches promise to eventually allow general inferences about the relative strength of different causal interactions during adaptive diversification.

Demographic processes modulate genome-wide levels and patterns of genetic variation via impacting effective population size independently of natural selection. Such processes include the perturbation of population distributions from external events shaping habitat landscape and internal factors shaping the probability of contemporaneous alleles in a population (coalescence). Several patterns have recently emerged: spatial and temporal heterogeneity in population structure have different influences on the persistence of new mutations and genetic variation, multi-locus analyses indicate that gene flow continues to occur during speciation and the incorporation of demographic processes into models of molecular evolution and association genetics approaches has improved statistical power to detect deviations from neutral-equilibrium expectations and decreased false positive rates.

The localization of Last Glacial Maximum (LGM) refugia is crucial information to understand a species' history and predict its reaction to future climate changes. However, many phylogeographical studies often lack sampling designs intensive enough to precisely localize these refugia. The hairy land snail Trochulus villosus has a small range centred on Switzerland, which could be intensively covered by sampling 455 individuals from 52 populations. Based on mitochondrial DNA sequences (COI and 16S), we identified two divergent lineages with distinct geographical distributions. Bayesian skyline plots suggested that both lineages expanded at the end of the LGM. To find where the origin populations were located, we applied the principles of ancestral character reconstruction and identified a candidate refugium for each mtDNA lineage: the French Jura and Central Switzerland, both ice-free during the LGM. Additional refugia, however, could not be excluded, as suggested by the microsatellite analysis of a population subset. Modelling the LGM niche of T. villosus, we showed that suitable climatic conditions were expected in the inferred refugia, but potentially also in the nunataks of the alpine ice shield. In a model selection approach, we compared several alternative recolonization scenarios by estimating the Akaike information criterion for their respective maximum-likelihood migration rates. The `two refugia' scenario received by far the best support given the distribution of genetic diversity in T. villosus populations. Provided that fine-scale sampling designs and various analytical approaches are combined, it is possible to refine our necessary understanding of species responses to environmental changes.

We present phylogenetic evidence supporting viral compartmentalization between the blood ( peripheral blood mononuclear cells or plasma) and multiple genitourinary sites in HIV-infected men. Four of the five subjects evaluated demonstrated compartmentalization of viral sequences between urogenital tract specimens ( tissue or fluid) and at least one blood category. HIV sequence migration from blood to urogenital tract was detected in four of five men, with migration from urogenital tract to blood in the fifth, and cross migration between both compartments noted in one man. These observations add 5 additional cases to the 27 total reported cases in which male urogenital tract compartmentalization has been studied, investigate surgical samples/specimens that have not been evaluated previously, and provide further evidence for restricted flow of HIV between the blood and the genital tract. As such, our study findings are important for understanding the long-term response to antiretroviral therapy, the design of vaccines, and the sexual transmission of HIV.

The morphological features of pollen and seed of Araucaria angustifolia have led to the proposal of limited gene dispersal for this species. We used nuclear microsatellite and AFLP markers to assess patterns of genetic variation in six natural populations at the intra- and inter-population level, and related our findings to gene dispersal in this species. Estimates of both fine-scale spatial genetic structure (SGS) and migration rate suggest relatively short-distance gene dispersal. However, gene dispersal differed among populations, and effects of more efficient dispersal within population were observed in at least one stand. In addition, even though some seed dispersal may be aggregated in this principally barochorous species, reasonable secondary seed dispersal, presumably facilitated by animals, and overlap of seed shadows within populations is suggested. Overall, no correlation was observed between levels of SGS and inbreeding, density or age structure, except that a higher level of SGS was revealed for the population with a higher number of juvenile individuals. A low estimate for the number of migrants per generation between two neighbouring populations implies limited gene flow. We expect that stepping-stone pollen flow may have contributed to low genetic differentiation among populations observed in a previous survey. Thus, strategies for maintenance of gene flow among remnant populations should be considered in order to avoid degrading effects of population fragmentation on the evolution of A. angustifolia.

To assess genetic diversity in the blue-listed purple martin (Progne subis) population in British Columbia, we analysed mitochondrial control region sequences of 93 individuals from British Columbia and 121 individuals collected from seven localities of the western and eastern North American subspecies P. s. arboricola and P. s. subis, respectively. Of the 47 haplotypes we detected, 34 were found exclusively in western populations, and 12 were found only in eastern populations. The most common eastern haplotype (25) was also found in three nestlings in British Columbia and one in Washington. Another British Columbia nestling had a haplotype (35) that differed by a C to T transition from haplotype 25. Coalescent analysis indicated that these five nestlings are probably descendents of recent immigrants dispersing from east to the west, because populations were estimated to have diverged about 200,000-400,000 ybp, making ancestral polymorphism a less likely explanation. Maximum likelihood estimates of gene flow among all populations detected asymmetrical gene flow into British Columbia not only of rare migrants from the eastern subspecies in Alberta but also a substantial number of migrants from the adjacent Washington population, and progressively lower numbers from Oregon in an isolation-by distance pattern. The influx of migrants from different populations is consistent with the migrant-pool model of recolonization which has maintained high genetic diversity in the small recovering population in British Columbia. Thus, the risk to this population is not from genetic erosion or inbreeding following a severe population crash, but from demographic stochasticity and extinction in small populations.

Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography. We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroupJ*(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture. We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11(th)-13(th) centuries CE introduced western European lineages into Lebanese Christians.

Genetic technologies developed in the last 20 years have lead to novel and exciting methods to identify genes and specific nucleotides within genes that control phenotypes in field collected organisms. In this review we define and explain two of these methods: linkage disequilibrium (D) mapping and quantitative trait nucleotide (QTN) mapping. The power to detect valid genotype-phenotype associations with LD or QTN mapping depends critically on the extent to which segregating sites in a genome assort independently. LD mapping depends on markers being in disequilibrium with the genes that condition expression of the phenotype. In contrast, QTN mapping depends critically upon most proximal loci being at equilibrium. We show that both patterns actually exist in the genome of Anopheles gambiae, the most important malaria vector in sub-Saharan Africa while segregating sites appear to be largely in equilibrium throughout the genome of Aedes aegypti, the vector of Dengue and Yellow fever flaviviruses. We discuss additional approaches that will be needed to identify genes and nucleotides that control phenotypes in field collected organisms, focusing specifically on ongoing studies of genes conferring resistance to insecticides.

Recent findings are consistent with a slow but constant shift towards reduced sensitivity of Mycosphaerella graminicola to azole fungicides, which target the CYP51 gene. The goal of this study was to elucidate the evolutionary mechanisms through which CYP51-based mutations associated with altered sensitivity have evolved in M. graminicola over space and time. To accomplish this, we sequenced and compared a portion of the CYP51 gene encompassing the main mutations associated with altered sensitivity towards demethylation inhibitor fungicides. The CYP51 gene showed an extraordinary dynamic shift consistent with a selective haplotype replacement both in space and in time. No mutations associated with increased resistance to azoles were found in non-European populations. These mutations were also absent in the oldest collections from Europe, whereas they dominated in the recent European populations. Intragenic recombination was identified as an important evolutionary process in populations affected by high fungicide selection, suggesting the creation of novel alleles among existing mutations as a potential source of novel resistance alleles. We propose that CYP51 mutations giving resistance in M. graminicola arose only locally (perhaps in Denmark or the UK) and were then spread eastward across Europe through wind-dispersed ascospores. We conclude that recurring cycles of recombination coupled with selection due to the widespread use of azole fungicides will increase the frequency of novel mutants or recombinants with higher resistance. Long-distance gene flow due to wind dispersal of ascospores will move the resulting new alleles to new areas following the prevailing wind directions. A selective replacement favouring haplotypes with various coding mutations at the target site for azole fungicides during the last 5-10 years is the most likely cause of the decrease in sensitivity reported for many azole fungicides in the same period.

Phrynocephalus vlangalii is restricted to dry sand or Gobi desert highlands between major mountain ranges in the Qinghai (Tibetan) Plateau. Mitochondrial DNA (mtDNA) sequence (partial ND2, tRNA(Trp) and partial tRNA(Ala)) was obtained from 293 Phrynocephalus sampled from 34 sites across the plateau. Partitioned Bayesian and maximum parsimony phylogenetic analyses revealed that P. vlangalii and two other proposed species (P. erythrus and P. putjatia) together form a monophyletic mtDNA clade which, in contrast with previous studies, does not include P. theobaldi and P. zetangensis. The main P. vlangalli clade comprises seven well-supported lineages that correspond to distinct geographical areas with little or no overlap, and share a most recent common ancestor at 5.06 +/- 0.68 million years ago (mya). This is much older than intraspecific lineages in other Tibetan animal groups. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruption of maternal gene flow. A combined approach based on tests of population expansion, estimation of node dates, and significance tests on clade areas indicated that phylogeographical structuring has been primarily shaped by three main periods of plateau uplift during the Pliocene and Pleistocene, specifically 3.4 mya, 2.5 mya and 1.7 mya. These periods corresponded to the appearance of several mountain ranges that formed physical barriers between lineages. Populations from the Qaidam Basin are shown to have undergone major demographic and range expansions in the early Pleistocene, consistent with colonization of areas previously covered by the huge Qaidam palaeolake, which desiccated at this time. The study represents one of the most detailed phylogeographical analyses of the Qinghai Plateau to date and shows how geological events have shaped current patterns of diversity.

Claviceps purpurea is an important pathogen of grasses and source of novel chemical compounds. Three groups within this species (G1, G2 and G3) have been recognized based on habitat association, sclerotia and conidia morphology, as well as alkaloid production. These groups have further been supported by Random Amplification of Polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers, suggesting this species may be more accurately described as a species complex. However, all divergent ecotypes can coexist in sympatric populations with no obvious physical barriers to prevent gene flow. In this study, we used both phylogenetic and population genetic analyses to test for speciation within C. purpurea using DNA sequences from ITS, a RAS-like locus, and a portion of beta-tubulin. The G1 types are significantly divergent from the G2/G3 types based on each of the three loci and the combined dataset, whereas the G2/G3 types are more integrated with one another. Although the G2 and G3 lineages have not diverged as much as the G1 lineage based on DNA sequence data, the use of three DNA loci does reliably separate the G2 and G3 lineages. However, the population genetic analyses strongly suggest little to no gene flow occurring between the different ecotypes, and we argue that this process is driven by adaptations to ecological habitats; G1 isolates are associated with terrestrial grasses, G2 isolates are found in wet and shady environments, and G3 isolates are found in salt marsh habitats.

The northeastern Atlantic and the Mediterranean Sea share geological histories and display great faunal affinities. The majority of the Mediterranean species have Atlantic origins, with a few species with tropical affinities. These include the parrotfish Sparisoma cretense and the wrasse Thalassoma pavo that are restricted to the subtropical northeastern Atlantic, the Macaronesian archipelagos (Azores, Madeira, and Canaries) and the southern Mediterranean. The Pleistocene glaciations have been described as having different effects on the fauna of the two regions. During glacial peaks, Mediterranean waters remained warmer than those of the adjacent Atlantic. Within the eastern Atlantic, the effects of Pleistocene glaciations were differentiated. Here, we perform a comparative analysis focusing on T. pavo and S. cretense populations from the northeastern Atlantic and the Mediterranean to assess the effects of Pleistocene glaciations in these two species. Sequences from the mitochondrial control region were obtained and analyzed combining phylogeographic and demographic approaches. Gene flow between Atlantic and Mediterranean populations was shown to be very high. The Mediterranean populations of T. pavo and S. cretense showed high levels of genetic diversity, even in the eastern basin, pointing to an ancient colonization event. This suggests that both species must have been able to persist in the Mediterranean during the cold Pleistocene periods. Historical migration estimates revealed a Mediterranean towards Atlantic trend in the case of T. pavo, which may reflect the re-colonization of areas in the Atlantic by fish that survived the cold phases in relatively warmer Mediterranean refugia. Our data also showed that within the Macaronesian Archipelagos, migrations occurred from Madeira towards the Azores, for both T. pavo and S. cretense, thus supporting a post-glacial colonization of the Azores by fish that persisted in the warmer region of Madeira. Similar geographic distributions, thermal affinities, and means of dispersion for T. pavo and S. cretense resulted in a similar response to the effects of Pleistocene glaciations, as evidenced by identical phylogeographic patterns.

CREATE is a Windows program for the creation of new and conversion of existing data input files for 52 genetic data analysis software programs. Programs are grouped into areas of sibship reconstruction, parentage assignment, genetic data analysis, and specialized applications. CREATE is able to read in data from text, Microsoft Excel and Access sources and allows the user to specify columns containing individual and population identifiers, birth and death data, sex data, relationship information, and spatial location data. CREATE's only constraints on source data are that one individual is contained in one row, and the genotypic data is contiguous. CREATE is available for download at http://www.lsc.usgs.gov/CAFL/Ecology/Software.html.

This study examined relationships between bathymetrically induced deep-ocean currents and the dispersal of the hydrothermal vent tubeworm Ridgeia piscesae along the northeast Pacific ridge system. A robust diagnostic model of deep-ocean circulation in this region predicted strong southeasterly currents following contours of the Blanco Transform Fault, a 450-km lateral offset that separates the Gorda and Juan de Fuca ridge systems. Such currents should facilitate the southward dispersal of R. piscesae larvae. Immigration rates for populations north and south of the Blanco Transform Fault were estimated from molecular population genetic data. Mitochondrial DNA evidence revealed population subdivision across the Blanco Transform Fault, and a strong directional bias in gene flow that was consistent with predictions of the circulation model. The distribution of mitochondrial diversity between the northern and southern populations of R. piscesae suggests that the Gorda Ridge tubeworms have maintained larger effective population sizes than the northern populations, a pattern that also exists in co-occurring limpets. Together, these data suggest that the northern vent fields may experience a higher frequency of habitat turnover and consequently more rapid losses of genetic diversity.

Marine species with planktonic larval durations of several months (teleplanic larvae) can potentially maintain demographic connectivity across large geographical distances. This perspective has important fundamental and applied implications, notably for the understanding of evolutionary and ecological processes in the marine realm, the implementation of marine protected areas, and fisheries management. Here we present, at the scale of the Northwest Atlantic, a spatial analysis of snow crab (Chionoecetes opilio, Majoidea) population genetic structure, a species that has a planktonic larval phase of 3 to 5 months. Eight microsatellite markers analysed on 847 C. opilio samples from 13 locations revealed an absence of significant genetic structure along the west coast of Greenland and within Atlantic Canada from southern Labrador to Nova Scotia. These results are consistent with a scenario of extensive demographic connectivity among C. opilio populations and have implications for the management of this species, which supports one of the most important Canadian and Greenlandic fisheries in terms of economic value. A genetic break is nevertheless identified between Greenland and Atlantic Canada, showing that genetic structure can develop within seas (the Labrador Sea in this case) despite the occurrence of very long planktonic larval stages.

Dispersal capabilities determine and maintain local gene flow, and this has implications for population persistence and/or recolonization following environmental perturbations (natural or anthropogenic), disease outbreaks, or other demographic collapses. To predict recolonization and understand dispersal capacity in a stream-breeding frog, we examined individual movement patterns and gene flow among four subpopulations of the Neotropical glassfrog, Centrolene prosoblepon, at a mid-elevation cloud forest site at E1 Cope, Panama. We measured male movement directly during a two year mark-recapture study, and indirectly with gene flow estimates from mitochondrial DNA sequences (mtDNA). Individuals of this species showed strong site fidelity: over two years, male frogs in all four headwater streams moved very little (mean = 2.33 m; mode = 0 m). Nine individuals changed streams within one or two years, moving 675-1 108 in. For those males moving more than 10 in, movement was biased upstream (p < 0.001). Using mtDNA ND1 gene sequences, we quantified gene flow within and among headwater streams at two spatial scales: among headwater streams within two adjacent watersheds (2.5 km) and among streams within a longitudinal gradient covering 5.0 km(2). We found high gene flow among headwater streams (phi(ST) = 0.007, p = 0.325) but gene flow was more limited across greater distances (phi(CT) = 0.322, p = 0.065), even within the same drainage network. Lowland populations of C prosoblepon potentially act as an important source of colonists for upland populations in this watershed.

Population augmentation with translocated individuals has been shown to alleviate the effects of bottlenecks and drift. The first step to determine whether restoration for genetic considerations is warranted is to genetically monitor reintroduced populations and compare results to those from the source. To assess the need for genetic restoration, we evaluated genetic diversity and structure of reintroduced (n = 3) and captive populations of the endangered black-footed ferret (Mustela nigripes). We measured genotypic changes among populations using seven microsatellite markers and compared phenotypic changes with eight morphometric characters. Results indicated that for the population which rapidly grew post-reintroduction, genetic diversity was equivalent to the captive, source population. When growth languished, only the population that was augmented yearly maintained diversity. Without augmentation, allelic diversity declined precipitously and phenotypic changes were apparent. Ferrets from the genetically depaupertate population had smaller limbs and smaller overall body size than ferrets from the two populations with greater diversity. Population divergence (F-ST = 0.10 +/- 0.01) was surprisingly high given the common source of populations. Thus, it appears that 5-10 years of isolation resulted in both genotypic divergence and phenotypic changes to populations. We recommend translocation of 30-40 captive individuals per annum to reintroduction sites which have not become established quickly. This approach will maximize the retention of genetic diversity, yet maintain the beneficial effects of local adaptation without being swamped by immigration.

Background: The Azores are an archipelago located in the North Atlantic Ocean (parallel 38) composed of nine islands, dispersed over three geographical groups: The Eastern group (Sao Miguel and Santa Maria), the Central group (Terceira, Graciosa, Pico, Sao Jorge and Faial) and the Western group (Flores and Corvo). Taking into consideration the geographical and settlement history differences of the archipelago, the genetic diversity pattern and the internal migration of the Azorean population were assessed, based on the analysis of 15 STR loci in 592 unrelated individuals. Results: The results of this evaluation reveal that Terceira displays the highest value of gene diversity (0.7979) and Corvo the lowest (0.7717). Gene flow analysis indicates that Corvo has the lowest value for migration, 23.35, where as Sao Miguel and Terceira have the highest values for emigration, 108.14 and 87.66, respectively. Taken together, the data demonstrate that, despite settlement diversity, no genetic difference between the populations of the nine islands is observable today. This may be explained by internal migration. Conclusion: Overall, the Azorean population can be analysed as a homogeneous genetic group, which consequently, would present, possibly, the same drug-reaction profile. In terms of genomic medicine, these results will have a significant impact on the design of future genetic and pharmacogenomic studies in the Azorean population.

Knowledge of DNA evolution is central to our understanding of biological history, but how fast does DNA change? Previously, pedigree and ancient DNA studies-focusing on evolution in the short term-have yielded molecular rate estimates substantially faster than those based on deeper phylogenies. It has recently been suggested that short-term, elevated molecular rates decay exponentially over 1-2 Myr to long-term, phylogenetic rates, termed “time dependency of molecular rates.” This transition has potential to confound molecular inferences of demographic parameters and dating of many important evolutionary events. Here, we employ a novel approach-geologically dated changes in river drainages and isolation of fish populations-to document rates of mitochondrial DNA change over a range of temporal scales. This method utilizes precise spatiotemporal disruptions of linear freshwater systems and hence avoids many of the limitations associated with typical DNA calibration methods involving fossil data or island formation. Studies of freshwater-limited fishes across the South Island of New Zealand have revealed that genetic relationships reflect past, rather than present, drainage connections. Here, we use this link between drainage geology and genetics to calibrate rates of molecular evolution across nine events ranging in age from 0.007 Myr (Holocene) to 5.0 Myr (Pliocene). Molecular rates of change in galaxiid fishes from calibration points younger than 200 kyr were faster than those based on older calibration points. This study provides conclusive evidence of time dependency in molecular rates as it is based on a robust calibration system that was applied to closely related taxa, and analyzed using a consistent and rigorous methodology. The time dependency observed here appears short-lived relative to previous suggestions (1-2 Myr), which has bearing on the accuracy of molecular inferences drawn from processes operating within the Quaternary and mechanisms invoked to explain the decay of rates with time.

Background: An increasing number of studies demonstrate that genetic differentiation and speciation in the sea occur over much smaller spatial scales than previously appreciated given the wide distribution range of many morphologically defined coral reef invertebrate species and the presumed dispersal-enhancing qualities of ocean currents. However, knowledge about the processes that lead to population divergence and speciation is often lacking despite being essential for the understanding, conservation, and management of marine biodiversity. Sponges, a highly diverse, ecologically and economically important reef-invertebrate taxon, exhibit spatial trends in the Indo-West Pacific that are not universally reflected in other marine phyla. So far, however, processes generating those unexpected patterns are not understood. Results: We unraveled the phylogeographic structure of the widespread Indo-Pacific coral reef sponge Leucetta chagosensis across its known geographic range using two nuclear markers: the rDNA internal transcribed spacers (ITS 1&2) and a fragment of the 28S gene, as well as the second intron of the ATP synthetase beta subunit-gene (ATPSb-iII). This enabled the detection of several deeply divergent clades congruent over both loci, one containing specimens from the Indian Ocean ( Red Sea and Maldives), another one from the Philippines, and two other large and substructured NW Pacific and SW Pacific clades with an area of overlap in the Great Barrier Reef/Coral Sea. Reciprocally monophyletic populations were observed from the Philippines, Red Sea, Maldives, Japan, Samoa, and Polynesia, demonstrating long-standing isolation. Populations along the South Equatorial Current in the south-western Pacific showed isolation-by-distance effects. Overall, the results pointed towards stepping-stone dispersal with some putative long-distance exchange, consistent with expectations from low dispersal capabilities. Conclusion: We argue that both founder and vicariance events during the late Pliocene and Pleistocene were responsible to varying degrees for generating the deep phylogeographic structure. This structure was perpetuated largely as a result of the life history of L. chagosensis, resulting in high levels of regional isolation. Reciprocally monophyletic populations constitute putative sibling ( cryptic) species, while population para- and polyphyly may indicate incipient speciation processes. The genetic diversity and biodiversity of tropical Indo-Pacific sponges appears to be substantially underestimated since the high level of genetic divergence is not necessarily manifested at the morphological level.

A major goal of population genetics research is to identify the relative influences of historical and contemporary processes that serve to structure genetic variation. Most population genetic models assume that populations exist in a state of migration-drift equilibrium. However, in the past this assumption has rarely been verified, and is likely rarely achieved in natural populations. We assessed the equilibrium status at both local and regional scales of the Atlantic killifish, Fundulus heteroclitus. This species is a model organism for the study of adaptive clinal variation, but has also experienced a complicated history of range expansion and secondary contact following allopatric divergence, potentially obscuring the influence of contemporary evolutionary processes. Presumptively neutral genetic markers (microsatellites) demonstrated zones of secondary intergradation among coastal populations centred around northern New Jersey and the Chesapeake Bay region. Analysis of genetic variation indicated isolation by distance among some populations and provided supporting evidence that the Delaware Bay, but not the Chesapeake Bay, has acted as a barrier to dispersal among coastal populations. Bayesian estimates indicated large effective population sizes and low migration rates, and were in good agreement with empirically derived estimates of population and neighbourhood size from mark-recapture studies. These data indicate that populations are not in migration-drift equilibrium at a regional scale, and suggest that contributing factors include large population size combined with relatively low migration rates. These conditions should be considered when interpreting the evolutionary significance of the distribution of genetic variation among F. heteroclitus populations.

Climate change during the late Quaternary has been implicated as the cause of both massive range shifts and extinction events. We combined molecular marker data and previously published fossil data to reconstruct the late Quaternary history of a grassland-dependent species, the black-footed ferret (Mustela nigripes), and to determine whether populations from Pleistocene refugia in the Columbia Basin, eastern Beringia, and Great Plains persisted into the Holocene and Recent eras. Using DNA extracted from 97 museum specimens of extirpated populations, we amplified 309 bp of the mtDNA control region, and 8 microsatellite markers from the nuclear genome. Overall haplotype diversity from 309 base pairs (bp) of mitochondrial DNA (mtDNA) control region was low (5 haplotypes, nucleotide diversity = 0.001 +/- 0.001 SD) and was contained within a single phylogenetic clade. The star phylogeny and unimodal mismatch distribution indicated that a rapid range expansion from a single Pleistocene refugium occurred. Microsatellite data corroborated this genetic pattern: populations from the mixed grasslands of the Great Plains had significantly higher expected heterozygosity and allelic richness than populations to the west (HE = 0.66 versus 0.41, AR = 4.3 versus 2.7, respectively), and 0, a measure of relative population size, was substantially greater in the east than west (2.4 versus 0.7). We infer from these data that black-footed ferrets rapidly colonized western ecoregions in a stepwise fashion from the Great Plains to the intermountain regions of the Rocky Mountains and the Colorado Plateau after the last ice age. It appears that glacial retreat and global warming caused both range expansion and localized extinction in this North American mustelid species.

Predators typically avoid dangerous species, and batesian mimicry evolves when a palatable species ( the `mimic') co- opts a warning signal from a dangerous species ( the `model') and thereby deceives its potential predators(1,2). Because predators would not be under selection to avoid the model and any of its look- alikes in areas where the model is absent ( that is, allopatry)(2-5), batesian mimics should occur only in sympatry with their model. However, contrary to this expectation, batesian mimics often occur in allopatry(6-8). Here we focus on one such example - a coral snake mimic(3,8). Using indirect DNA- based methods, we provide evidence suggesting that mimics migrate from sympatry, where mimicry is favoured(3,9), to allopatry, where it is disfavoured(10). Such gene flow is much stronger in nuclear genes than in maternally inherited mitochondrial genes, indicating that dispersal by males may explain the presence of mimetic phenotypes in allopatry. Despite this gene flow, however, individuals from allopatry resemble the model less than do individuals from sympatry. We show that this breakdown of mimicry probably reflects predator- mediated selection acting against individuals expressing the more conspicuous mimetic phenotype in allopatry. Thus, although gene flow may explain why batesian mimics occur in allopatry, natural selection may often override such gene flow and promote the evolution of non- mimetic phenotypes in such areas.

Sleeper sharks are a poorly studied group of deep-sea sharks. The subgenus, Somniosus, contains three morphologically similar species: S. microcephalus found in the Arctic and North Atlantic; S. pacificus in the North Pacific; and S. antarcticus in the Southern Ocean. These sharks have been reported mainly in temperate to polar waters and occasionally in subtropical locations. They have not been recorded in tropical waters. This study investigates the relationships among the accepted species of Somniosus through analysis of mitochondrial cytochrome b sequence variation. Seventy-five samples were examined from four sampling locations in the North Pacific, Southern Ocean and North Atlantic. Twenty-one haplotypes were found. A minimum spanning parsimony network separated these haplotypes into two divergent clades, an S. microcephalus and an S. pacificus/antarcticus clade, strongly supporting the distinction of S. microcephalus as a separate species from the Pacific sleeper shark species. Analysis of genetic structure within the S. pacificus/antarcticus clade (analysis of molecular variance, allele frequency comparisons, and a nested clade analysis) showed limited or no differences amongst three populations. Further examination of genetic variation at more variable mtDNA and nuclear markers is needed to examine the species status of S. pacificus and S. antarcticus.

Micro-evolutionary processes that underpin genetic and morphological variation in highly mobile pelagic vertebrates are virtually unknown. Previous findings preferentially invoke vicariant isolation due to large-scale physical barriers such as continental landmasses, followed by genetic drift. However increasingly, evidence for divergence by non-random processes (e.g. selection, plasticity) is being presented. Wedge-tailed shearwaters are wide-ranging seabirds with breeding colonies located such that they experience a variety of environmental pressures and conditions. Previous work on this species has provided evidence of inter-colony divergence of adult morphology and foraging modes, as well as chick developmental patterns, suggesting that reinforcement among colonies is possible. In order to evaluate the micro-evolutionary processes driving this observed variation, our study compared patterns of gene flow with morphological and environmental variation among four colonies of wedge-tailed shearwater breeding within the Indo-Pacific Ocean basin. Estimates of gene flow differed according to the genetic marker used; most likely, this is a function of different mutation rates. Nuclear introns suggest that gene flow among wedge-tailed shearwater breeding colonies within the Indo-Pacific Ocean basin is substantial, however microsatellite markers imply that gene flow is reduced. In general, levels of genetic divergence were relatively low and did not correlate with geographic distance, morphological distance or environmental differences (sea-surface temperature and chlorophyll a concentration) among colonies. We suggest that genetic drift alone is unlikely to be the major source of morphological variation seen in this species. Instead, we propose that non-random processes (selection, plasticity) underpin morphological diversity seen in this and possibly other seabird species.

Aim Oceanic islands represent a special challenge to historical biogeographers because dispersal is typically the dominant process while most existing methods are based on vicariance. Here, we describe a new Bayesian approach to island biogeography that estimates island carrying capacities and dispersal rates based on simple Markov models of biogeographical processes. This is done in the context of simultaneous analysis of phylogenetic and distributional data across groups, accommodating phylogenetic uncertainty and making parameter estimates more robust. We test our models on an empirical data set of published phylogenies of Canary Island organisms to examine overall dispersal rates and correlation of rates with explanatory factors such as geographic proximity and area size. Location Oceanic archipelagos with special reference to the Atlantic Canary Islands. Methods The Canary Islands were divided into three island-groups, corresponding to the main magmatism periods in the formation of the archipelago, while non-Canarian distributions were grouped into a fourth `mainland-island'. Dispersal between island groups, which were assumed constant through time, was modelled as a homogeneous, time-reversible Markov process, analogous to the standard models of DNA evolution. The stationary state frequencies in these models reflect the relative carrying capacity of the islands, while the exchangeability (rate) parameters reflect the relative dispersal rates between islands. We examined models of increasing complexity: Jukes-Cantor (JC), Equal-in, and General Time Reversible (GTR), with or without the assumption of stepping-stone dispersal. The data consisted of 13 Canarian phylogenies: 954 individuals representing 393 taxonomic (morphological) entities. Each group was allowed to evolve under its own DNA model, with the island-model shared across groups. Posterior distributions on island model parameters were estimated using Markov Chain Monte Carlo (MCMC) sampling, as implemented in MrBayes 4.0, and Bayes Factors were used to compare models. Results The Equal-in step, the GTR, and the GTR step dispersal models showed the best fit to the data. In the Equal-in and GTR models, the largest carrying capacity was estimated for the mainland, followed by the central islands and the western islands, with the eastern islands having the smallest carrying capacity. The relative dispersal rate was highest between the central and eastern islands, and between the central and western islands. The exchange with the mainland was rare in comparison. Main conclusions Our results confirm those of earlier studies suggesting that inter-island dispersal within the Canary Island archipelago has been more important in explaining diversification within lineages than dispersal between the continent and the islands, despite the close proximity to North Africa. The low carrying capacity of the eastern islands, uncorrelated with their size or age, fits well with the idea of a historically depauperate biota in these islands but more sophisticated models are needed to address the possible influence of major recent extinction events. The island models explored here can easily be extended to address other problems in historical biogeography, such as dispersal among areas in continental settings or reticulate area relationships.

A wide range of vectors is currently introducing a plethora of alien marine species into indigenous marine species assemblages. Over the past two decades, molecular studies of non-native seaweeds, including cryptic invaders, have successfully identified the species involved and their sources; we briefly review these studies. As yet, however, little research has been directed towards examining the genetic consequences of seaweed invasions. Here we provide an overview of seaweed invasions from a genetic perspective, focusing on invader species for which the greatest amount of information is available. We review invasion processes, and rationalize evolutionary and genetic consequences for the indigenous and invader species into two main groups: (1) changes in gene-pool composition, in population structure and allele frequencies; and (2) changes in genome organization at the species level through hybridization, and in individual gene expression profiles at the levels of expressed messenger RNA and the proteome (i.e., all proteins synthesized) and thus the phenotype. We draw on studies of better-known aquatic and terrestrial organisms to point the way forward in revealing the genetic consequences of seaweed invasions. We also highlight potential applications of more recent methodological and statistical approaches, such as microarray technology, assignment tests and mixed stock analysis.

The Black and Caspian Seas have experienced alternating periods of isolation and interconnection over many Milankovitch climate oscillations and most recently became separated when the meltwater overflow from the Caspian Sea ceased at the end of the last glaciation. Climate-induced habitat changes have indisputably had profound impacts on distribution and demography of aquatic species, yet uncertainties remain about the relative roles of isolation and dispersal in the response of species shared between the Black and Caspian Sea basins. We examined these issues using phylogeographical analysis of an anadromous cyprinid fish Rutilus frisii. Bayesian coalescence analyses of sequence variation at two nuclear and one mitochondrial genes suggest that the Black and Caspian Seas supported separate populations of R. frisii during the last glaciation. Parameter estimates from the fitted isolation-with-migration model showed that their separation was not complete, however, and that the two populations continued to exchange genes in both directions. These analyses also suggested that majority of migrations occurred during the Pleistocene, showing that the variation shared between the Black and Caspian Seas is the result of ancient dispersal along the temporary natural connections between the basins, rather than of incomplete lineage sorting or recent human-mediated dispersal. Gene flow between the refugial populations was therefore an important source of genetic variation, and we suggest that it facilitated the evolutionary response of the populations to changing climate.

Individuals of many species show high levels of fidelity to natal populations, often due to reliance on patchily distributed habitat features. In many of these species, the negative impacts of inbreeding are mitigated through specialized behaviours such as seasonal mating dispersal. Quantifying population structure for species with these characteristics can potentially elucidate social and environmental factors that interact to affect mating behaviour and population connectivity. In the northern part of their range, timber rattlesnakes are communal hibernators with high natal philopatry. Individuals generally recruit to the same hibernaculum as their mother and remain faithful to that hibernaculum throughout their lives. We examined the genetic structure of Crotalus horridus hibernacula in the northeastern USA using microsatellite loci. Sampled hibernacula exhibited only modest levels of differentiation, indicating a significant level of gene flow among them. We found no significant correlation between genetic differentiation and geographical distance, but did find significant positive correlation between genetic differentiation and a cost-based distance metric adjusted to include the amount of potential basking habitat between hibernacula. Therefore, thermoregulation sites may increase gene flow by increasing the potential for contact among individuals from different populations. Parentage analyses confirmed high levels of philopatry of both sexes to their maternal hibernaculum; however, approximately one-third of paternity assignments involved individuals between hibernacula, confirming that gene flow among hibernacula occurs largely through seasonal male mating dispersal. Our results underscore the importance of integrating individual-level behaviours and landscape features with studies of fine-scale population genetics in species with high fidelity to patchily distributed habitats.

During the last 10 years, an increasing number of studies have explored evolutionary aspects of biological invasions. It is becoming increasingly clear that evolutionary processes play an important role during the establishment of non-native species. Genetic drift during the colonization process followed by strong selection imposed through a change in biotic conditions and co-evolutionary disequilibrium set the conditions for rapid evolutionary change in introduced populations. Different hypotheses, which have been proposed to explain how evolutionary and genetic processes, can facilitate invasiveness are explored and their relevance for fish invasions is discussed. Empirical evidence increasingly suggests that admixture after multiple introductions, hybridization between native and non-native species and enemy release can all catalyse the evolution of invasiveness. A number of studies also suggest that genetic bottlenecks might represent less of genetic paradox than previously thought. Much of the theoretical developments and empirical evidence concerning the importance of evolution during biological invasions has been provided from studies on invasive plants. Despite their prominence, fish invasions have received little attention from evolutionary biologists. Recent advances in population genetic analysis such as non-equilibrium methods and genomic techniques such as microarray technology provide suitable tools to address such issues. (c) 2007 The Author Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Background: Marine pelagic fishes exhibit rather complex patterns of genetic differentiation, which are the result of both historical processes and present day gene flow. Comparative multilocus analyses based on both nuclear and mitochondrial genetic markers are probably the most efficient and informative approach to discerning the relative role of historical events and life-history traits in shaping genetic heterogeneity. The European sardine (Sardina pilchardus) is a small pelagic fish with a relatively high migratory capability that is expected to show low levels of genetic differentiation among populations. Previous genetic studies based on meristic and mitochondrial control region haplotype frequency data supported the existence of two sardine subspecies ( S. p. pilchardus and S. p. sardina). Results: We investigated genetic structure of sardine among nine locations in the Atlantic Ocean and Mediterranean Sea using allelic size variation of eight specific microsatellite loci. Bayesian clustering and assignment tests, maximum likelihood estimates of migration rates, as well as classical genetic-variance-based methods ( hierarchical AMOVA test and R-ST pairwise comparisons) supported a single evolutionary unit for sardines. These analyses only detected weak but significant genetic differentiation, which followed an isolation-by-distance pattern according to Mantel test. Conclusion: We suggest that the discordant genetic structuring patterns inferred based on mitochondrial and microsatellite data might indicate that the two different classes of molecular markers may be reflecting different and complementary aspects of the evolutionary history of sardine. Mitochondrial data might be reflecting past isolation of sardine populations into two distinct groupings during Pleistocene whereas microsatellite data reveal the existence of present day gene flow among populations, and a pattern of isolation by distance.

We estimate parameters of a general isolation-with-migration model using resequence data from mitochondrial DNA (mtDNA), the Y chromosome, and two loci on the X chromosome in samples of 25-50 individuals from each of 10 human populations. Application of a coalescent-based Markov chain Monte Carlo technique allows simultaneous inference of divergence times, rates of gene flow, as well as changes in effective population size. Results from comparisons between sub-Saharan African and Eurasian populations estimate that 1500 individuals founded the ancestral Eurasian population similar to 40 thousand years ago (KYA). Furthermore, these small Eurasian founding populations appear to have grown much more dramatically than either African or Oceanian populations. Analyses of sub-Saharan African populations provide little evidence for a history, of population bottlenecks and suggest that die), began diverging from one another upward of 50 KYA. We surmise that ancestral African populations had already been geographically structured prior to the founding of ancestral Eurasian populations. African populations are shown to experience low levels of mitochondrial DNA gene flow, but high levels of Y chromosome gene flow. In particular, Y chromosome gene flow appears to be asymmetric, i.e., from the Bantu-speaking population into other African populations. Conversely, mitochondrial gene flow is more extensive between non-African populations, but appears to be absent between European and Asian Populations.

We assessed population genetic subdivision among four colonies of Common Eiders (Somateria niollissima v-nigrum) breeding in the Yukon-Kuskokwim Delta (YKD), Alaska, using microsatellite genotypes and DNA sequences with differing modes of inheritance. Significant, albeit low, levels of genetic differentiation were observed between mainland populations and Kigigak Island for nuclear intron lamin A and mitochondrial DNA (mtDNA) control region. Intercolony variation in haplotypic frequencies also was observed at mtDNA. Positive growth signatures assayed from microsatellites, nuclear introns, and mtDNA indicate recent colonization of the YKD, and may explain the low levels of structuring observed. Gene flow estimates based on microsatellites, nuclear introns, and mtDNA suggest asymmetrical gene flow between mainland colonies and Kigigak Island, with more individuals on average dispersing from mainland populations to Kigigak Island than vice versa. The directionality of gene flow observed may be explained by the colonization of the YKD from northern glacial refugia or by YKD metapopulation dynamics.

We evaluate the performance of maximum likelihood (ML) analysis of allele frequency data in a linear array of populations. The parameters are a mutation rate and either the dispersal rate in a stepping stone model or a dispersal rate and a scale parameter in a geometric dispersal model. An approximate procedure known as maximum product of approximate conditional (PAC) likelihood is found to perform as well as ML. Mis-specification biases may occur because the importance sampling algorithm is formally defined in term of mutation and migration rates scaled by the total size of the population, and this size may differ widely in the statistical model and in reality. As could be expected, ML generally performs well when the statistical model is correctly specified. Otherwise, mutation rate estimates are much closer to mutation probability scaled by number of demes in the statistical model than scaled by number of demes in reality when mutation probability is high and dispersal is most limited. This mis-specification bias actually has practical benefits. However, opposite results are found in opposite conditions. Migration rate estimates show roughly similar trends, but they may not always be easily interpreted as low-bias estimates of dispersal rate under any scaling. Estimation of the dispersal scale parameter is also affected by mis-specification of the number of demes, and the different biases compensate each other in such a way that good estimation of the so-called neighborhood size (or more precisely the product of population density and mean-squared parent-offspring dispersal distance) is achieved. Results congruent with these findings are found in an application to a damselfly data set.

Common raven (Corvus corax) populations in Mojave Desert regions of southern California and Nevada have increased dramatically over the past five decades. This growth has been attributed to increased human development in the region, as ravens have a commensal relationship with humans and feed extensively at landfills and on road-killed wildlife. Ravens, as a partially subsidized predator, also represent a problem for native desert wildlife, in particular threatened desert tortoises (Gopherus agassizii). However, it is unclear whether the more than 15-fold population increase is due to in situ population growth or to immigration from adjacent regions where ravens have been historically common. Ravens were sampled for genetic analysis at several local sites within five major areas: the West Mojave Desert (California), East Mojave Desert (southern Nevada), southern coastal California, northern coastal California (Bay Area), and northern Nevada (Great Basin). Analyses of mtDNA control region sequences reveal an increased frequency of raven `Holarctic clade' haplotypes from south to north inland, with `California clade' haplotypes nearly fixed in the California populations. There was significant structuring among regions for mtDNA, with high F-ST values among sampling regions, especially between the Nevada and California samples. Analyses of eight microsatellite loci reveal a mostly similar pattern of regional population structure, with considerably smaller, but mostly significant, values. The greater mtDNA divergences may be due to lower female dispersal relative to males, lower N-e, or effects of high mutation rates on maximal values of F-ST. Analyses indicate recent population growth in the West Mojave Desert and a bottleneck in the northern California populations. While we cannot rule out in situ population growth as a factor, patterns of movement inferred from our data suggest that the increase in raven populations in the West Mojave Desert resulted from movements from southern California and the Central Valley. Ravens in the East Mojave Desert are more similar to ones from northern Nevada, indicating movement between those regions. If this interpretation of high gene flow into the Mojave Desert is correct, then efforts to manage raven numbers by local control may not be optimally effective.

The bay scallop Argopecten irradians concentricus Say is a commercially and recreationally important species along the East Coast of the US that consistently shows evidence of recruitment limitation. To determine if limited planktonic larval exchange between populations inhabiting lagoonal basins or sounds contributes to recruitment limitation in central North Carolina, a hypervariable portion of mtDNA (885 bp) was sequenced from 219 adults from 4 sounds (Topsail, Bogue, Back, and Pamlico), 3 of which (Bogue, Back, and Pamlico) are connected by inshore waterways. Although the largest sound (Pamlico) harbored the greatest genetic diversity, diversity was high in all 4 sounds, with no evidence of recent bottlenecks. An analysis of molecular variance indicates significant genetic structure among sounds (phi(CT) = 0. 0069, p = 0.023); all pairwise comparisons among sounds were significant, with the exception of those involving Pamlico Sound. Despite being connected by a short (3 km) inshore waterway, adjacent Bogue and Back Sounds were highly significantly differentiated (phi(CT)=0.0145, p = 0.000). Coalescent-based estimates of gene flow indicated that most sounds exchange <= 4 migrants each generation. Bogue and Back Sound populations, which were heavily impacted by a localized red tide outbreak in 1983 and which subsequently experienced a recruitment failure, each receive <4 migrants each generation from all other sounds combined. Dynamic physical processes in the vicinity of Beaufort Inlet can explain such limited larval exchange between Bogue and Back Sounds, but if dispersal is primarily controlled by tidally dominated surface flow, net dispersal distances may be limited throughout the region. Therefore, patterns of gene flow and genetic differentiation are consistent with the hypothesis that individual sounds are demographically independent and are closed with respect to fishery management issues.

Background. Theoretical work suggests that data from multiple nuclear loci provide better estimates of population genetic parameters than do single loci, but just how many loci are needed and how much sequence is required from each has been little explored. Methodology/Principle Findings. To investigate how much data is required to estimate the population genetic parameter theta (4N(e)mu) accurately under ideal circumstances, we simulated datasets of DNA sequences under three values of theta per site (0.1, 0.01, 0.001), varying in both the total number of base pairs sequenced per individual and the number of equal-length loci. From these datasets we estimated theta using the maximum likelihood coalescent framework implemented in the computer program MIGRATE. Our results corroborated the theoretical expectation that increasing the number of loci impacted the accuracy of the estimate more than increasing the sequence length at single loci. However, when the value of theta was low (0.001), the per-locus sequence length was also important for estimating theta accurately, something that has not been emphasized in previous work. Conclusions/Significance. Accurate estimation of theta required data from at least 25 independently evolving loci. Beyond this, there was little added benefit in terms of decreasing the squared coefficient of variation of the coalescent estimates relative to the extra effort required to sample more loci.

The Iberian Peninsula has been described as a glacial refugium for numerous organisms. In particular, there is evidence both from pollen records and genetic studies that shows the existence of Mediterranean conifers (Pinus halepensis Miller, Pinus pinaster Aiton, and Pinus pinea L) in southeastern Spain during the last glacial stage. Data from eight polymorphic allozyme markers were used to study the spatial genetic structure of I I native populations of maritime pine, P. pinaster, in this region. Models of isolation by distance were adjusted to different groups of populations to test specific hypotheses about the role of mountain ranges in shaping the spatial genetic structure of maritime pine in southeastern Spain. In addition, pair-wise gene interchange was analyzed using migration matrix models and maximum likelihood methods to make joint estimates of dispersal rates and population sizes. A complex pattern in the distribution of gene diversity was found, involving historical isolation due to geographical variables for particular populations. The role of mountain ranges in glacial refugia i) reducing the risk of a population bottleneck by altitudinal migration in response to climatic change, and ii) acting as geographical barriers to gene flow, is discussed.

Phylogenetic and geographic evidence suggest that many parthenogenetic organisms have evolved recently and have spread rapidly. These patterns play a critical role in our understanding of the relative merits of sexual versus asexual reproductive modes, yet their interpretation is often hampered by a lack of detail. Here we present a detailed phylogeographic study of a vertebrate parthenogen, the Australian gecko Heteronotia binoei, in combination with statistical and biophysical modeling of its distribution during the last glacial maximum. Parthenogenetic H. binoei occur in the Australian arid zone and have the widest range of any known vertebrate parthenogen. They are broadly sympatric with their sexual counterparts, from which they arose via hybridization. We have applied nested clade phylogeographic, effective migration, and mismatch distribution analyses to mitochondrial DNA ( mtDNA) sequences obtained for 319 individuals sampled throughout the known geographic ranges of two parthenogenetic mitochondrial lineages. These analyses provide strong evidence for past range expansion events from west to east across the arid zone, and for continuing eastward range expansion. Parthenogen formation and range expansion events date to the late Pleistocene, with one lineage expanding from the northwest of its present range around 240,000 years ago and the second lineage expanding from the far west around 70,000 years ago. Statistical and biophysical distribution models support these inferences of recent range expansion, with suitable climatic conditions during the last glacial maximum most likely limited to parts of the arid zone north and west of much of the current ranges of these lineages. Combination of phylogeographic analyses and distribution modeling allowed considerably stronger inferences of the history of this complex than either would in isolation, illustrating the power of combining complementary analytical approaches.

Determining the genetic structure of tropical bird populations is important for assessing potential genetic effects of future habitat fragmentation and for testing hypotheses about evolutionary mechanisms promoting diversification. Here we used 10 microsatellite DNA loci to describe levels of genetic differentiation for five populations of the lek-mating blue manakin (Chiroxiphia caudata), sampled along a 414-km transect within the largest remaining continuous tract of the highly endangered Atlantic Forest habitat in southeast Brazil. We found small but significant levels of differentiation between most populations. F-ST values varied from 0.0 to 0.023 (overall F-ST = 0.012) that conformed to a strong isolation by distance relationship, suggesting that observed levels of differentiation are a result of migration-drift equilibrium. N(e)m values estimated using a coalescent-based method were small (<= 2 migrants per generation) and close to the minimum level required to maintain genetic similarity between populations. An implication of these results is that if future habitat fragmentation reduces dispersal between populations to even a small extent, then individual populations may undergo a loss of genetic diversity due to an increase in the relative importance of drift, since inbreeding effective population sizes are relatively small (N-e similar to 1000). Our findings also demonstrate that population structuring can occur in a tropical bird in continuous habitat in the absence of geographical barriers possibly due to behavioural features of the species.

Nuclear and chloroplast microsatellite markers were used to study population structure and gene flow among seven Cretan populations of the Aegean endemic plant species Brassica cretica (Brassicaceae). Both nuclear and chloroplast markers revealed exceptionally high levels of population differentiation (overall F-ST = 0.628 and 1.000, respectively) and relatively little within-population diversity (overall H-S = 0.211 and 0.000, respectively). Maximum-likelihood estimates of directional migration rates were low among all pairs of populations (average Nm = 0.286). There was no evidence that differences in flower colour between populations had any influence on historical levels of gene flow. In addition, a haplotype network showed that all five chloroplast haplotypes found in the sample were closely related. Together, these results suggest that current patterns of diversification in B. cretica are mainly a result of genetic drift during the last half million years. The main conclusions from the present study are consistent with the prevailing hypothesis that plant diversification in the Aegean region is driven by random rather than adaptive differentiation among isolated populations.

In tropical rainforests, insects show especially high species richness and local endemism of species relative to vertebrates. One possible cause is that insects respond to historical fluctuations of rainforests on a smaller spatial scale than do vertebrates. To evaluate this hypothesis, we combine environmental niche models and mitochondrial DNA phylogeography for two pairs of sister species of the dung beetle genus Temnoplectron (T. aeneopiceum-T. subvolitans and T. politulum-T. reyi) from the rainforests of northeastern Australia, where climate-driven rainforest fluctuations in the Quaternary have strongly influenced genetic and species diversity of vertebrates. Within both species pairs, the bioclimatic niche was conserved, but the T. aeneopiceum-T. subvolitans species pair had the narrower environmental range, and thus more restricted potential distribution. Coalescent analyses indicated Late Pliocene or Early Pleistocene divergences for both species pairs, and earlier speciation in (T. aeneopiceum-T. subvolitans) than in (T. politulum-T. reyi). Phylogeographic structure in (T. aeneopiceum-T. subvolitans) was more pronounced than in (T. politulum-T. reyi), with significant isolation-by-distance in the former species-pair only. Nested clade and coalescence analyses indicated local range expansions for the T. aeneopiceum-subvolitans species pair and range-wide expansion for both T. politulum and T. reyi. We suggest that stronger phylogeographic structure and earlier divergence in (T. aeneopiceum-T. subvolitans) than in (T. politulum-T. reyi) reflects a stronger influence of environmental barriers to gene flow under the present climate and greater sensitivity to warmer and drier periods of the Quaternary. The two species pairs evidently responded to Quaternary rainforest fluctuations at spatial scales similar to those seen within low-vagility species of vertebrate. Despite this similarity of scale, these insect lineages are reproductively isolated at parapatric boundaries, whereas analogous lineages of vertebrates often are not. We suggest that rapid evolution of genitalia may facilitate geographic speciation in rainforest beetles.

To reveal the role of diverged body size and genital morphology in reproductive isolation among closely related species, we examined patterns of, and factors limiting, introgressive hybridization between sympatric Ohomopterus ground beetles in central Japan using mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences. We sampled 17 local assemblages that consisted of two to five species and estimated levels of interspecific gene flow using the genetic distance, D-A, and maximum-likelihood estimates of gene flow. Sharing of haplotypes or haplotype lineages was detected between six of seven species that occurred in the study areas, indicating mitochondrial introgression. The intensity and direction of mitochondrial gene flow were variable among species pairs. To determine the factors affecting introgression patterns, we tested the relationships between interspecific DA and five independent variables: difference in body size, difference in genital size, phylogenetic relatedness (nuclear gene sequence divergence), habitat difference, and species richness of the assemblage. Body and genital size differences contributed significantly to preventing gene flow. Thus, mechanical isolation mechanisms reduce the chance of introgressive hybridization between closely related species. Our results highlight the role of morphological divergence in speciation and assemblage formation processes through mechanical isolation.

FaBox is a collection of simple and intuitive web services that enable biologists and medical researchers to quickly perform typical task with sequence data. The services makes it easy to extract, edit, and replace sequence headers and join or divide data sets based on header information. Other services include collapsing a set of sequences into haplotypes and automated formatting of input files for a number of population genetics programs, such as ARLEQUIN, TCS and MRBAYES. The toolbox is expected to grow on the basis of requests for particular services and converters in the future.

Background: The soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of R. solani AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of R. solani AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of R. solani AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of R. solani AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89). Results: Populations of R. solani AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of R. solani AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of R. solani AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Phi(ST) = 0.257, significant at P < 0.05) but not for locus pP42F (Phi(ST) = 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of R. solani AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of R. solani AG-3. Conclusion: The two sisters populations of the basidiomycete fungus R. solani AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species.

For more than a century, archaeologists have studied the cultural and skeletal remains of the prehistoric Native Americans known as the “Hopewell Moundbuilders.” While many aspects of the Hopewell phenomenon are now well understood, questions still remain about the genetic makeup, burial practices, and social structure of Hopewell communities. To help answer these questions, we extracted mitochondrial DNA (mtDNA) from the skeletal remains of 39 individuals buried at the Pete Klunk Mound Group in Illinois. The pattern of mtDNA variation at this site suggests that matrilineal relationships did not strongly influence burial practices. Because different forms of mortuary activity were not associated with distinct genetic lineages, this study provides no evidence of a maternally inherited or ascribed status system in this society. The genetic data collected here also help clarify another aspect of Illinois Hopewell social structure by suggesting a matrilocal system of post-marital residence. Finally, when these data were considered in conjunction with mtDNA data previously collected from the Hopewell Mound Group in Ohio (Mills 2003), they demonstrated that migration and gene flow did accompany the cultural exchange between Hopewell communities in the Illinois and Ohio Valleys.

Using the island model of population demography, I report that the demographic parameters migration rate and effective population size can be jointly estimated with equilibrium probabilities of identity in state calculated using a sample of genotypes collected at a single point in time from a single generation. The method, which uses moment-type estimators, applies to dioecious populations in which females and males have identical demography and monoecious populations with no selfing and requires that offspring genotypes are sampled following reproduction and prior to migration. I illustrate the estimation procedure using the infinite-island model with no mutation and the finite-island model with three kinds of mutation models. In the infinite-island model with no mutation, the estimators can be expressed as simple functions of estimates of the F-statistic parameters F-IT and F-ST. In the finite-island model with mutation among k alleles, mutation rate, migration rate, and effective population size can be simultaneously estimated. The estimates of migration rate and effective population size are somewhat robust to violations in assumptions that may arise in empirical applications such as different kinds of mutation models and deviations from temporal equilibrium.

We examined the genetic structure of snowy plovers (Charadrius alexandrinus) in North America, the Caribbean, and the west coast of South America to quantify variation within and among breeding areas and to test the validity of three previously recognized subspecies. Sequences (676 bp) from domains I and II of the mitochondrial control region were analyzed for 166 snowy plovers from 20 breeding areas. Variation was also examined at 10 microsatellite loci for 144 snowy plovers from 14 breeding areas. The mtDNA and microsatellite data provided strong evidence that the Puerto Rican breeding group is genetically divergent from sites in the continental U.S. (net sequence divergence = 0.38%; F (ST) for microsatellites = 0.190). Our data also revealed high levels of differentiation between sites from South America and North America (net sequence divergence = 0.81%; F (ST) for microsatellites = 0.253). In contrast, there was little genetic structure among breeding sites within the continental U.S. Our results suggest that snowy plovers in Florida should be considered part of C. a. nivosus (rather than part of C. a. tenuirostris, where they are currently placed), whereas snowy plovers from Puerto Rico should be considered part of C. a. tenuirostris. Snowy plovers in South America should remain a separate subspecies (C. a. occidentalis). Although U.S. Pacific and Gulf Coast breeding areas were not genetically distinct from other continental U.S. sites, demographic isolation, unique coastal habitats, and recent population declines suggest they warrant special concern.

The northern riffleshell (Epioblasma torulosa rangiana) is a critically endangered unionoid species in need of conservation throughout its range. It is the only unionoid to be federally protected in both Canada and the U.S. We use sequences from two mtDNA genes and 15 microsatellite loci to assess genetic variation among 86 individuals from the four populations in the three remaining drainages in which E. t. rangiana is known to be reproducing. All of these populations are in formerly glaciated landscapes that emerged < 10 kya. The mtDNA sequence data do not indicate significant geographic structure among the populations. However, allelic data from the microsatellite loci reveal highly significant population structuring. Individuals of E. t. rangiana can be assigned to their own river of origin with 98.8% accuracy. Significant isolation-by-distance occurs. This analysis will be useful to conservation managers in documenting the genetic structure, patterns of isolation, and genetic variability within and among populations of E. t. rangiana.

Assessing the genetic consequences of habitat fragmentation is a crucial step in conservation planning for species in endangered habitats. We tested for the impact of natural habitat fragmentation on gene flow and genetic diversity in seven northern breeding locations of the sagebrush Brewer's sparrow, Spizella breweri breweri. Genetic analyses using five highly variable DNA microsatellite loci suggested that individuals sampled within a sagebrush landscape fragmented by natural elements such as coniferous forest, comprise a single genetic population and that gene flow among them is unimpeded. We posit that juvenile dispersal links seemingly isolated breeding locales of this species, and discuss implications of our findings for conservation of migratory songbirds in the northern portion of their ranges in light of potential shifts in distribution due to climate change.

Metapopulation dynamics are increasingly invoked in management and conservation of endangered species. In this context, asymmetrical gene flow patterns can be density dependent, with migration occurring mainly from larger into smaller populations, which may depend on it for their persistence. Using genetic markers, such patterns have recently been documented for various organisms including salmonids, suggesting this may be a more general pattern. However, metapopulation theory does not restrict gene flow asymmetry to `source-sink' structures, nor need these patterns be constant over longer evolutionary timescales. In anadromous salmonids, gene flow can be expected to be shaped by various selective pressures underlying homing and dispersal ('straying') behaviours. The relative importance of these selective forces will vary spatially and for populations of different census size. Furthermore, the consequences of life-history variation among populations for dispersal and hence gene flow remain poorly quantified. We examine population structure and connectivity in Atlantic salmon (Salmo salar L.) from Newfoundland and Labrador, a region where populations of this species are relatively pristine. Using genetic variation at 13 microsatellite loci from samples (N = 1346) collected from a total of 20 rivers, we examine connectivity at several regional and temporal scales and test the hypothesis that the predominant direction of gene flow is from large into small populations. We reject this hypothesis and find that the directionality of migration is affected by the temporal scale over which gene flow is assessed. Whereas large populations tend to function as sources of dispersal over contemporary timescales, such patterns are often changed and even reversed over evolutionary, coalescent-derived timescales. These patterns of population structure furthermore vary between different regions and are compatible with demographic and life-history attributes. We find no evidence for sex-biased dispersal underlying gene flow asymmetry. Our findings caution against generalizations concerning the directionality of gene flow in Atlantic salmon and emphasize the need for detailed regional study, if such information is to be meaningfully applied in conservation and management of salmonids.

We studied population genetic variation and structure in the fire ant Solenopsis invicta using nuclear genotypic and mitochondrial DNA (mtDNA) sequence data obtained from samples collected throughout its native range. Geographic populations are strongly differentiated at both genomes, with such structure more pronounced in Brazil than in Argentina. Higher-level regional structure is evident from the occurrence of isolation-by-distance patterns among populations, the recognition of clusters of genetically similar, geographically adjacent populations by ordination analysis, and the detection of an mtDNA discontinuity between Argentina and Brazil coinciding with a previously identified landform of biogeographical relevance. Multiple lines of evidence from both genomes suggest that the ancestors of the ants we studied resembled extant northern Argentine S. invicta, and that existing Brazilian populations were established more recently by serial long-distance colonizations and/or range expansions. The most compelling evidence for this is the corresponding increase in F-K (a measure of divergence from a hypothetical ancestor) and decrease in genetic diversity with distance from the Corrientes population in northern Argentina. Relatively deep sequence divergence among several mtDNA clades, coupled with geographical partitioning of many of them, suggests prolonged occupation of South America by S. invicta in more-or-less isolated regional populations. Such populations appear, in some cases, to have come into secondary contact without regaining the capacity to freely interbreed. We conclude that nominal S. invicta in its native range comprises multiple entities that are sufficiently genetically isolated and diverged to have embarked on independent evolutionary paths.

Within its distribution range in the northeastern Atlantic, the stalked barnacle Pollicipes pollicipes shows a well-defined pattern of genetic variation, comprising (a) a subtropical/temperate northern assemblage, made up of populations distributed between 47 degrees N and 28 degrees N along the French, Iberian, North African and Canary Islands coastlines, and (b) a single isolated and highly divergent tropical population in the Cape Verde Islands (16 degrees N), at the southernmost limit of the species' distribution. However, within the northern assemblage several populations show a level of genetic differentiation that allows rejection of the hypothesis of genetic homogeneity. The congruence observed between genetic and hydrographic patterns suggests a crucial role of hydrodynamics, and of the dispersal of the planktonic larvae, in the determination of population structure. Along the southern European Atlantic coast, the Iberian Poleward Current and mesoscale hydrographic structures are, respectively, facilitating gene flow at the regional level and genetic differentiation at the local level. On the Atlantic coast of North Africa, the homogenizing equatorward flow of the Canary Current does not extend as far as the Cape Verde Islands. A demographic expansion is dated to the late Pleistocene, preceding the Eemian interglacial, and is oldest in the case of the long-standing Cape Verde population, sustained by a stable tropical habitat. The divergence between the Cape Verde population and the remaining populations is thus ancient, and suggests that oceanic current patterns may constitute a generalized physical barrier to the dispersal of marine organisms between Cape Verde and the rest of Macaronesia.

Phylogeographic studies designed to estimate rates and patterns of genetic differentiation within species often reveal unexpected and graphically striking cases of allele or haplotype sharing between species (introgression) via hybridization and backcrossing. Does introgression between species significantly influence population genetic structure relative to more conventional sources of differentiation (drift) and similarity (dispersal) among populations within species ? Here we use mtDNA sequences from four species in two genera of sea urchins and sea stars to quantify the relative magnitude of gene flow across oceans and across species boundaries in the context of the trans-Arctic interchange of marine organisms between the Pacific and Atlantic oceans. In spite of the much smaller distances between sympatric congeners, rates of gene flow between sympatric species via heterospecific gamete interactions were small and significantly lower than gene flow across oceans via dispersal of planktonic larvae. We conclude that, in these cases at least, larvae are more effective than gametes as vectors of gene flow.

Transylvania's ethnic mosaic is composed of Romanians, German Saxons and Hungarians. The ethnic groups of the Hungarian minority that settled in Romania show differences in dialects, customs and religious affiliations. In this study entire mtDNA control region sequences from 360 individuals of Hungarian ethnicity from two populations (the Csango and the Szekely), settled in the historical region of Transylvania in Romania, were generated and analyzed following high quality sequencing standards. Phylogenetic analyses were used for haplogroup determination, quasi-median network analyses were applied for the visualization of character conflicts, and median joining reconstructions were used for depicting haplotype structures. Affiliation of haplotypes to major west Eurasian haplogroups was confirmed using coding region SNPs. Gene flow between the two populations was low and biased towards a higher migration rate from the Csango to the Szekely than vice versa. Phylogeographic analyses revealed effects of genetic isolation within the Csango population, which is, in its genetic structure, clearly different from the Szekely population. The pronounced genetic divergence between the two populations is in sharp contrast to the expectation of high genetic similarity due to the close geographic proximity of their native homelands. The population data will be incorporated in the EMPOP database (www.empop.org).

The impact of gene flow and population size fluctuations in shaping genetic variation during adaptive radiation, at both the genome-wide and gene-specific levels, is very poorly understood. To examine how historical population size and gene flow patterns within and between loci have influenced lineage divergence in the Hawaiian silversword alliance, we have investigated the nucleotide sequence diversity and divergence patterns of four floral regulatory genes (ASAP1-A, ASAP1-B, ASAP3-A, ASAP3-B) and a structural gene (ASCAB9). Levels and patterns of molecular divergence across these five nuclear loci were estimated between two recently derived species (Dubautia ciliolata and Dubautia arborea) which are presumed to be sibling species. This multilocus analysis of genetic variation, haplotype divergence and historical demography indicates that population expansion and differential gene flow occurred subsequent to the divergence of these two lineages. Moreover, contrasting patterns of allele- sharing for regulatory loci vs. a structural locus between these two sibling species indicate alternative histories of genetic variation and partitioning among loci where alleles of the floral regulatory loci are shared primarily from D. arborea to D. ciliolata and alleles of the structural locus are shared in both directions. Taken together, these results suggest that adaptively radiating species can exhibit contrasting allele migration rates among loci such that allele movement at specific loci may supersede genetic divergence caused by drift and that lineage divergence during adaptive radiation can be associated with population expansion.

Genetic differentiation is generally assumed to be low in highly mobile species, but this simplistic view may obscure the complex conditions and mechanisms allowing genetic exchanges between specific populations. Here, we combined data from satellite-tracked migratory caribou (Rangifer tarandus), microsatellite markers, and demographic simulations to investigate gene flow mechanisms between seven caribou herds of eastern Canada. Our study included one montane, two migratory, and four sedentary herds. Satellite-tracking data indicated possibilities of high gene flow between migratory herds: overlap of their rutting ranges averaged 10% across years and 9.4% of females switched calving sites at least once in their lifetime. Some migratory individuals moved into the range of the sedentary herds, suggesting possibilities of gene flow between these herds. Genetic differentiation between herds was weak but significant (F-ST = 0.015): migratory and montane herds were not significantly distinct (F-ST all <= 0.005), whereas sedentary herds were more differentiated (F-ST = 0.018-0.048). Geographical distances among sedentary herds limited gene flow. Historical estimates of gene flow were higher from migratory herds into sedentary herds (4Nm all > 9) than vice-versa (4Nm all < 5), which suggests migratory herds had a demographic impact on sedentary herds. Demographic simulations showed that an effective immigration rate of 0.0005 was sufficient to obtain the empirical F-ST of 0.015, while a null immigration rate increased the simulated F-ST to > 0.6. In conclusion, the weak genetic differentiation between herds cannot be obtained without some genetic exchanges among herds, as demonstrated by genetic and spatial data.

Background: Ethnic minorities in Northern Thailand, often referred to as Hill Tribes, are considered an ideal model to study the different genetic impact of sex-specific migration rates expected in matrilocal (women remain in their natal villages after the marriage and men move to their wife's village) and patrilocal societies (the opposite is true). Previous studies identified such differences, but little is known about the possible interaction with another cultural factor that may potentially affect genetic diversity, i.e. linguistic differences. In addition, Hill Tribes started to migrate to Thailand in the last centuries from different Northern areas, but the history of these migrations, the level of genetic legacy with their places of origin, and the possible confounding effects related to this migration history in the patterns of genetic diversity, have not been analysed yet. Using both original and published data on the Hill Tribes and several other Asian populations, we focused on all these aspects. Results: Genetic variation within population at mtDNA is lower in matrilocal, compared to patrilocal, tribes. The opposite is true for Y-chromosome microsatellites within the Sino-Tibetan linguistic family, but Hmong-Mien speaking patrilocal groups have a genetic diversity very similar to the matrilocal samples. Population divergence ranges between 5% and 14% at mtDNA sequences, and between 5% and 36% at Y-chromosomes STRs, and follows the sex-specific differences expected in patrilocal and matrilocal tribes. On the average, about 2 men and 14 women, and 4 men and 4 women, are exchanged in patrilocal and matrilocal tribes every generation, respectively. Most of the Hill Tribes in Thailand seem to preserve a genetic legacy with their likely geographic origin, with children adoption probably affecting this pattern in one tribe. Conclusion: Overall, the sex specific genetic signature of different postmarital habits of residence in the Hill Tribes is robust. However, specific perturbations related to linguistic differences, population specific traits, and the complex migratory history of these groups, can be identified. Additional studies in different populations are needed, especially to obtain more precise estimates of the migration parameters.

False killer whales (Pseudorca crassidens (Owen, 1846)) are incidentally taken in the North Pacific pelagic long-line fishery, but little is known about their population structure to assess the impact of these takes. Using mitochondrial DNA (mtDNA) control region sequence data, we quantified genetic variation for the species and tested for genetic differentiation among geographic strata. Our data set of 124 samples included 115 skin-biopsy samples collected from false killer whales inhabiting the eastern North Pacific Ocean (ENP), and nine samples collected from animals sampled at sea or on the beach in the western North Pacific, Indian, and Atlantic oceans. Twenty-four (24). haplotypes were identified, and nucleotide diversity was low (pi = 0.37%) but comparable with that of closely related species. Phylogeographic concordance in the distribution of haplotypes was revealed and a demographically isolated population of false killer whales associated with the main Hawaiian islands was identified (Phi(ST) = 0.47, p < 0.0001). This result supports recognition of the existing management unit, which has geo-political boundaries corresponding to the USA's exclusive economic zone (EEZ) of Hawai'i. However, a small number of animals sampled within the EEZ but away from the near-shore island area, which is defined as <25 nautical miles (1 nautical mile = 1.852 km) from shore, had haplotypes that were the same or closely related to those found elsewhere in the ENP, which suggests that there may be a second management unit within the Hawaiian EEZ. Biologically meaningful boundaries for the population(s) cannot be identified until we better understand the distribution and ecology of false killer whales.

Estimation of effective population sizes (N-e) and temporal gene flow (N(e)m, m) has many implications for understanding population structure in evolutionary and conservation biology. However, comparative studies that gauge the relative performance of N-e, N(e)m or m methods are few. Using temporal genetic data from two salmonid fish population systems with disparate population structure, we (i) evaluated the congruence in estimates and precision of long- and short-term N-e, N(e)m and m from six methods; (ii) explored the effects of metapopulation structure on N-e estimation in one system with spatiotemporally linked subpopulations, using three approaches; and (iii) determined to what degree interpopulation gene flow was asymmetric over time. We found that long-term N-e estimates exceeded short-term N-e within populations by 2-10 times; the two were correlated in the system with temporally stable structure (Atlantic salmon, Salmo salar) but not in the highly dynamic system (brown trout, Salmo trutta). Four temporal methods yielded short-term N-e estimates within populations that were strongly correlated, and these were higher but more variable within salmon populations than within trout populations. In trout populations, however, these short-term N-e estimates were always lower when assuming gene flow than when assuming no gene flow. Linkage disequilibrium data generally yielded short-term N-e estimates of the same magnitude as temporal methods in both systems, but the two were uncorrelated. Correlations between long- and short-term geneflow estimates were inconsistent between methods, and their relative size varied up to eightfold within systems. While asymmetries in gene flow were common in both systems (58-63% of population-pair comparisons), they were only temporally stable in direction within certain salmon population pairs, suggesting that gene flow between particular populations is often intermittent and/or variable. Exploratory metapopulation N-e analyses in trout demonstrated both the importance of spatial scale in estimating N-e and the role of gene flow in maintaining genetic variability within subpopulations. Collectively, our results illustrate the utility of comparatively applying N-e, N(e)m and m to (i) tease apart processes implicated in population structure, (ii) assess the degree of continuity in patterns of connectivity between population pairs and (iii) gauge the relative performance of different approaches, such as the influence of population subdivision and gene flow on N-e estimation. They further reiterate the importance of temporal sampling replication in population genetics, the value of interpreting N-e or m in light of species biology, and the need to address long-standing assumptions of current N-e, N(e)m or m models more explicitly in future research.

Surveys of nucleotide diversity in the wild ancestor of maize, Zea mays ssp. parviglumis, have revealed genomewide departures from the standard neutral equilibrium (NE) model. Here we investigate the degree to which Population structure may account for the excess of rare polymorphisms frequently observed in species-wide samples. On the basis of sequence data from five nuclear and two chloroplast loci, we found significant population genetic structure among seven subpopulations from two geographic regions. Comparisons of estimates of population genetic parameters from species-wide samples and subpopulation-specific samples showed that population genetic subdivision influenced observed patterns of nucleotide polymorphism. In particular, Tajima's D was significantly higher (closer to zero) in subpopulation-specific samples relative to species-wide samples, and therefore more closely corresponded to NE expectations. In spite of these overall patterns, the extent to which levels and patterns of polymorphism within subpopulations differed from species-wide samples and NE expectations depended strongly on the geographic region (Jalisco vs. Balsas) from which subpopulations were sampled. This may be due to the demographic history of subpopulations in those regions. Overall, these results suggest that explicitly accounting for population structure may be important for studies examining the genetic basis of ecologically and agronomically important traits as well as for identifying loci that have been the targets of selection.

Tertiary geological events and Quaternary climatic fluctuations have been proposed as important factors of speciation in the North American flora and fauna. Few studies, however, have rigorously tested hypotheses regarding the specific factors driving divergence of taxa. Here, we test explicit speciation hypotheses by correlating geologic events with divergence times among species in the continentally distributed trilling chorus frogs (Pseudacris). In particular, we ask whether marine inundation of the Mississippi Embayment, uplift of the Appalachian Mountains, or modification of the ancient Teays-Mahomet River system contributed to speciation. To examine the plausibility of ancient rivers causing divergence, we tested whether modern river systems inhibit gene flow. Additionally, we compared the effects of Quaternary climatic factors (glaciation and aridification) on levels of genetic variation. Divergence time estimates using penalized likelihood and coalescent approaches indicate that the major lineages of chorus frogs diversified during the Tertiary, and also exclude Quaternary climate change as a factor in speciation of chorus frogs. We show the first evidence that inundation of the Mississippi Embayment contributed to speciation. We reject the hypotheses that Cenozoic uplift of the Appalachians and that diversion of the Teays-Mahomet River contributed to speciation in this clade. We find that by reducing gene flow, rivers have the potential to cause divergence of lineages. Finally, we demonstrate that populations in areas affected by Quaternary glaciation and aridification have reduced levels of genetic variation compared to those from more equable regions, suggesting recent colonization.

The Transverse Ranges in southern California have been identified as having a prominent phylogeographic role. Numerous studies have identified distinct north-south and/or east-west lineage breaks involving the Transverse Ranges. However, in evaluating their findings, most authors have regarded this complex system somewhat simplistically. In this study we more deeply investigate these breaks using two approaches: first we examine the phylogeographic history of Sepedophilus castaneus (Coleoptera: Staphylinidae) and then implement a comparative phylogeography approach applying Brooks parsimony analysis to the topologies of nine additional taxa. Phylogenetic analysis, nested clade analysis, and AMOVAs for S. castaneus agree that there is a major lineage break between the eastern and western Transverse Ranges, localized between the Sierra Pelona and the San Gabriel Mountains. The comparative phylogeographic analysis supports a generally strong concordance of area relationships with geographic proximity. It is notable, however, that the Transverse Ranges as a group do not show phylogenetic cohesion, but rather they are split into three main regions: an eastern region (San Gabriel, San Bernardino, and San Jacinto Mountains), a central region (central Transverse Ranges and Sierra Pelona) that is often grouped with the Tehachapi and Sierra Nevada populations, and a western region (northwestern Transverse Ranges and Santa Ynez Mountains) that is consistently grouped with coast range areas to the north. The lineage break between east and west Transverse Ranges is attributable to the presence of a marine embayment in what is now the Santa Clara River valley 5-2.5 million years ago.

Background: The dusky dolphin ( Lagenorhynchus obscurus) is distributed along temperate, coastal regions of New Zealand, South Africa, Argentina, and Peru where it feeds on schooling anchovy, sardines, and other small fishes and squid tightly associated with temperate ocean sea surface temperatures. Previous studies have suggested that the dusky dolphin dispersed in the Southern Hemisphere eastward from Peru via a linear, temperate dispersal corridor provided by the circumpolar west-wind drift. With new mitochondrial and nuclear DNA sequence data, we propose an alternative phylogeographic history for the dusky dolphin that was structured by paleoceanographic conditions that repeatedly altered the distribution of its temperate prey species during the Plio-Pleistocene. Results: In contrast to the west-wind drift hypothesis, phylogenetic analyses support a Pacific/Indian Ocean origin, with a relatively early and continued isolation of Peru from other regions. Dispersal of the dusky dolphin into the Atlantic is correlated with the history of anchovy populations, including multiple migrations from New Zealand to South Africa. Additionally, the cooling of the Eastern Equatorial Pacific led to the divergence of anchovy populations, which in turn explains the north-south equatorial transgression of L. obliquidens and the subsequent divergence of L. obscurus in the Southern Hemisphere. Conclusion: Overall, our study fails to support the west-wind drift hypothesis. Instead, our data indicate that changes in primary productivity and related abundance of prey played a key role in shaping the phylogeography of the dusky dolphin, with periods of ocean change coincident with important events in the history of this temperate dolphin species. Moderate, short-term changes in sea surface temperatures and current systems have a powerful effect on anchovy populations; thus, it is not infeasible that repeated fluctuations in anchovy populations continue to play an important role in the history of coastal dolphin populations.

Vocal learning is thought to have evolved in three clades of birds (parrots, hummingbirds, and oscine passerines), and three clades of mammals (whales, bats, and primates). Behavioural data indicate that, unlike other suboscine passerines, the three-wattled bellbird Procnias tricarunculata (Cotingidae) is capable of vocal learning. Procnias tricarunculata shows conspicuous vocal ontogeny, striking geographical variation in song, and rapid temporal change in song within a population. Deprivation studies of vocal development in P. tricarunculata are impractical. Here, we report evidence from mitochondrial DNA sequences and nuclear microsatellite loci that genetic variation within and among the four allopatric breeding populations of P. tricarunculata is not congruent with variation in vocal behaviour. Sequences of the mitochondrial DNA control region document extensive haplotype sharing among localities and song types, and no phylogenetic resolution of geographical populations or behavioural groups. The vocally differentiated, allopatric breeding populations of P. tricarunculata are only weakly genetically differentiated populations, and are not distinct taxa. Mitochondrial DNA and microsatellite variation show small (2.9% and 13.5%, respectively) but significant correlation with geographical distance, but no significant residual variation by song type. Estimates of the strength of selection that would be needed to maintain the observed geographical pattern in vocal differentiation if songs were genetically based are unreasonably high, further discrediting the hypothesis of a genetic origin of vocal variation. These data support a fourth, phylogenetically independent origin of avian vocal learning in Procnias. Geographical variations in P. tricarunculata vocal behaviour are likely culturally evolved dialects.

Commercially harvested marine bivalve populations show a broad range of population-genetic patterns that may be driven by planktonic larval dispersal (gene flow) or by historical (genetic drift) and ecological processes (selection). We characterized microsatellite genetic variation among populations and year classes of the commercially harvested Arctic surfclam, Mactromeris polynyma, in order to test the relative significance of gene flow and drift on three spatial scales: within commercially harvested populations in the northwest Atlantic; among Atlantic populations; and between the Atlantic and Pacific oceans. We found small nonsignificant genetic subdivision among eight populations from the northwest Atlantic (F (ST) = 0.002). All of these Atlantic populations were highly significantly differentiated from a northeast Pacific population (F (ST) = 0.087); all populations showed high inbreeding coefficients (F (IS) = 0.432). We tested one likely source of heterozygote deficits by aging individual clams and exploring genetic variation among age classes within populations (a temporal Wahlund effect). Populations showed strikingly different patterns of age structure, but we found little differentiation among age classes. In one case, we were able to analyze genetic diversity between age classes older or younger than the advent of intensive commercial harvesting. The results generally suggest spatially broad and temporally persistent genetic homogeneity of these bivalves. We discuss the implications of the results for the biology and management of surfclam populations.

The population genetic structure of the loggerhead sea turtle (Caretta caretta) nesting in the eastern Mediterranean was assessed by sequencing a fragment of the control region of the mitochondrial DNA (n = 190) and seven microsatellites (n = 112). The two types of markers revealed genetic structuring (mtDNA: gamma(st) = 0.212, P < 0.001; nDNA F (st) = 0.006, P < 0.001), thus indicating that both females and males are philopatric and that gene flow between populations is restricted. Mitochondrial DNA data indicate that the female populations nesting on the islands of Crete and Cyprus have suffered a recent bottleneck or colonization event. However, no bottleneck or founder effect was revealed by nuclear markers, thus indicating male-mediated gene flow from other populations that would increase nuclear genetic variability. Crete, and to a lower extent Cyprus, are thought to play a central role in such male-mediated gene flow that may reduce the negative effect of genetic drift or inbreeding on the small populations of Lebanon and Israel. This population structure indicates that assessing population relevance only on the basis of genetic variability and size would be misleading, as some populations not fulfilling those requirements may play a relevant role in genetic exchange and hence contribute to the overall genetic variability.

Blue-spotted salamanders (Ambystoma laterale) are a widespread and relatively common species throughout northeastern North America. The distribution of this species is marked by a pair of peripherally isolated populations at the southwestern boundary of its range in Iowa, a state where these salamanders are endangered. Because small peripatric populations suffer greater risks of extinction, the genetic state of the isolates was compared to that of a reference population that appears to be in geographic contiguity with the primary distribution of the species. Five polymorphic microsatellite loci were used to examine population genetic structure. Whereas allelic richness exhibited by each locus was qualitatively similar across study populations, genetic data indicate that the scaled effective population sizes of the peripheral isolates were demonstrably smaller compared to that of the reference population. One of the Iowa isolates shows evidence of a recent bottleneck and of substantial inbreeding; this population may therefore be subject to a particularly heightened risk of extirpation.

A number of evolutionary mechanisms have been suggested for generating low but significant genetic structuring among marine fish populations. We used nine microsatellite loci and recently developed methods in landscape genetics and coalescence-based estimation of historical gene flow and effective population sizes to assess temporal and spatial dynamics of the population structure in European flounder (Platichthys flesus L.). We collected 1062 flounders from 13 localities in the northeast Atlantic and Baltic Seas and found temporally stable and highly significant genetic differentiation among samples covering a large part of the species' range (global F-ST = 0.024, P < 0.0001). In addition to historical processes, a number of contemporary acting evolutionary mechanisms were associated with genetic structuring. Physical forces, such as oceanographic and bathymetric barriers, were most likely related with the extreme isolation of the island population at the Faroe Islands. A sharp genetic break was associated with a change in life history from pelagic to benthic spawners in the Baltic Sea. Partial Mantel tests showed that geographical distance per se was not related with genetic structuring among Atlantic and western Baltic Sea samples. Alternative factors, such as dispersal potential and/or environmental gradients, could be important for generating genetic divergence in this region. The results show that the magnitude and scale of structuring generated by a specific mechanism depend critically on its interplay with other evolutionary mechanisms, highlighting the importance of investigating species with wide geographical and ecological distributions to increase our understanding of evolution in the marine environment.

This study is aimed at evaluating the likelihood that kin-biased distribution will be expressed or detected in a range of brown trout (Salmo trutta) populations as a function of family size. Microsatellite analysis indicated that fewer fall- and half-siblings were found in populations with larger effective population sizes, while more full- and half-siblings were found in populations with lower effective population size. It is suggested that kin-biased distribution and hence kin-biased behaviours are not likely to be expressed equally frequently in all populations since the number of close relatives will vary among populations and, hence, the opportunity for relatives to interact differs among populations. These findings can, at least partly, explain the discrepancy among previous studies of kin-biased distribution in wild salmonids under natural conditions. Effective population size could, hence, be used to predict the salmonid populations in which kin-biased distribution are more likely to occur and be detected. (c) 2007 The Author Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Analysis of genetic data can reveal past and ongoing demographic connections between reef populations. The history, extent, and geography of isolation and exchange help to determine which populations are evolutionarily distinct and how to manage threatened reefs. Here the genetic approaches undertaken to understand connectivity among reefs are reviewed, ranging from early allozyme studies on genetic subdivision, through the use of sequence data to infer population histories, to emerging analyses that pull the influences of the past connections away from the effects of ongoing dispersal. Critically, some of these new approaches can infer migration and isolation over recent generations, thus offering the opportunity to answer many questions about reef connectivity and to better collaborate with ecologists and oceanographers to address problems that remain.

Long-term effective population size is expected, and has been shown, to correlate positively with various measures of-population fitness. Here we examine the interacting effects of population size (as a surrogate for genetic factors) and prey consumption rates (as a surrogate for environmental quality) on fecundity in two sympatric species of wolf spider, Rabidosa punctulata and Rabidosa rabida. Population size was estimated in each of seven genetically isolated populations in each of 3 years using mark-recapture methods. Fecundity was estimated as the mean number of live offspring produced by similar to 15 females sampled from each population of each species each year for 3 years. Prey consumption rates were estimated by sampling similar to 300 spiders per population per year and assaying the proportion of spiders with prey. Larger populations have higher fecundity and more genetic diversity than smaller populations. Variation among populations in fecundity for a given year could be attributed most strongly to differences in population size, with variation in prey consumption rates and the interaction between population size and prey consumption playing smaller but still important roles. During the most stressful environmental conditions, the smallest populations of both species experienced disproportionately low-fecundity rates, more than doubling the estimated number of lethal equivalents during those years. The evidence presented in this paper for inbreeding-environment interactions at the population level and further evidence for a log-linear relationship between population size and fitness have important implications for conservation.

The Japanese wood pigeon (Columba janthina) is endemic to the islands of East Asia and it is included in the Japanese and Asian Red Lists because of its narrow habitat range that is restricted to mature forests on small islands and because of the destruction of these habitats. We examined the genetic structure of Columba janthina by studying 463 base pairs of the mitochondrial control region sequences. We analyzed 154 samples from eight populations and identified 27 haplotypes. Three population groups were identified based on the pairwise Phi(ST) values. A substantial gene flow, as reflected by the low and non-significant Phi(ST) values, is maintained among the northern group that includes six populations found on the Okinawa, Tokara, Goto, Setouchi, Oki, and Izu islands. In contrast, the southeastern group found on the Ogasawara Islands had large Phi(ST) values with every population from other regions (0.910 < Phi(ST) < 0.962). The southwestern group found on the Sakishima Islands also had significant but small Phi(ST) values with every population from the northern group (0.081 < Phi(ST) < 0.205). The Mantel test showed a highly significant correlation between the Phi(ST) values and the route length of the habitat network, as well as the linear distance with correction of the habitat gap effect, indicating the importance of the closely connected structure of the habitats. The three groups mentioned above could be considered as independent management units, and the southeastern group has the highest conservation priority due to its narrow distribution range and small population size.

The Balearic shearwater Puffinus rnauretanicus is one of the most critically endangered seabirds in the world. The species is endemic to the Balearic archipelago, and conservation concerns are the low number of breeding pairs, the low adult survival, and the possible hybridization with a sibling species, the morphologically smaller Yelkouan shearwater (P. yelkouan). We sampled almost the entire breeding range of the species and analyzed the genetic variation at two mitochondrial DNA regions. No genetic evidence of population decline was found. Despite the observed philopatry, we detected a weak population structure mainly due to connectivity among colonies higher than expected, but also to a Pleistocene demographic expansion. Some colonies showed a high imbalance between immigration and emigration rates, suggesting spatial heterogeneity in patch quality. Genetic evidence of maternal introgression from the sibling species was reinforced, but almost only in a peripheral colony and not followed, at least to date, by the spread of the introgressed mtDNA lineages. Morphometric differences were not correlated with mtDNA haplotypes and introgression. is probably due to a secondary contact between the two species several generations ago. Overall, results suggested that the very recent demographic decline in this critically endangered species has not yet decreased its genetic variability, and connectivity found among most colonies should help to reduce species extinction risk. Spreading of introgression. should be monitored, but the species is not jeopardized at the moment by genetic factors and the major conservation actions should concentrate at enhancing adult survival. (C) 2007 Elsevier Ltd. All rights reserved.

The polychaete tubeworm Hydroides elegans (Haswell) is a biofouling species with relatively limited larval dispersal. Four highly polymorphic microsatellite loci were used to make inferences about the migration and global population structure of 137 individuals from seven sub-populations located in the Atlantic, Pacific, and Indian Oceans and in the Mediterranean Sea. The results of the genetic analyses suggest minimal population sub-structure (F-st = 0.09). Estimates of pairwise F-st and migration rates using the coalescent-based method of MIGRATE suggest that there is little genetic differentiation between certain populations. Variation in relatedness among pairs of populations is consistent with a suite of local and global factors. The most likely explanation for close genetic relatedness among certain populations over such vast distances is the regular and consistent transport of adults and larvae on the hulls and in the ballast water of ships, respectively.

We present a new approach for estimation of the population-scaled mutation rate, theta, from microsatellite genotype data, using the recently introduced `' product of approximate conditionals `' framework. Com P parisons with other methods on simulated data demonstrate that this new approach is attractive in terms of both accuracy and speed of computation. Our simulation experiments also demonstrate that, despite the theoretical advantages of full-likelihood-based methods, methods based on certain summary statistics (specifically, the sample homozygosity) can perform very competitively in practice.

There has been a great increase in both the number of population genetic analysis programs and the size of data sets being studied with them. Since the file formats required by the most popular and useful programs are variable, automated reformatting or conversion between them is desirable. (FORMATOMATIC) is an easy to use program that can read allelic data files in (GENEPOP), (RAW ( CSV)) or (CONVERT) formats and create data files in nine formats: RAW (( CSV), ARLEQUIN, GENEPOP, IMMANC / BAYESASS +, MIGRATE, NEWHYBRIDS, MSVAR, BAPS) and (STRUCTURE.) Use of formatomatic should greatly reduce time spent reformatting data sets and avoid unnecessary errors.

The origins of pathogens and their past and present migration patterns are often unknown. We used phylogenetic haplotype clustering in conjunction with model-based coalescent approaches to reconstruct the genetic history of the barley leaf pathogen Rhynchosporium secalis using the avirulence gene NIP1 and its flanking regions. Our results falsify the hypothesis that R. secalis emerged in association with its host during the domestication of barley 10 000 to 15 000 years ago in the Fertile Crescent and was introduced into Europe through the migration of Neolithic farmers. Estimates of time since most recent common ancestor (2500-5000 BP) placed the emergence of R. secalis clearly after the domestication of barley. We propose that modern populations of R. secalis originated in northern Europe following a host switch, most probably from a wild grass onto cultivated barley shortly after barley was introduced into northern Europe. R. secalis subsequently spread southwards into already established European barley-growing areas.

1. Better tools are needed to predict population connectivity in complex landscapes. `Least-cost modelling' is one commonly employed approach in which dispersal costs are assigned to distinct habitat types and the least-costly dispersal paths among habitat patches are calculated using a geographical information system (GIS). Because adequate data on dispersal are usually lacking, dispersal costs are often assigned solely from expert opinion. Spatially explicit, high-resolution genetic data may be used to infer variation in animal movements. We employ such an approach to estimate habitat-specific migration rates and to develop least-cost connectivity models for desert bighorn sheep Ovis canadensis nelsoni. 2. Bighorn sheep dispersal is thought to be affected by distance and topography. We incorporated both factors into least-cost GIS models with different parameter values and estimated effective geographical distances among 26 populations. We assessed which model was correlated most strongly with gene flow estimates among those populations, while controlling for the effect of anthropogenic barriers. We used the best-fitting model to (i) determine whether migration rates are higher over sloped terrain than flat terrain; (ii) predict probable movement corridors; (iii) predict which populations are connected by migration; and (iv) investigate how anthropogenic barriers and translocated populations have affected landscape connectivity. 3. Migration models were correlated most strongly with migration when areas of at least 10% slope had 1/10th the cost of areas of lower slope; thus, gene flow occurred over longer distances when `escape terrain' was available. Optimal parameter values were consistent across two measures of gene flow and three methods for defining population polygons. 4. Anthropogenic barriers disrupted numerous corridors predicted to be high-use dispersal routes, indicating priority areas for mitigation. However, population translocations have restored high-use dispersal routes in several other areas. Known intermountain movements of bighorn sheep were largely consistent with predicted corridors. 5. Synthesis and applications. Population genetic data provided sufficient resolution to infer how landscape features influenced the behaviour of dispersing desert bighorn sheep. Anthropogenic barriers that block high-use dispersal corridors should be mitigated, but population translocations may help maintain connectivity. We conclude that developing least-cost models from similar empirical data could significantly improve the utility of these tools.

The constraining effect of gene flow on adaptive divergence is often inferred but rarely quantified. We illustrate ways of doing so using stream populations of threespine stickleback (Gasterosteus aculeatus) that experience different levels of gene flow from a parapatric lake population. In the Misty Lake watershed (British Columbia, Canada), the inlet stream population is morphologically divergent from the lake population, and presumably experiences little gene flow from the lake. The outlet stream population, however, shows an intermediate phenotype and may experience more gene flow from the lake. We first used microsatellite data to demonstrate that gene flow from the lake is low into the inlet but high into the outlet, and that gene flow from the lake remains relatively constant with distance along the outlet. We next combined gene flow data with morphological and habitat data to quantify the effect of gene flow on morphological divergence. In one approach, we assumed that inlet stickleback manifest well-adapted phenotypic trait values not constrained by gene flow. We then calculated the deviation between the observed and expected phenotypes for a given habitat in the outlet. In a second approach, we parameterized a quantitative genetic model of adaptive divergence. Both approaches suggest a large impact of gene flow, constraining adaptation by 80-86% in the outlet (i.e., only 14-20% of the expected morphological divergence in the absence of gene flow was observed). Such approaches may be useful in other taxa to estimate how important gene flow is in constraining adaptive divergence in nature.

The threespine stickleback (Gasterosteus aculeatus) species complex is well suited for identifying the types of phenotypic divergence and isolating barriers that contribute to reproductive isolation at early stages of speciation. In the present study, we characterize the patterns of genetic and phenotypic divergence as well as the types of isolating barriers that are present between two sympatric pairs of threespine sticklebacks in Hokkaido, Japan. One sympatric pair consists of an anadromous and a resident freshwater form and shows divergence in body size between the forms, despite the lack of genetic differentiation between them. The second sympatric pair consists of two anadromous forms, which originated before the last glacial period and are currently reproductively isolated. These two anadromous forms have diverged in many morphological traits as well as in their reproductive behaviours. Both sexual isolation and hybrid male sterility contribute to reproductive isolation between the anadromous species pair. We discuss the shared and unique aspects of phenotypic divergence and reproductive isolation in the Japanese sympatric pairs compared with postglacial stickleback species pairs. Further studies of these divergent species pairs will provide a deeper understanding of the mechanisms of speciation in sticklebacks. (C) 2007 The Linnean Society of London.

Pelobates fuscus is a fossorial amphibian that inhabits much of the European plain areas. To unveil traces of expansion and contraction events of the species' range, we sequenced 702 bp of the mitochondrial cytochrome b gene. To infer the population history we applied phylogeographical methods, such as nested clade phylogeographical analysis (NCPA), and used summary statistics to analyse population structure under a neutral model of evolution. Populations were assigned to different drainage systems and we tested hypotheses of explicit refugial models using information from analysis of molecular variance, nucleotide diversity, effective population size estimation, NCPA, mismatch distribution and Bayesian dating. Coalescent simulations were used as post hoc tests for plausibility of derived or a priori assumed biogeographical hypotheses. Our combination of all approaches enabled the reconstruction of the colonization history and phylogeography of P. fuscus and confirmed a previous assumption of the existence of two major genetic lineages within P. fuscus. Using the Afro-European vicariance of Pelobates cultripes and Pelobates varaldii and applying Bayesian dating we estimated the divergence of these phylogeographical lineages to the Pliocene. We suggest the existence of three different glacial refugia: (i) the area between the Caspian and Black Seas as the origin for the expansion of the `eastern lineage'; (ii) the Danube system as a centre of diversity for part of the `western lineage'; (iii) the Po Valley, the largest centre of genetic variability. This fits the hypothesis that climatic fluctuation was a key event for differentiation processes in P. fuscus.

Under discussion are such population groups as management unit (stock) and evolutionarily significant unit, along with the problem of short-term ans long-term goals of conservation activities and wildlife management. The short-term goals may differ from the long-term goals. Management units (stocks) are demographically independent populations, though genetically they may be interconnected to a high degree. It is at this level of population organization that the short-term nature management goals are reached: the preservation of stable reproduction of management units, and the exclusion of excessive pressure on small groups. The evolutionarily significant units have independent conservation status determined by significant reproductive isolation and unique adaptations. It is at this level that long-term management goals are reached: the conservation of the native population structure, the evolutionarily significant differences, the maximum genetic diversity, and, thus, the evolutionary potential.

A number of dolphin species, though highly mobile, show genetic structure among parapatric and sometimes sympatric populations. However, little is known about the temporal patterns of population structure for these species. Here, we apply Bayesian inference and data from ancient DNA to assess the structure and dynamics of bottlenose dolphin (Tursiops truncatus) populations in the coastal waters of the UK. We show that regional population structure in UK waters is consistent with earlier studies suggesting local habitat dependence for this species in the Mediterranean Sea and North Atlantic. One genetically differentiated UK population went extinct at least 100 years ago and has not been replaced. The data indicate that this was a local extinction, and not a case of historical range shift or contraction. One possible interpretation is a declining metapopulation and conservation need for this species in the UK.

Human immunodeficiency virus (HIV) infects different organs and tissues. During these infection events, subpopulations of HIV type 1 (HIV-1) develop and, if viral trafficking is restricted between subpopulations, the viruses can follow independent evolutionary histories, i.e., become compartmentalized. This phenomenon is usually detected via comparative sequence analysis and has been reported for viruses isolated from the central nervous system (CNS) and the genital tract. Several approaches have been proposed to study the compartmentalization of HIV sequences, but to date, no rigorous comparison of the most commonly employed methods has been made. In this study, we systematically compared inferences made by six different methods for detecting compartmentalization based on three data sets: (i) a sample of 45 patients with sequences gathered from the CNS, (ii) sequences from the female genital tract of 18 patients, and (iii) a set of simulated sequences. We found that different methods often reached contradictory conclusions. Methods based on the topology of a phylogenetic tree derived from clonal sequences were generally more sensitive in detecting compartmentalization than those that relied solely upon pairwise genetic distances between sequences. However, as the branching structure in a phylogenetic tree is often uncertain, especially for short, low-diversity, or recombinant sequences, tree-based approaches may need to be modified to take phylogenetic uncertainty into account. Given the frequently discordant predictions of different methods and the strengths and weaknesses of each particular methodology, we recommend that a suite of several approaches be used for reliable inference of compartmentalized population structure.

Nested clade phylogeographic analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so, a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA. We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key. We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (restricted gene flow with isolation by distance and contiguous range expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy.

Cephalopod movement occurs during all phases of the life history, with the abundance and location of cephalopod populations strongly influenced by the prevalence and scale of their movements. Environmental parameters, such as sea temperature and oceanographic processes, have a large influence on movement at the various life cycle stages, particularly those of oceanic squid. Tag recapture studies are the most common way of directly examining cephalopod movement, particularly in species which are heavily fished. Electronic tags, however, are being more commonly used to track cephalopods, providing detailed small- and large-scale movement information. Chemical tagging of paralarvae through maternal transfer may prove to be a viable technique for tracking this little understood cephalopod life stage, as large numbers of individuals could be tagged at once. Numerous indirect methods can also be used to examine cephalopod movement, such as chemical analyses of the elemental and/or isotopic signatures of cephalopod hard parts, with growing interest in utilising these techniques for elucidating migration pathways, as is commonly done for fish. Geographic differences in parasite fauna have also been used to indirectly provide movement information, however, explicit movement studies require detailed information on parasite-host specificity and parasite geographic distribution, which is yet to be determined for cephalopods. Molecular genetics offers a powerful approach to estimating realised effective migration rates among populations, and continuing developments in markers and analytical techniques hold the promise of more detailed identification of migrants. To date genetic studies indicate that migration in squids is extensive but can be blocked by major oceanographic features, and in cuttlefish and octopus migration is more locally restricted than predictions from life history parameters would suggest. Satellite data showing the location of fishing lights have been increasingly used to examine the movement of squid fishing vessels, as a proxy for monitoring the movement of the squid populations themselves, allowing for the remote monitoring of oceanic species.

This paper presents a methodology for model fitting and inference in the context of Bayesian models of the type f(Y vertical bar X,theta) f (X vertical bar theta)f(theta), where Y is the (set of) observed data, theta is a set of model parameters and X is an unobserved (latent) stationary stochastic process induced by the first order transition model f(X(t+1)vertical bar X-(t),theta), where X-(t) denotes the state of the process at time (or generation) t. The crucial feature of the above type of model is that, given theta, the transition model f(X(t+1 vertical bar|X-(t) stop,theta) is known but the distribution of the stochastic process in equilibrium, that is f(X|theta), is, except in very special cases, intractable, hence unknown. A further point to note is that the data Y has been assumed to be observed when the underlying process is in equilibrium. In other words, the data is not collected dynamically over time. We refer to such specification as a latent equilibrium process (LEP) model. It is motivated by problems in population genetics (though other applications are discussed), where it is of interest to learn about parameters such as mutation and migration rates and population sizes, given a sample of allele frequencies at one or more loci. In such problems it is natural to assume that the distribution of the observed allele frequencies depends on the true (unobserved) population allele frequencies, whereas the distribution of the true allele frequencies is only indirectly specified through a transition model. As a hierarchical specification, it is natural to fit the LEP within a Bayesian framework. Fitting such models is usually done via Markov chain Monte Carlo (MCMC). However, we demonstrate that, in the case of LEP models, implementation of MCMC is far from straightforward. The main contribution of this paper is to provide a methodology to implement MCMC for LEP models. We demonstrate our approach in population genetics problems with both simulated and real data sets. The resultant model fitting is computationally intensive and thus, we also discuss parallel implementation of the procedure in special cases.

Habitat connectivity and corridors are often assumed to be critical for the persistence of patchily distributed populations, but empirical evidence for this assumption is scarce. We assessed the importance of connectivity among habitat patches for dispersal by a mature-forest obligate, the Boreal Owl (Aegolius funereus). Boreal Owls demonstrated a lack of genetic structure (theta = 0.004 +/- 0.002 [SE]) among subpopulations, regardless of matrix type and extent, which indicates that unforested matrix does not act as a barrier to dispersal for this vagile species. We found only slightly higher genetic distances (Cavalli-Sforza chord distances ranged from 0.015 to 0.025) among patchily distributed Rocky Mountain subpopulations as compared with largely contiguous boreal-forest subpopulations (0.013 to 0.019) and no evidence of a genetic split across the expansive high plains of Wyoming. Even the most isolated subalpine patches are connected via gene flow. As northern boreal forests continue to experience intensive harvest of mature stands, geographic dispersion of Boreal Owl habitat may begin to more closely resemble that found in the Rocky Mountains. We suggest that decreased connectivity poses much less of a threat to continued abundance of this mature-forest obligate than overall loss of nesting and foraging habitat. Assessment of the importance of corridors and connectivity should be conducted on a species-by-species basis, given the variation in response of species to discontinuity of habitat, even among closely related taxa or guilds.

Isolated granitic rock outcrops or `inselbergs' may provide a window into the molecular ecology and genetics of continental radiations under simplified conditions, in analogy to the use of oceanic islands in studies of species radiations. Patterns of variability and gene flow in inselberg species have never been thoroughly evaluated in comparison to related taxa with more continuous distribution ranges, or to other species in the same kingdom in general. We use nuclear microsatellites to study population differentiation and gene flow in two diploid, perennial plants adapted to high-altitude neotropical inselbergs, Alcantarea imperialis and Alcantarea geniculata (Bromeliaceae). Population differentiation is pronounced in both taxa, especially in A. imperialis. Gene flow in this species is considerably lower than expected from the literature on plants in general and Bromeliaceae in particular, and too low to prevent differentiation due to drift (N(e)m < 1), unless selection coefficients/effect sizes of favourable alleles are great enough to maintain species cohesion. Low gene flow in A. imperialis indicates that the ability of pollinating bats to promote gene exchange between inselbergs is smaller than previously assumed. Population subdivision in one inselberg population of A. imperialis appears to be associated with the presence of two colour morphs that differ in the coloration of rosettes and bracts. Our results indicate a high potential for inselbergs as venues for studies of the molecular ecology and genetics of continental radiations, such as the one that gave rise to the extraordinary diversity of adaptive strategies and phenotypes seen in Bromeliaceae.

I present a simple approach to overcome the high cost and low efficiency of cloning polymerase chain reaction (PCR) products for individuals in wide-scale population genetic analyses. The methodology reduces the number of cloning reactions per individual by engineering a suite of genetic markers that differ in size and pooling these PCR products prior to cloning. Alleles from each gene are then recovered by screening transformed bacterial colonies and identifying the inserts corresponding to each gene based on size. I demonstrate the utility of this technique by presenting the results I obtained from cloning four nuclear genes in 118 individuals from three species of sea urchins (Strongylocentrotus purpuratus, S. droebachiensis and S. pallidus). Of the 472 different PCR products I cloned, I recovered at least one allele for 432 of them (91.5%) by screening between 16 and 32 bacterial colonies for each individual. There existed a bias with respect to recovery efficiency: the two largest fragments (1130-800 bp) were recovered 100% of the time, while the two smaller fragments (580-650 bp) were recovered in 85.6% and 81.4% of the experiments, respectively. I discuss the promise of this application for wide-scale genetic analyses.

Natural populations of wild common buckwheat have been found growing adjacent to cultivated populations of common buckwheat. Gene flow between the cultivated and natural populations would be expected in such cases. To evaluate the amount of gene flow, two sets composed of a cultivated buckwheat population and an adjacent natural population of wild common buckwheat were chosen, one from Yanjing village in the Sanjiang area, which is presumed to be the original birthplace of common buckwheat, and one from Jinhe village, Yanyuan district of Sichuan province in China. The genotypes of 45 individuals from each population were examined at eight microsatellite marker loci to estimate the magnitude of gene flow between the cultivated and wild common buckwheat populations. The Bayesian method with a Markov chain Monte Carlo approach estimated that the magnitude of gene flow between the populations in the Sanjiang area at 0.0020.008 was not significantly different from that found in Yanyuan district at 0.0020.008. The gene flow between cultivated populations was higher, usually at 0.002-0.044 (exceptionally high at 0.255 between cultivated populations of Yanjing and Jinhe), than that found between a cultivated population and a natural population (0.002-0.008) or between two natural populations (0.002-0.003). Therefore, the genetic similarity found between the cultivated populations and natural populations observed in the Sanjiang area (Konishi et al., 2005) was not due to recent gene flow between them. This in turn suggests that the close genetic relationship found in the Sanjiang area may be due to the common ancestry of the natural populations and cultivated common buckwheat.

While many studies have examined the barrier effects of large rivers on animal dispersal and gene flow, few Studies have considered the barrier effects of small streams. We used displacement experiments and analyses of genetic population structure to examine the effects of first-order and second-order streams on the dispersal of terrestrial red-backed salamanders, Plethodon cinereus (Green, 1818). We marked red-backed salamanders from near the edges of one first-order stream and one second-order stream, and experimentally displaced them either across the stream or an equal distance farther into the forest. A comparison of return rates indicated that both streams were partial barriers to salamander movement, reducing return rates by approximately 50%. Analysis of six microsatellite loci from paired plots on the same side and on opposite sides of the second-order stream suggested that the stream did contribute to genetic differentiation of salamander populations. Collectively, our results imply that low-order streams do influence patterns of movement and gene flow in red-backed salamanders. We suggest that given the high density of first-order and second-order streams in most landscapes, these features may have important effects on species that, like red-backed salamanders, have limited dispersal and large geographic ranges.

The Namaqua sandgrouse, Pterocles namaqua, is a highly nomadic granivore of semiarid to arid habitats. As a result of nomadic movements in response to rainfall, the size of the breeding population in any one area fluctuates dramatically between breeding seasons. This high mobility in response to spatial and temporal abundance of food resources is expected to result in little population genetic structuring. Namaqua sandgrouse also shows a seasonally predictable partial migration between the southeast and northwest regions of South Africa, and a further possible north-south migration between southwestern South Africa and central Namibia. It is unclear whether birds migrating between these regions breed in only one or both regions. If populations breed in only one region of their migratory range, then population genetic structuring is predicted to occur. This study addresses Namaqua sandgrouse movements with the analysis of mitochondrial DNA control region sequences. In general, little population genetic structure was evident, yet strong signals of population growth were detected. Several populations have private alleles, which is in direct contradiction to the spatial genetic pattern expected under high levels of gene flow. We suggest that the inference of high levels of female gene flow could be an artifact of population growth and that additional loci will allow a greater understanding of Namaqua sandgrouse movements.

The Grid Services Base Library (GSBL) is a procedural application programming interface (API) that abstracts many of the high-level functions performed by Globus Grid services, thus dramatically lowering the barriers to writing Grid services. The library has been extensively tested and used for computational biology research in a Globus Toolkit-based Grid system, in which no fewer than twenty Grid services written with this API are deployed. (c) 2006 Elsevier B.V. All rights reserved.

We investigate multi locus patterns of differentiation between parental populations of two swallowtail butterfly species that differ at a number of ecologically important sex-linked traits. Using a new coalescent-based approach, we show that there is significant heterogeneity in estimated divergence times among five Z-linked markers, rejecting a purely allopatric speciation model. We infer that the Z chromosome is a mosaic of regions that differ in the extent of historical gene flow, potentially due to isolating barriers that prevent the introgression of species-specific traits that result in hybrid incompatibilities. Surprisingly, a candidate region for a strong barrier to introgression, Ldh, does not show a significantly deeper divergence time than other markers on the Z chromosome. Our approach can be used to test alternative models of speciation and can potentially assign chronological order to the appearance of factors contributing to reproductive isolation between species.

The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically acknowledging the shared but unknown species tree from which gene trees are sampled is much reduced compared with treating the history of each locus independently of an overarching species tree. The analysis also yields a concentrated posterior distribution of the yeast species tree whose mode is congruent with the concatenated gene tree but can do so with less than half the loci required by the concatenation method. Using simulations, we show that, with large numbers of loci, highly resolved species trees can be estimated under conditions in which concatenation of sequence data will positively mislead phylogeny, and when the proportion of gene trees matching the species tree is <10%. However, when gene tree/species tree congruence is high, species trees can be resolved with just two or three loci. These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories.

Historical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long-distance dispersal. Porpidia flavicunda is a lichen-forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA-sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Quebec, Baffin Island, Western Greenland and Northern Scandinavia. DNA-sequence data sets of three nuclear gene fragments (LSU, RPB2 and beta-tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long-distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance.

We present a new approach for estimating mixing between populations based on non-recombining markers, specifically Y-chromosome microsatellites. A Markov chain Monte Carlo (MCMC) Bayesian statistical approach is used to calculate the posterior probability distribution of population parameters of interest, including the effective population size and the time to most recent common ancestor (MRCA). To test whether two populations are homogeneously mixed we introduce a “mixing” statistic defined for each coalescent event that weights the contribution of that ancestor's descendants to the two subpopulations, and an associated population “purity” statistic. Using simulated data with low levels of migration between two populations, we demonstrate that our method is more sensitive than other commonly used distance-based methods such as R-ST and D-SW. To illustrate our method, we analysed mixing between 11 pre-defined Chinese ethnic/regional populations, using 5 microsatellite markers from the non-recombining region of the Y-chromosome (NRY), demonstrating a significant clustering of a subset of subpopulations with a high mutual relative degree of mixing (homogeneous mixing with support > 0.99). Our analysis suggests that there is a strong correlation between effective population size and mixing with other subpopulations. Thus, despite considerable mixing between these groups, the purity statistic still identifies significant heterogeneity, suggesting that periods of historical isolation continue to leave a recoverable signal despite modern introgression.

Larval dispersal is critical for the maintenance of species populations in patchy and ephemeral hydrothermal vent habitats. On fast-spreading ridges, such as the East Pacific Rise, rates of habitat turnover are comparable to estimated life-spans of many of the inhabiting species. Traditionally, dispersal questions have been addressed with two very different approaches, larval studies and population genetics. Population genetic studies of vent-endemic species have been informative for determining whether patterns of dispersal are suggestive of stepping stone or island models and estimating rates of gene flow (effective migrants per generation) over broad geographic ranges. However, these studies leave fundamental questions unanswered about the specific mechanisms by which larvae disperse and species maintain their populations and biogeographic ranges. With the goal of examining genetic structure and elucidating alternative larval dispersal mechanisms, we employed a genomic DNA fingerprinting technique, amplified fragment length polymorphisms (AFLPs). To assess the potential utility of AFLPs, and genetic structure of the hydrothermal vent tubeworm Riftia pachyptila, genomic `fingerprints' were recovered from 29 individuals from five vent fields spanning a distance of up to c. 5000 km along the East Pacific Rise. In contrast to previous population genetic studies that found little to no genetic structure using allozymes and mitochondrial DNA, genetic analyses of 630 polymorphic AFLP loci identified distinct subclades within R. pachyptila populations. Significant levels of differentiation were observed among populations from all vent regions as well as within each region. Discrete assemblages of tube-worms separated by as little as c. 400 m within a given vent region were genetically distinguishable and cohorts (based on size-frequency distribution) within an aggregation were found to be most closely related. These results suggest that mechanisms of larval dispersal act to retain cohort fidelity in R. pachyptila.

Asian-origin avian influenza (AI) viruses are spread in part by migratory birds. In Alaska, diverse avian hosts from Asia and the Americas overlap in a region of intercontinental avifaunal mixing. This region is hypothesized to be a zone of Asia-to-America virus transfer because birds there can mingle in waters contaminated by wild-bird-origin Al viruses. Our 7 years of Al virus surveillance among waterfowl and shorebirds in this region (1998-2004; 8,254 samples) showed remarkably low infection rates (0.06%). Our findings suggest an Arctic effect on viral ecology, caused perhaps by low ecosystem productivity and low host densities relative to available water. Combined with a synthesis of avian diversity and abundance, intercontinental host movements, and genetic analyses, our results suggest that the risk and probably the frequency of intercontinental virus transfer in this region are relatively low.

Purpose: The aim of this study was to evaluate the performance of the NONMEM prior functionality compared to a full Bayesian method when applied to population physiological models using diazepam as a case study. Methods: Whole-body physiologically based pharmacokinetic (WBPBPK) models for diazepam were initially developed, tested and calibrated for rats and man using a full Bayesian analysis as implemented in WINBUGS. The final models were implemented in NONMEM and the results from the two analyses compared in terms of parameter estimates, measures of parameter precision and run times. Results: NONMEM population parameter estimates were in close agreement with those produced by the Bayesian analysis although there was a substantial shortening of run time for both the animal WBPBPK model (4.5 vs. 21 h) and human WBPBPK models (2 vs. 167 h). The adequacy of the model and the final parameter estimates were judged to be sufficient by the model's ability to describe individual tissue concentration-time profiles. The model provided a good overall description of the plasma concentration-time data in both rat and man with comparable parameter precision. A limited nonparametric bootstrap (n=50) was performed to assess parameter sensitivity, bias and imprecision. No systematic bias was seen when comparing bootstrap means to final parameter estimates. Conclusions: The ease of implementation and reductions in run time hopefully provide a further step forward in allowing the wider use of these complex and information-rich models together with clinical data in the future.

The range of the grey parrot (Psittacus erithacus), one of the most heavily harvested bird species for the international pet trade, spans the forest belt of Central and West Africa and includes the oceanic island of Principe (Gulf of Guinea). Morphological variation led to the recognition of two mainland subspecies (P. e. erithacus and P. e. timneh). The population from Principe was originally described as a separate species (P. princeps) but is currently included in the nominate race. We used 1932 bp of the mitochondrial genome to clarify the genealogical affinities between the two currently-recognized mainland subspecies and the Principe population. Sampling included 20 individuals from Principe, 17 from P. e. erithacus, and 13 from P. e. timneh. We found that the two mainland subspecies form two independent lineages, having diverged up to 2.4 million years ago (Ma), and that the Principe population is composed of two lineages that diverged in allopatry. The most common lineage is descended from the first colonizers and evolved in isolation for up to 1.4 Ma. Contrary to current understanding, this `Principe lineage' is more closely related to the timneh than to the erithacus subspecies. The second lineage consists of P. e. erithacus birds from the nearby mainland that colonized the island in recent times. The evolutionary dynamics of the grey parrot population of Principe are primarily characterized by isolation, with new genetic variation being added through rare immigration events. The heavily harvested Principe grey parrot population should therefore be treated as an independent conservation unit.

Although fragmented rainforest environments represent hotspots for invertebrate biodiversity, few genetic studies have been conducted on rainforest invertebrates. Thus, it is not known if invertebrate species in rainforests are highly genetically fragmented, with the potential for populations to show divergent selection responses, or if there are low levels of gene flow sufficient to maintain genetic homogeneity among fragmented populations. Here we use microsatellite markers and DNA sequences from the mitochondrial ND5 locus to investigate genetic differences among Drosophila birchii populations from tropical rainforests in Queensland, Australia. As found in a previous study, mitochondrial DNA diversity was low with no evidence for population differentiation among rainforest fragments. The pattern of mitochondrial haplotype variation was consistent with D. birchii having undergone substantial past population growth. Levels of nuclear genetic variation were high in all populations while F-ST values were very low, even for flies from geographically isolated areas of rainforest. No significant differentiation was observed between populations on either side of the Burdekin Gap (a long-term dry corridor), although there was evidence for higher gene diversity in low-latitude populations. Spatial autocorrelation coefficients were low and did not differ significantly from random, except for one locus which revealed a clinal-like pattern. Comparisons of microsatellite differentiation contrasted with previously established clinal patterns in quantitative traits in D. birchii, and indicate that the patterns in quantitative traits are likely to be due to selection. These results suggest moderate gene flow in D. birchii over large distances. Limited population structure in this species appears to be due to recent range expansions or cycles of local extinctions followed by recolonizations/expansions. Nevertheless, patterns of local adaptation have developed in D. birchii that may result in populations showing different selection responses when faced with environmental change.

Pine and oak woodlands are common North American floral communities with distinct regional species composition. The white-breasted nuthatch (Aves: Sitta carolinensis) is a common resident bird of North American pine and oak woodlands, and is distributed continentally across the highly disjunct distribution of these woodlands. We propose three historical hypotheses to explain the evolution of the white-breasted nuthatch in its principal habitat. (i) The species evolved in situ in the regional pine-oak communities and the isolation of populations in these regions is captured in cryptic genetic variation. (ii) Migration of individuals between regions is frequent enough to maintain the widespread distributions and prevent regional divergence. (iii) The species have recently expanded to occupy their current distributions and an insufficient amount of time has passed for divergence to occur. Phylogenetic analysis of mitochondrial DNA (ND2 gene) variation (N = 216) in the white-breasted nuthatch reveals four reciprocally monophyletic clades concordant with the distribution of the regional North American pine and oak woodlands, and supports hypothesis 1 of in situ evolution of populations in the regional pine and oak communities. Within-clade population structure and demographic history are also discussed.

The connectivity among marine populations is determined by the dispersal capabilities of adults as well as their eggs and larvae. Dispersal distances and directions have a profound effect on gene flow and genetic differentiation within species. Genetic homogeneity over large areas is a common feature of coral reef fishes and can reflect high dispersal capability resulting in high levels of gene flow. If fish larvae return to their parental reef, gene flow would be restricted and genetic differentiation could occur. Larabicus quadrilineatus (Labridae) is considered as an endemic fish species of the Red Sea and Gulf of Aden. The juveniles of this species are cleaner fish that feed on ectoparasites of other fishes. Here, we investigated the genetic population structure and gene flow in L. quadrilineatus among five locations in the Red Sea to infer connectivity among them. To estimate genetic diversity, we analysed 369 bp of 237 mitochondrial DNA control region sequences. Haplotype and nucleotide diversities were higher in the southern than in the northern Red Sea. Analysis of molecular variance (AMOVA) detected the highest significant genetic variation between northern and central/southern populations (Phi(CT) = 0.01; P < 0.001). Migration analysis revealed a several fold higher northward than southward migration, which could be explained by oceanographic conditions and spawning season. Even though the Phi(ST) value of 0.01 is rather low and implies a long larval dispersal distance, estimates based on the isolation-by-distance model show a very low mean larval dispersal distance (0.44-5.1 km) compared to other studies. In order to enable a sustainable ornamental fishery on the four-line wrasse, the results of this study suggest that populations in the northern and southern Red Sea should be managed separately as two different stocks. The rather low larval dispersal distance of about 5 km needs to be considered in the design of marine protected areas to enable connectivity and self-seeding.

Brown trout populations in the Hardanger Fjord, Norway, have declined drastically due to increased exposure to salmon lice from salmonid aquaculture. We studied contemporary samples from seven populations and historical samples (1972 and 1983) from the two largest populations, one of which has declined drastically whereas the other remains stable. We analysed 11 microsatellite loci, including one tightly linked to the UBA gene of the major histocompatibility class I complex (MHC) and another locus linked to the TAP2A gene, also associated with MHC. The results revealed asymmetric gene flow from the two largest populations to the other, smaller populations. This has important conservation implications, and we predict that possible future population recoveries will be mediated primarily by the remaining large population. Tests for selection suggested diversifying selection at UBA, whereas evidence was inconclusive for TAP2A. There was no evidence for temporally fluctuating selection. We assessed the distribution of adaptive divergence among populations. The results showed the most pronounced footprints of selection between the two largest populations subject to the least immigration. We suggest that asymmetric gene flow has an important influence on adaptive divergence and constrains local adaptive responses in the smaller populations. Even though UBA alleles may not affect salmon louse resistance, the results bear evidence of adaptive divergence among populations at immune system genes. This suggests that similar genetic differences could exist at salmon louse resistance loci, thus rendering it a realistic scenario that differential population declines could reflect differences in adaptive variation.

Bayesian methods have become extremely popular in molecular ecology studies because they allow us to estimate demographic parameters of complex demographic scenarios using genetic data. Articles presenting new methods generally include sensitivity studies that evaluate their performance, but they tend to be limited and need to be followed by a more thorough evaluation. Here we evaluate the performance of a recent method, BAYESASS, which allows the estimation of recent migration rates among populations, as well as the inbreeding coefficient of each local population. We expand the simulation study of the original publication by considering multi-allelic markers and scenarios with varying number of populations. We also investigate the effect of varying migration rates and F-ST more thoroughly in order to identify the region of parameter space where the method is and is not able to provide accurate estimates of migration rate. Results indicate that if the demographic history of the species being studied fits the assumptions of the inference model, and if genetic differentiation is not too low (F-ST >= 0.05), then the method can give fairly accurate estimates of migration rates even when they are fairly high (about 0.1). However, when the assumptions of the inference model are violated, accurate estimates are obtained only if migration rates are very low (m = 0.01) and genetic differentiation is high (F-ST >= 0.10). Our results also show that using posterior assignment probabilities as an indication of how much confidence we can place on the assignments is problematical since the posterior probability of assignment can be very high even when the individual assignments are very inaccurate.

Dispersal is often viewed as a process on which the landscape has little effect. This is particularly apparent in populations' genetic and ecological studies, where isolation by distance is generally tested using a Euclidean distance between populations. However, landscapes can be richly textured mosaics of patches, associated with different qualities (e.g. different costs crossing patches) and different structures (shape, size and arrangement). An important challenge, therefore, is to determine if accounting for this additional complexity enriches our understanding of the dispersal processes. In this study, we quantify the effect of landscape structure on dispersal distances between 15 populations of the greater white-toothed shrew (Crocidura russula) in a highly fragmented landscape in Switzerland. We use a spatially explicit individual-based model to simulate C. russula dispersal. This model is designed to account for movement behavior in heterogeneous landscapes. We explore the relationship between simulation results and genetic differentiation between actual subpopulations. Finally, we test if simulated dispersal distances are better predictors of genetic differentiation than traditional Euclidean distances. The ecological distances measured by the model show a clear relationship with genetic differentiation between C. russula subpopulations. This relationship is stronger than the one obtained by the usual Euclidean distance. (c) 2006 Elsevier B.V. All rights reserved.

Previous genetic studies indicate Steller sea lions (Eumetopias jubatus (Schreber, 1776)) comprise three phylogeo-graphically distinct populations. However, differences in population trends and ecology and the limited extent of recorded dispersal suggest structure may be present at smaller scales. We examined sequence variation within a longer segment (531 bp) of the mtDNA control region in greater numbers (n = 1654) of sea lions from across Alaska than earlier investigations to investigate fine-scale dispersal patterns in Steller sea lions. We detected high levels of haplotypic diversity (h = 0.934) and confirmed phylogeographic differentiation between southeastern and western Alaska (Phi(st) = 0.23, P < 0.0001), but also found significant differentiation at regional and local scales. Rookeries in the Gulf of Alaska, eastern Bering Sea, and eastern Aleutians were distinct from rookeries in the central and western Aleutians (F-st = 0.021, P < 0.0001; Phi(st) = 0.017, P < 0.0001). The location of this split coincides with an oceanographic divergence between continental shelf and ocean basin waters and with differences in sea lion foraging ecology and population trends. A number of rookeries were also significantly differentiated from nearby rookeries (F-st = 0.02-0.025, P < 0.05), signifying substantial female-mediated philopatry, in some cases, at local scales. These findings have important implications for understanding the ecology of Steller sea lions in relation to marine ecosystems and the causes of population declines, and they provide guidance for management, including the identification of management stocks.

In 1988, Felsenstein described a framework for assessing the likelihood of a genetic data set in which all of the possible genealogical histories of the data are considered, each in proportion to their probability. Although not analytically solvable, several approaches, including Markov chain Monte Carlo methods, have been developed to find approximate solutions. Here, we describe an approach in which Markov chain Monte Carlo simulations are used to integrate over the space of genealogies, whereas other parameters are integrated out analytically. The result is an approximation to the full joint posterior density of the model parameters. For many purposes, this function can be treated as a likelihood, thereby permitting likelihood-based analyses, including likelihood ratio tests of nested models. Several examples, including an application to the divergence of chimpanzee subspecies, are provided.

Lingcod, Ophiodon elongatus Girard, have a 3-month pelagic larval stage and are an important recreational and commercial species on the west coast of North America. Cytochrome-c oxidase I sequences from tissue samples were used to characterize population structure and infer patterns of gene flow from California to Alaska. No significant genetic structure was found when estimates of Wright's F-ST (i.e., Phi(ST)) were generated among all populations sampled. Nesting populations within regions, however, indicated that the inner coast of Washington State is distinct, a result corroborating previous allozyme work. Coalescent-based estimates of gene flow indicate that although migration can be high from an evolutionary perspective, nearly half of all comparisons among populations showed no gene flow in at least one direction. From an ecological perspective, moderate migration rates (Nm < 10) among most populations provide surprisingly limited connectivity at large (similar to 1,000 km) and small (similar to 100 km) spatial scales. Coalescent-based estimates also show that gene flow between the inner and the outer coasts is asymmetric, a result consistent with prevailing surface currents. Because the expected inter-locus variances for coalescent-based estimates of gene flow are likely large, future work will benefit from analyses of nuclear DNA markers. However, limited demographic connectivity on large spatial scales may help explain why stock recovery has been uneven, with greater recovery in the northern (87% rebuilt) than in the southern (24% rebuilt) fishery region, supporting a regional management strategy. These results suggest that despite a 3-month pelagic larval stage, some areas may be effectively closed with respect to both population dynamics and fishery management issues.

Landscape genetics has emerged as a new research area that integrates population genetics, landscape ecology and spatial statistics. Researchers in this field can combine the high resolution of genetic markers with spatial data and a variety of statistical methods to evaluate the role that landscape variables play in shaping genetic diversity and population structure. While interest in this research area is growing rapidly, our ability to fully utilize landscape data, test explicit hypotheses and truly integrate these diverse disciplines has lagged behind. Part of the current challenge in the development of the field of landscape genetics is bridging the communication and knowledge gap between these highly specific and technical disciplines. The goal of this review is to help bridge this gap by exposing geneticists to terminology, sampling methods and analysis techniques widely used in landscape ecology and spatial statistics but rarely addressed in the genetics literature. We offer a definition for the term `landscape genetics', provide an overview of the landscape genetics literature, give guidelines for appropriate sampling design and useful analysis techniques, and discuss future directions in the field. We hope, this review will stimulate increased dialog and enhance interdisciplinary collaborations advancing this exciting new field.

Dispersal in birds and mammals tends to be female-biased in monogamous species and male-biased in polygamous species. However results for other taxa, most notably fish, are equivocal. We employed molecular markers and physical tags to test the hypothesis that Atlantic salmon, a promiscuous species with intense male-male competition for access to females, displays male-biased dispersal. We found significant variation in sex ratios and in asymmetric gene flow between neighbouring salmon populations, but little or no evidence for sex-biased dispersal. We show that conditions favouring male dispersal will often be offset by those favouring female dispersal, and that spatial and temporal variation in sex ratios within a metapopulation may favour the dispersal of different sexes in source and sink habitats. Thus, our results reconcile previous discrepancies on salmonid dispersal and highlight the need to consider metapopulation dynamics and sex ratios in the study of natal dispersal of highly fecund species.

Since the late 1990s, molecular techniques have fuelled debate about the role of Pleistocene glacial cycles in structuring contemporary avian diversity in North America. The debate is still heated; however, there is widespread agreement that the Pleistocene glacial cycles forced the repeated contraction, fragmentation, and expansion of the North American biota. These demographic processes should leave genetic `footprints' in modern descendants, suggesting that detailed population genetic studies of contemporary species provide the key to elucidating the impact of the late Quaternary (late Pleistocene-Holocene). We present an analysis of mitochondrial DNA (mtDNA) variation in the mountain chickadee (Poecile gambeli) in an attempt to examine the genetic evidence of the impact of the late Quaternary glacial cycles. Phylogenetic analyses reveal two strongly supported clades of P. gambeli: an Eastern Clade (Rocky Mountains and Great Basin) and a Western Clade (Sierra Nevada and Cascades). Post-glacial introgression is apparent between these two clades in the Mono Lake region of Central California. Within the Eastern Clade there is evidence of isolation-by-distance in the Rocky Mountain populations, and of limited gene flow into and around the Great Basin. Coalescent analysis of genetic variation in the Western Clade indicates that northern (Sierra Nevada/Cascades) and southern (Transverse/Peninsular Ranges) populations have been isolated and evolving independently for nearly 60 000 years.

We have developed a Bayesian version of our likelihood-based Markov chain Monte Carlo genealogy sampler LAMARC and compared the two versions for estimation of Theta = 4N(e)mu, exponential growth rate, and recombination rate. We used simulated DNA data to assess accuracy of means and support or credibility intervals. In all cases the two methods had very similar results. Some parameter combinations led to overly narrow support or credibility intervals, excluding the truth more often than the desired percentage, for both methods. However, the Bayesian approach rejected the generative parameter values significantly less often than the likelihood approach, both in cases where the level of rejection was normal and in cases where it was too high.

The spatial genetic structure of the widespread orchid Serapias vomeracea ssp. vomeracea and of the two rare S. vomeracea ssp. laxiflora and ssp. orientalis was examined using nuclear microsatellites. The three taxa showed low mean allele number (3.2), frequent significant deviations from the HW equilibrium (13 out of 20 populations) and intermediate to high gene diversity. F-statistics indicated either low or highly unpredictable levels of gene flow, in line with a not significant isolation by distance. Demographic tests suggested that most of populations experienced a size decline and show a small effective population size. The heterozygote excess detected in many populations could be the consequence of non-random mating due to the nonrewarding pollination strategy of Serapias. Hence, the divergence of lineages within the genus could be driven by a combination of stochastic forces such as drift and bottlenecks, as well as locally selective forces.

The crab-eating fox is a medium-sized Neotropical canid with generalist habits and a broad distribution in South America. We have investigated its genetic diversity, population structure and demographic history across most of its geographic range by analysing 512 base pairs (bp) of the mitochondrial DNA (mtDNA) control region, 615 bp of the mtDNA cytochrome b gene and 1573 total nucleotides from three different nuclear fragments. MtDNA data revealed a strong phylogeographic partition between northeastern Brazil and other portions of the species' distribution, with complete separation between southern and northern components of the Atlantic Forest. We estimated that the two groups diverged from each other c. 400 000-600 000 years ago, and have had contrasting population histories. A recent demographic expansion was inferred for the southern group, while northern populations seem to have had a longer history of large population size. Nuclear sequence data did not support this north-south pattern of subdivision, likely due at least in part to secondary male-mediated historical gene flow, inferred from multilocus coalescent-based analyses. We have compared the inferred phylogeographic patterns to those observed for other Neotropical vertebrates, and report evidence for a major north-south demographic discontinuity that seems to have marked the history of the Atlantic Forest biota.

The Fertile Crescent represents the center of origin and earliest known place of domestication for many cereal crops. During the transition from wild grasses to domesticated cereals, many host-specialized pathogen species are thought to have emerged. A sister population of the wheat-adapted pathogen Mycosphaerella graminicola was identified on wild grasses collected in northwest Iran. Isolates of this wild grass pathogen from 5 locations in Iran were compared with 123 M. graminicola isolates from the Middle East, Europe, and North America. DNA sequencing revealed a close phylogenetic relationship between the pathogen populations. To reconstruct the evolutionary history of M. graminicola, we sequenced 6 nuclear loci encompassing 464 polymorphic sites. Coalescence analyses indicated a relatively recent origin of M. graminicola, coinciding with the known domestication of wheat in the Fertile Crescent around 8,000-9,000 BC. The sympatric divergence of populations was accompanied by strong genetic differentiation. At the present time, no genetic exchange occurs between pathogen populations on wheat and wild grasses although we found evidence that gene flow may have occurred since genetic differentiation of the populations.

This study examined the degree and pattern of variability in trophic morphology in Arctic charr (Salvelinus alpinus L.) at three spatial scales: across 22 populations from Scotland and between and within two adjacent catchments (Laxford and Shin) in northern Scotland. In addition, the variability at six microsatellite loci between and within the Laxford and Shin systems was determined. Habitat use by charr differed significantly between populations. The pattern of variability in trophic morphology, known to influence foraging ability in charr, showed a very high degree of between-population variation with at least 52% of population pairs showing significant differences in head shape. Trophic morphology and genetic variation was also high over small geographical scales; variation being as high between charr from lakes within the same catchment, as between adjacent catchments. The pattern of both phenotypic and genotypic variation suggests a mosaic of variation across populations with geographically close populations often as distinct from each other as populations with much greater separation. Very low levels of effective migrants between populations, even within the same catchment, suggest that this variation is being maintained by very low straying rates between phenotypically and genetically distinct populations, even when there is no apparent barrier to movement. We conclude that the genetic and phenotypic integrity of charr populations across Scotland is high and that this adaptive radiation constitutes a `hidden' element of diversity in northern freshwater systems. Two consequences of this are that the population (rather than the species) makes a more rational unit for the consideration of conservation strategies and that the habitat requirements and therefore management needs may differ significantly between populations.

The range dynamics of a species can either be governed by the spatial tracing of the fundamental environmental niche or by adaptation that allows to occupy new niches. Therefore, the investigation of spatial variation in the realized environmental niche is central to the understanding of species range limit dynamics. However, the study of intraspecific niche variation has been neglected in most phylogeographical studies. We studied the spatial distribution of the realized environmental niche in three land snail species of the genus Candidula, integrating phylogeographical methods, morphometrics, and spatial biodiversity informatics. The phylogeographical analyses showed significant range expansions in all species. These expansions were accompanied in Candidula gigaxii by a shift in the realized environmental niche, the species Candidula unifasciata followed its ancestral niche during expansion while the climate changed in the area of origin and Candidula rugosiuscula tracked the ancestral environmental conditions. The significant niche shifts were associated with potentially adaptive changes of shell morphology. We propose our presented approach as a practicable framework to test hypotheses on intraspecific niche evolution. (c) 2007 The Linnean Society of London.

The impact of islands on the population structure of Anopheles flavirostris (Ludlow) (Diptera: Culicidae), the primary malaria vector in the Philippines, was assessed. A phylogenetic analysis of 16 cytochrome oxidase subunit I (CO1) haplotypes revealed three clades: one basal clade containing genetically disparate haplotypes from Mindanao, and two derived clades, one of which was largely confined to the largest island, Luzon, and one that was widespread except for Luzon. For the Luzon clade, nested clade analysis revealed an isolation-by-distance effect, and a mismatch distribution analysis diagnosed a recent demographic expansion (sum of squared deviation, SDD = 0.0093, P = 0.075), which mirrors demographic attributes found in mainland primary malaria vectors and could inflate estimates of gene flow from F-ST. For the widespread clade, evidence of range expansion and past fragmentation and/or long distance colonization from the Visayas or Mindanao to Palawan is suggested. A south-to-north range expansion of An. flavirostris is suggested; estimates of coalescence for the Luzon clade was 214 000 years ago (ya) (95% confidence interval 35 600-298 000 ya), i.e. late Pleistocene. Present day rather than Pleistocene island association and some, but not all, sea barriers appeared to be important for An. flavirostris population structure. Our results suggest that endemic island malaria vector species need to be considered before any generalizations are made about the population structure of primary and secondary vectors.

Populations of lake sturgeon Acipenser Julvescens have undergone dramatic declines in abundance and distribution in the Great Lakes basin and are a species of conservation concern throughout their range. While information regarding the genetic population structure of this species is critical for the development of effective management plans, little information currently exists. We examined both microsatellite and mitochondrial DNA (mtDNA) variation as a means of estimating population genetic diversity within, and the degree of spatial population structuring among, 11 remnant lake sturgeon populations in the upper Great Lakes basin. Multiple measures of genetic diversity were consistently high across populations and were not significantly correlated with estimates of current adult population size. Despite substantial population declines, life history characteristics, including longevity and itemparity, appear to have buffered lake sturgeon populations from losses of genetic diversity. Significant levels of interpopulation variance in both microsatellite allele and mtDNA haplotype frequencies (mean genetic differentiation index = 0.055 over eight microsatellite loci; mean haplotype frequencies = 0.134 for mtDNA) were detected. Population structure is most likely a function of high levels of natal fidelity, a trend observed in other species of sturgeon Acipenser spp. We discuss the implications of these results with regard to the management and conservation of lake sturgeon in the Great Lakes.

One proposed mechanism of speciation is divergent sexual selection, whereby divergence in female preferences and male signals results in behavioural isolation. Despite the appeal of this hypothesis, evidence for it remains inconclusive. Here, we present several lines of evidence that sexual selection is driving behavioural isolation and speciation among populations of an Amazonian frog (Physalaemus petersi). First, sexual selection has promoted divergence in male mating calls and female preferences for calls between neighbouring populations, resulting in strong behavioural isolation. Second, phylogenetic analysis indicates that populations have become fixed for alternative call types several times throughout the species' range, and coalescent analysis rejects genetic drift as a cause for this pattern, suggesting that this divergence is due to selection. Finally, gene flow estimated with microsatellite loci is an average of 30 times lower between populations with different call types than between populations separated by a similar geographical distance with the same call type, demonstrating genetic divergence and incipient speciation. Taken together, these data provide strong evidence that sexual selection is driving behavioural isolation and speciation, supporting sexual selection as a cause for speciation in the wild.

Genetic studies of recently established populations are challenging because the assumption of equilibrium underlying many analyses is likely to be violated. Using microsatellites, we investigated determinants of genetic structure and migration among invasive European-Chinese mitten crab populations, applying a combination of traditional population genetic analyses and nonequilibrium Bayesian methods. Consistent with their recent history, invasive populations showed much lower levels of genetic diversity than a native Chinese population, indicative of recent bottlenecks. Population differentiation was generally low but significant and especially pronounced among recently established populations. Significant differentiation among cohorts from the same geographical location (River Thames) suggests the low effective population size and associated strong genetic drift that would be anticipated from a very recent colonization. An isolation-by-distance pattern appears to be driven by an underlying correlation between geographical distance and population age, suggesting that cumulative homogenizing gene flow reduces founder bottleneck-associated genetic differentiation between longer-established populations. This hypothesis was supported by a coalescent analysis, which supported a drift + gene flow model as more likely than a model excluding gene flow. Furthermore, admixture analysis identified several recent migrants between the UK and Continental European population clusters. Admixture proportions were significantly predicted by the volume of shipping between sites, indicating that human-mediated transport remains a significant factor for dispersal of mitten crabs after the initial establishment of populations. Our study highlights the value of nonequilibrium methods for the study of invasive species, and also the importance of evaluating nonequilibrium explanations for isolation by distance patterns.

Peregrine falcon populations underwent devastating declines in the mid-20th century due to the bioaccumulation of organochlorine contaminants, becoming essentially extirpated east of the Great Plains and significantly reduced elsewhere in North America. Extensive re-introduction programs and restrictions on pesticide use in Canada and the United States have returned many populations to predecline sizes. A proper population genetic appraisal of the consequences of this decline requires an appropriate context defined by (i) meaningful demographic entities; and (ii) suitable reference populations. Here we explore the validity of currently recognized subspecies designations using data from the mitochondrial control region and 11 polymorphic microsatellite loci taken from 184 contemporary individuals from across the breeding range, and compare patterns of population genetic structure with historical patterns inferred from 95 museum specimens. Of the three North American subspecies, the west coast marine subspecies Falco peregrinus pealei is well differentiated genetically in both time periods using nuclear loci. In contrast, the partitioning of continental Falco peregrinus anatum and arctic Falco peregrinus tundrius subspecies is not substantiated, as individuals from these subspecies are historically indistinguishable genetically. Bayesian clustering analyses demonstrate that contemporary genetic differentiation between these two subspecies is mainly due to changes within F. p. anatum (specifically the southern F. p. anatum populations). Despite expectations and a variety of tests, no genetic bottleneck signature is found in the identified populations; in fact, many contemporary indices of diversity are higher than historical values. These results are rationalized by the promptness of the recovery and the possible introduction of new genetic material.

Microsatellite markers were first Used to partition individuals of European grayling Thymallus thymallus, from the Danube, Rhine and Main, and Elbe drainage systems into subpopulations and to estimate individual immigrants ancestrics over the last few generations. Subsequently, the studied populations were `purged' from recent immigrants and the proportions of evolutionary lineages within the `purged' populations were re-estimated by applying, mtDNA markers. The results confirmed a high level of admixture of the divergent mtDNA lineages (i.e. natural secondary contact) in populations sampled at the contact zones of the drainages. In addition, a substantial amount of introgression was observed for several populations that were known to be affected by stocking of European grayling from different origins. (c) 2006 The Authors Journal compilation (c) The Fisheries Society of the British Isles.

Using 11 microsatellite markers, genetic analyses of three successive year-classes of gag Mycteroperca microlepis juveniles across the north-eastern Gulf of Mexico revealed a lack of spatial structure and very little temporal variation between year-classes. These results are consistent with long-term effective population sizes on the order of 30 000 adults. The importance of reproductive-style and sex-ratio variation is discussed as an important influence on long-term effective sizes. (c) 2006 The Author Journal compilation (c) 2006 The Fisheries Society of the British Isles.

The genetic diversity and genetic structure of plant populations are influenced by processes of regeneration. Assessing the genetic composition of populations regenerated by different modes is important for successful forest management and conservation. In this study, we compared the genetic diversity and genetic structure of six populations in mixed stands with those of four post-fire stands of the noble hardwood species Betula maximowicziana. We collected plant tissues from 491 adults and 266 seedlings, germinated from soil samples, for a total of 10 populations, and genotyped them using 11 microsatellite loci. Genetic diversity parameters (e.g., H-E, R-s, F-IS) in the post-fire stands were similar to those in the mixed stands. In contrast, other parameters, including the number of private alleles (P-A), the number of loci showing significant linkage disequilibrium (LD) and effective population size (Ne) differed between the mixed and post-fire stands. The average P-A, LD and Ne values were 1.2, 2.0 and 315.7, respectively, for the mixed stands, and 0.3, 5.0 and 282.2, respectively, for the post-fire stands. Evidence of a significant bottleneck was detected in two of four adult populations in the post-fire stands, possibly as a result of a catastrophic founder effect due to fire disturbance on their genetic constitution. Buried seed populations maintained the same level of genetic variability as adult populations, but with lower genetic differentiation among them. Spatioternporal gene flow, characterized by wind-mediated dispersal and the persistence of viable seeds in the soil, are key factors maintaining the genetic diversity of B. maximowicziana populations. Our study reveals that post-fire stands and buried seeds will be useful genetic resources in the future. (c) 2006 Elsevier B.V. All rights reserved.

Our understanding of the evolution of genes of the major histocompatibility complex (MHC) is rapidly increasing, but there are still enigmatic questions remaining, particularly regarding the maintenance of high levels of MHC polymorphisms in small, isolated populations. Here, we analyze the genetic variation at eight microsatellite loci and sequence variation at exon 2 of the MHC class IIB (DAB) genes in two wild populations of the Trinidadian guppy, Poecilia reticulata. We compare the genetic variation of a small (N-e approximate to 100) and relatively isolated upland population to that of its much larger (N. 2400) downstream counterpart. As predicted, microsatellite diversity in the upland population is significantly lower and highly differentiated from the population further downstream. Surprisingly, however, these guppy populations are not differentiated by MHC genetic variation and show very similar levels of allelic richness. Computer simulations indicate that the observed level of genetic variation can be maintained with overdominant selection acting at three DAB loci. The selection coefficients differ dramatically between the upland (s >= 0.2) and lowland (s <= 0.01) populations. Parasitological analysis on wild-caught fish shows that parasite load is significantly higher on upland than on lowland fish, which suggests that large differences in selection intensity may indeed exist between populations. Based on the infection intensity, a substantial proportion of the upland fish would have suffered direct or indirect fitness consequences as a result of their high parasite loads. Selection by parasites plays a particularly important role in the evolution of guppies in the upland habitat, which has resulted in high levels of MHC diversity being maintained in this population despite considerable genetic drift.

Effective spatial management of coral reefs including design of marine protected areas requires an understanding of interpopulation genetic connectivity. We assessed gene flow along 355 km of the Florida reef system and between Florida and Belize in three commensal invertebrates occupying the same host sponge (Callyspongia vaginalis) but displaying contrasting reproductive dispersal strategies: the broadcast-spawning brittle star Ophiothrix lineata and two brooding amphipods Leucothoe kensleyi and Leucothoe ashleyae. Multiple analytical approaches to sequence variation in the mitochondrial COI gene demonstrated a high degree of overall connectivity for all three species along the Florida reef system. Ophiothrix lineata showed significant genetic structuring between Florida and Belize, and a pattern of isolation by distance but no significant genetic structuring along the Florida coastline. Bayesian estimates of migration detected a strong southerly dispersal bias for O. lineata along the Florida reef system, contrary to the general assumption of northerly gene flow in this region based on the direction of the Florida Current. Both amphipods, despite direct development, also showed high gene flow along the Florida reef system. Multiple inferences of long-distance dispersal from a nested clade analysis support the hypothesis that amphipod transport, possibly in detached sponge fragments, could generate the high levels of overall gene flow observed. However, this transport mechanism appears much less effective across deep water as connectivity between Florida and Belize (1072 km) is highly restricted.

Several recent studies have shown that amphibian populations may exhibit high genetic subdivision in areas with recent fragmentation and urban development. Less is known about the potential for genetic differentiation in continuous habitats. We studied genetic differentiation of red-backed salamanders (Plethodon cinereus) across a 2-km transect through continuous forest in Virginia, USA. Mark-recapture studies suggest very little dispersal for this species, whereas homing experiments and post-Pleistocene range expansion both suggest greater dispersal abilities. We used six microsatellite loci to examine genetic population structure and differentiation between eight subpopulations of red-backed salamanders at distances from 200 m to 2 km. We also used several methods to extrapolate dispersal frequencies and test for sex-biased dispersal. We found small, but detectable differentiation among populations, even at distances as small as 200 m. Differentiation was closely correlated with distance and both Mantel tests and assignment tests were consistent with an isolation-by-distance model for the population. Extrapolations of intergenerational variance in spatial position (sigma(2) < 15 m(2)) and pair-wise dispersal frequencies (4Nm < 25 for plots separated by 300 m) both suggest limited gene flow. Additionally, tests for sex-biased dispersal imply that dispersal frequency is similarly low for both sexes. We suggest that these low levels of gene flow and the infrequent dispersal observed in mark-recapture studies may be reconciled with homing ability and range expansion if dispersing animals rarely succeed in breeding in saturated habitats, if dispersal is flexible depending on the availability of habitat, or if dispersal frequency varies across the geographic range of red-backed salamanders.

We study the ancestral genetic process for samples from two large, subdivided populations that are connected by migration to, from, and within a small set of subpopulations, or demes. We consider convergence to an ancestral limit process as the numbers of demes in the two large, subdivided populations tend to infinity. We show that the ancestral limit process for a sample includes a recent instantaneous adjustment to the sample size and structure followed by a more ancient process that is identical to the usual structured coalescent, but with different scaled parameters. This justifies the application of a modified structured coalescent to some hierarchically structured populations. (c) 2006 Elsevier Inc. All rights reserved.

The genus Tripterygion (Risso 1826) is restricted to the eastern Atlantic and the Mediterranean, and comprises only three species. T. melanuros and T. tripteronotus are essentially endemic to the Mediterranean, while Tripterygion delaisi occurs in the Atlantic and in the Mediterranean. Two subspecies of T. delaisi have been described (T. d. xanthosoma in the Mediterranean and T. d. delaisi in the Atlantic). Several scenarios have been proposed for the evolution of T. delaisi subspecies, but so far its subspeciation process is not clear. In this study we present a population survey of T. delaisi including specimens from the two recognized subspecies. We combined a phylogeographic approach with estimates of the direction of migration (between the Atlantic and the Mediterranean) and of the coalescence time of the two subspecies, using polymorphic mitochondrial and nuclear genes. The results of this study clearly support the existence of two Tripterygion delaisi clades, one in the eastern Atlantic islands and another in the Atlantic coasts of Europe and in the Mediterranean. Historical migration between the islands and Western Europe plus Mediterranean was restricted, and showed a westbound trend, with a higher number of migrants going from the Western Europe plus Mediterranean into the islands. We estimated the time of coalescence of both groups of T. delaisi to be more recent than the onset of Pleistocene glaciations (1.7 Mya). Our results are consistent with previous hypothesis that consider successive dispersal events of a Tripterygion ancestor from the western African coast colonizing the Atlantic islands and the Mediterranean, promoting the evolutionary divergence between these areas.

Using the structured serial coalescent with Bayesian MCMC and serial samples, we estimate population size when some demes are not sampled or are hidden, ie ghost demes. It is found that even with the presence of a ghost deme, accurate inference was possible if the parameters are estimated with the true model. However with an incorrect model, estimates were biased and can be positively misleading. We extend these results to the case where there are sequences from the ghost at the last time sample. This case can arise in HIV patients, when some tissue samples and viral sequences only become available after death. When some sequences from the ghost deme are available at the last sampling time, estimation bias is reduced and accurate estimation of parameters associated with the ghost deme is possible despite sampling bias. Migration rates for this case are also shown to be good estimates when migration values are low.

Background: The past decade has seen a remarkable increase in the number of recognized mouse lemur species ( genus Microcebus). As recently as 1994, only two species of mouse lemur were recognized according to the rules of zoological nomenclature. That number has now climbed to as many as fifteen proposed species. Indeed, increases in recognized species diversity have also characterized other nocturnal primates - galagos, sportive lemurs, and tarsiers. Presumably, the movement relates more to a previous lack of information than it does to any recent proclivity for taxonomic splitting. Due to their nocturnal habits, one can hypothesize that mouse lemurs will show only minimal variation in pelage coloration as such variation should be inconsequential for the purposes of mate and/ or species recognition. Even so, current species descriptions for nocturnal strepsirrhines place a good deal of emphasis on relatively fine distinctions in pelage coloration. Results: Here, we report results from a multi- year study of mouse lemur populations from Beza Mahafaly in southern Madagascar. On the basis of morphological and pelage variation, we initially hypothesized the presence of up to three species of mouse lemurs occurring sympatrically at this locality, one of which appeared to be undescribed. Genetic analysis reveals definitively, however, that all three color morphs belong to a single recognized species, Microcebus griseorufus. Indeed, in some cases, the three color morphs can be characterized by identical mitochondrial haplotypes. Conclusion: Given these results, we conclude that investigators should always proceed with caution when using a single data source to identify novel species. A synthetic approach that combines morphological, genetic, geographic, and ecological data is most likely to reveal the true nature of species diversity.

Identifying ecological factors associated with population genetic differentiation is important for understanding microevolutionary processes and guiding the management of threatened populations. We identified ecological correlates of several population genetic parameters for three interacting species (two garter snakes and an anuran) that occupy a common landscape. Using multiple regression analysis, we found that species interactions were more important in explaining variation in population genetic parameters than habitat and nearest-neighbour characteristics. Effective population size was best explained by census size, while migration was associated with differences in species abundance. In contrast, genetic distance was poorly explained by the ecological correlates that we tested, but geographical distance was prominent in models for all species. We found substantially different population dynamics for the prey species relative to the two predators, characterized by larger effective sizes, lower gene flow and a state of migration-drift equilibrium. We also identified an escarpment formed by a series of block faults that serves as a barrier to dispersal for the predators. Our results suggest that successful landscape-level management should incorporate genetic and ecological data for all relevant species, because even closely associated species can exhibit very different population genetic dynamics on the same landscape.

Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually - similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers.

It is well known theoretically that gene flow can impede genetic differentiation between populations. In this study, we show that in a highly mobile bird species, where dispersal is well documented, there is a strong genetic and morphological differentiation over a very short geographical scale (less than 5 km). Allocation tests revealed that birds caught in one area were assigned genetically to the same area with a very high probability, in spite of current gene flow. Populations were also morphologically differentiated. The results suggest that the relationship between gene flow and differentiation can be rather complicated and non-intuitive.

We used mitochondrial DNA control-region sequences to investigate the genetic structure of Mexican Spotted Owl (Strix occidentalis lucida) populations in the southwestern United States. This subspecies is federally listed as threatened, and its preferred habitat is naturally fragmented. We found that intrapopulation genetic diversity was high in all but the southeastern Arizona “sky island” populations, where it was variable. Genetic variance partitioning indicated that similar to 17% of the variation was distributed among populations and 7.5% was distributed among physiographic regions. Patterns of genetic correlation with geographic distance indicated that gene flow was substantial among populations within the relatively continuous habitat zone of the Mogollon Rim-Upper Gila Mountains in central Arizona and west-central New Mexico. However, there was significant isolation-by-distance elsewhere, and estimates of genetic divergence increased exponentially with geographic distance among fragmented populations on the scale of a few hundreds of kilometers; this implies that gene flow is restricted among those habitat fragments. Genetic heterogeneity among southeastern Arizona populations suggest that they have regularly received immigrants from the central Arizona populations. The Colorado population either was larger than thought or, more likely, has continuously received immigrants from elsewhere and is not a self-sustaining population.

The analysis of genetic diversity within species is vital for understanding evolutionary processes at the population level and at the genomic level. A large quantity of data can now be produced at an unprecedented rate, requiring the use of dedicated computer programs to extract all embedded information. Several statistical packages have been recently developed, which offer a panel of standard and more sophisticated analyses. We describe here the functionalities, special features and assumptions of more than 20 such programs, indicate how they can interoperate, and discuss new directions that could lead to improved software and analyses.

An explosive growth is occurring in the quantity, quality and complexity of molecular variation data that are being collected. Historically, such data have been analysed by using model-based methods. Models are useful for sharpening intuition, for explanation and for prediction: they add to our understanding of how the data were formed, and they can provide quantitative answers to questions of interest. We outline some of these model-based approaches, including the coalescent, and discuss the applicability of the computational methods that are necessary given the highly complex nature of current and future data sets.

Habitat fragmentation and climate change are two major threats on biodiversity. Fragmentation limits the number of patches and their decreased connectivity cannot always maintain populations at dynamic equilibrium. The natural extreme fragmentation of marine cave habitats represents an opportunity to understand how these processes interact. The hypothesis of a low gene flow among populations due to a high level of fragmentation was tested by analysing sequence variation in a fragment of the mitochondrial gene of the cytochrome oxidase subunit I in 170 individuals (23 localities across the NW Mediterranean) of two marine cave-dwelling mysids of the genus Hemimysis. The species Hemimysis margalefi recently replaced its congener Hemimysis speluncola, a species shift that could be related to the warming of the Mediterranean Sea and to differences in their thermal tolerances. There were too few H. speluncola samples to further discuss their genetic structuring, but for H. margalefi, the present study revealed high levels of genetic diversity and genetic structuring, as shown by the eight genetically distinct groups identified. The Croatian group might constitute a sibling species due to a strong divergence (15%). Nevertheless, these groups present reduced but orientated gene flow according to the general circulation in the Mediterranean, and fit a stepping-stone model. At local scale (Marseille area, France), gene flow among caves is dependent on unexpected local hydrodynamic barriers, that determine metapopulation sizes. Through the example of mysid species inhabiting marine caves, the present work confirms the strong influence of habitat disjunction (natural fragmentation) on population structure, and stresses the importance of coastal geomorphological features in inducing complex interactions between the circulation of water masses and the circulation of genes.

Several processes have been described that could explain geographical variation and speciation within small islands, including fragmentation of populations through volcanic eruptions. Massive landslides, or debris avalanches, could cause similar effects. Here we analyse the potential impact of the 0.8 million-year-ago (Ma) Guimar valley debris avalanche on the phylogeography of the lizard Gallotia galloti on the Canary Island of Tenerife. Distributions of mitochondrial DNA lineages (based on cytochrome b sequences) were analysed on a 60-km southeastern coast transect centred on this area. Three main clades were detected, which can be divided into northern (one clade) and southern (two clades) groups that introgress across the valley. Maximum-likelihood estimates of migration rates (scaled for mutation rate) revealed highly asymmetric patterns, indicating that long-term gene flow into this region from both the northern and the southern populations greatly exceeded that in the opposite directions, consistent with recolonization of the area. The ancestral Tenerife node on the G. galloti tree is estimated at 0.80 Ma, matching closely with the geological estimate for the debris avalanche. Morphological variation (body dimensions and scalation) was also analysed and indicated a stepped cline in female scalation across the valley, although the patterns for male scalation and male and female body dimensions were not as clear. Together these findings provide support for the hypothesis that the debris avalanche has shaped the phylogeography of G. galloti and may even have been a primary cause of the within-island cladogenesis through population fragmentation and isolation. Current estimates of timing of island unification mean that the original hypothesis that within-island diversity is explained by the secondary contact of populations from the two ancient precursor islands of Teno and Anaga is less plausible for this and some other Tenerife species. Large-scale landslides have occurred on many volcanic islands, and so may have been instrumental in shaping within-island diversities.

Previous studies have investigated the human population history of eastern North America by examining mitochondrial DNA (mtDNA) variation among Native Americans, but these studies could only reconstruct maternal population history. To evaluate similarities and differences in the maternal and paternal population histories of this region, we obtained DNA samples from 605 individuals, representing 16 indigenous populations. After amplifying the amelogenin locus to identify males, we genotyped 8 binary polymorphisms and 10 microsatellites in the male-specific region of the Y chromosome. This analysis identified 6 haplogroups and 175 haplotypes. We found that sociocultural factors have played a more important role than language or geography in shaping the patterns of Y chromosome variation in eastern North America. Comparisons with previous mtDNA studies of the same samples demonstrate that male and female demographic histories differ substantially in this region. Postmarital residence patterns have strongly influenced genetic structure, with patrilocal and matrilocal populations showing different patterns of male and female gene flow. European contact also had a significant but sex-specific impact due to a high level of male-mediated European admixture. Finally, this study addresses long-standing questions about the history of Iroquoian populations by suggesting that the ancestral Iroquoian population lived in southeastern North America.

The HIV evolutionary processes continuously unfold, leaving a measurable footprint in viral gene sequences. A variety of statistical models and inference techniques have been developed to reconstruct the HIV evolutionary history and to investigate the population genetic processes that shape viral diversity. Remarkably different population genetic forces are at work within and among hosts. Population-level HIV phylogenies are mainly shaped by selectively neutral epidemiologic processes, implying that genealogy-based population genetic inference can be useful to study the HIV epidemic history. Such evolutionary analyses have shed light on the origins of HIV, and on the epidemic spread of viral variants in different geographic locations and in different populations. The HIV genealogies reconstructed from within-host sequences indicate the action of selection pressure. In addition, recombination has a significant impact on HIV genetic diversity. Accurately quantifying both the adaptation rate and the population recombination rate of HIV will contribute to a better understanding of immune escape and drug resistance. Characterizing the impact of HIV transmission on viral genetic diversity will be a key factor in reconciling the different population genetic processes within and among hosts.

We have studied levels and distribution of genetic variation in nine isolated populations of Brown trout in NW Spain. In the present study, we have tried to test the importance of preservation of genetic variability for the survival of a set of isolated Brown trout (Salmo trutta) populations from the same river drainage. We screened genetic variation in three different markers, mitochondrial, microsatellites and Major Histocompatibility Complex (MHC), presumed to be under different selective pressures. Overall, genetic diversity varied considerably across populations and the distribution of genetic variation was similar at MHC and microsatellites; highly polymorphic populations at the microsatellite loci were also highly polymorphic at the MHC. We also observed high levels of differentiation among populations. Although we found evidence suggesting that balancing selection has influenced the long term evolution of the MHC, genetic drift seems to have eroded the effect of selection, becoming the predominant evolutionary force shaping genetic variation in some of the smaller populations. Despite current lack of variation at the MHC, these small populations seem to have remained viable for a long time.

Despite growing interest in the effects of landscape heterogeneity on genetic structuring, few tools are available to incorporate data on landscape composition into population genetic studies. Analyses of isolation by distance have typically either assumed spatial homogeneity for convenience or applied theoretically unjustified distance metrics to compensate for heterogeneity. Here I propose the isolation-by-resistance (IBR) model as an alternative for predicting equilibrium genetic structuring in complex landscapes. The model predicts a positive relationship between genetic differentiation and the resistance distance, a distance metric that exploits precise relationships between random walk times and effective resistances in electronic networks. As a predictor of genetic differentiation, the resistance distance is both more theoretically justified and more robust to spatial heterogeneity than Euclidean or least cost path-based distance measures. Moreover, the metric can be applied with a wide range of data inputs, including coarse-scale range maps, simple maps of habitat and nonhabitat within a species' range, or complex spatial datasets with habitats and barriers of differing qualities. The IBR model thus provides a flexible and efficient tool to account for habitat heterogeneity in studies of isolation by distance, improve understanding of how landscape characteristics affect genetic structuring, and predict genetic and evolutionary consequences of landscape change.

Small populations at the edge of a species' distribution can represent evolutionary relics left behind after range contractions due to climate change or human exploitation. The distinctiveness and genetic diversity of a small population of bottlenose whales in the Gully, a submarine canyon off Nova Scotia, was quantified by comparison to other North Atlantic populations using 10 microsatellites and mitrochondrial DNA (mtDNA) control region sequences (434 bp). Both markers confirmed the distinctiveness of the Gully (n = 34) from the next nearest population, off Labrador (n = 127; microsatellites - F-ST = 0.0243, P < 0.0001; mtDNA - Phi(ST) = 0.0456, P < 0.05). Maximum likelihood microsatellite estimates suggest that less than two individuals per generation move between these areas, refuting the hypothesis of population links through seasonal migration. Both males and females appear to be philopatric, based on significant differentiation at both genomes and similar levels of structuring among the sexes for microsatellites. mtDNA diversity was very low in all populations (h = 0.51, pi = 0.14%), a pattern which may be due to selective sweeps associated with this species' extreme deep-diving ecology. Whaling had a substantial impact on bottlenose whale abundance, with over 65 000 animals killed before the hunt ceased in the early 1970s. Genetic diversity was similar among all populations, however, and no signal for bottlenecks was detected, suggesting that the Gully is not a relic of a historically wider distribution. Instead, this unique ecosystem appears to have long provided a stable year-round habitat for a distinct population of bottlenose whales.

Microsatellites have gained wide application for elucidating population structure in nonmodel organisms. Since they are generally noncoding, neutrality is assumed but rarely tested. In Atlantic cod (Gadus morhua L.), microsatellite studies have revealed highly heterogeneous estimates of genetic differentiation among loci. In particular one locus, Gmo 132, has demonstrated elevated genetic differentiation. We investigated possible hitchhiking selection at this and other microsatellite loci in Atlantic cod. We employed 11 loci for analysing samples from the Baltic Sea, North Sea, Barents Sea and Newfoundland covering a large part of the species' distributional range. The `classical' Lewontin-Krakauer test for selection based on variance in estimates of F-ST and G'(ST) (standardized genetic differentiation) revealed only one significant pairwise test (North Sea-Barents Sea), and the source of the elevated variance could not be ascribed exclusively to Gmo 132. In contrast, different variants of the recently developed ln R theta. test for selective sweeps at microsatellite loci revealed a high number of significant outcomes of pair-wise tests for Gmo 132. Further, the presence of selection was indicated in at least one other locus. The results suggest that many previous estimates of genetic differentiation in cod based on microsatellites are inflated, and in some cases relationships among populations are obscured by one or more loci being the subject to hitch-hiking selection. Likewise, temporal estimates of effective population sizes in Atlantic cod may be flawed. We recommend, generally, to use a higher number of microsatellite loci to elucidate population structure in marine fishes and other nonmodel species to allow for identification of outlier loci that are subject to selection.

The brittle-star Acrocnida brachiata (Montagu) lives in sandy-bottom habitat of both intertidal and subtidal zones along the coasts of the northwestern Europe. An allozyme frequency-based survey (five enzyme loci) was combined with a mitochondrial (mt) COI haplotype analysis (598-bp sequences) on 17 populations to trace back past colonization pathways from the actual population structure of the species. Both genetic markers display a sharp genetic break between intertidal (clade I) and subtidal populations (clade S). This break corresponds to an allele frequency inversion at three enzyme loci (Hk, Pgm and Pgi) and a deep divergence of about 20% in mtCOI sequences between most of the intertidal populations and other samples. The geographic distribution of clade I seems to be more restricted than clade S as it is absent from the intertidal of the eastern English Channel and North Sea and may be replaced by clade S in south Brittany. Applying previously published rates of mutation, divergence between the two clades is estimated to pre-date 5 million years ago and may be due to allopatric speciation processes at the Mio-Pliocene transition. The occurrence of putative hybrids in a few localities, however, suggests incomplete cryptic speciation with secondary contact zones. The relative importance of colonization history vs. habitat specialization are discussed in the light of neutral evolution as tested from mtCOI gene sequences. While differential selection seems to have contributed little to the separation of the lineages, it may have played a role in the emergence of adaptive polymorphisms in the hybrid zone. Furthermore, congruent spatial patterns of differentiation were observed in both clades suggesting a recent increase in population size. These findings are in agreement with a recent expansion of the populations during or after the formation of the English Channel, from a southern refuge for the subtidal clade whereas the intertidal clade may have persisted further north. As previously suspected for a species with a very short pelagic larval phase, contemporary gene flow between distant or adjacent populations appears to be extremely reduced or even absent.

The North American freshwater limpet genus Laevapex (Walker, 1903) is a ubiquitous inhabitant of lentic and slow-moving lotic habitats east of the Rocky Mountains, but uncertainty clouds its systematic affinities, the phylogenetic validity of its constituent nominal species, and its degree of genetic connectivity among drainages. We addressed these issues by sampling the genus throughout much of its collective range and constructing representative nuclear and mitochondrial (mt) gene trees, in addition to performing morphometric analyses of shell shape variation. Our results identify neotropical Gundlachia and South American Uncancylus as sister lineages for Laevapex and reveal a pronounced sub-familial dichotomy within the Ancylidae, separating these three New World genera from a Holarctic (Ferrissia (Ancylus, Rhodacmea)) sister clade. Five nominal taxa (L. fuscus, L. diaphanus, L. peninsulae, L. sp., and “F” arkansasensis), indistinguishable in our morphometrie analyses, were polyphyletic in the mt gene trees, exhibited modest levels (< 3.9%) of genetic divergence in the primary (103 of 109 individuals) mt clade and, with one minor exception, they appeared fixed for a single nuclear ITS-2 genotype. Although complicated by the presence of rare, highly divergent mt lineages (of either introgressive or persistent ancestral polymorphic origin) in some populations, the molecular data were consistent with a taxonomic conclusion that these five nominal taxa represent a single polymorphic lineage of the type species L. Juscus. AMOVA analyses indicated that 56% of the observed mt variation could be attributed to among population differences, only two of 36 haplotypes were detected in more than one sampling location, and estimates of among-population mt gene flow were generally low at both regional and continental scales. Unrooted network analyses revealed a number of mt tip clades, one restricted to the southwestern part of the range, the remainder having overlapping distributions in eastern North America. All of the eastern tip clades occurred in the Mid-Atlantic region, and these samples displayed by far the highest levels of collective mt diversity. However, directional gene flow estimates indicated that this region has been a recipient (especially from Alabama populations), rather than a source of haplotypic diversity, implying that it likely represents a center of overlap, not a primary ice age refugium, for this limpet species. (c) 2006 Elsevier Inc. All rights reserved.

Biological diversity is quantified for reasons ranging from primer design, to bioprospecting, and community ecology. As a common index for all levels, we suggest Shannon's H-S, already used in information theory and biodiversity of ecological communities. Since Lewontin's first use of this index to describe human genetic variation, it has been used for variation of viruses, splice-junctions, and informativeness of pedigrees. However, until now there has been no theory to predict expected values of this index under given genetic and demographic conditions. We present a new null theory for H-S at the genetic level, and show that this index has advantages including (i) independence of measures at each hierarchical level of organization; (ii) robust estimation of genetic exchange over a wide range of conditions; (iii) ability to incorporate information on population size; and (iv) explicit relationship to standard statistical tests. Utilization of this index in conjunction with other existing indices offers powerful insights into genetic processes. Our genetic theory is also extendible to the ecological community level, and thus can aid the comparison and integration of diversity at the genetic and community levels, including the need for measures of community diversity that incorporate the genetic differentiation between species.

The global migration patterns of the fungal wheat pathogen Phaeosphaeria nodorum were analysed using 12 microsatellite loci. Analysis of 693 isolates from nine populations indicated that the population structure of P. nodorum is characterized by high levels of genetic diversity and a low degree of subdivision between continents. To determine whether genetic similarity of populations was a result of recent divergence or extensive gene flow, the microsatellite data were analysed using an isolation-with-migration model. We found that the continental P. nodorum populations diverged recently, but that enough migration occurred to reduce population differentiation. The migration patterns of the pathogen indicate that immigrants originated mainly from populations in Europe, China and North America.

River systems are vulnerable to natural and anthropogenic habitat fragmentation and will often harbor populations deviating markedly from simplified theoretical models. We investigated fine-scale population structure in the sedentary river fish Cottus gobio using microsatellites and compared migration estimates from three F-ST estimators, a coalescent maximum-likelihood method and Bayesian recent migration analyses. Source-sink structure was evident via asymmetry in migration and genetic diversity with smaller upstream locations emigration biased and larger downstream subpopulations immigration biased. Patterns of isolation by distance suggested that the system was largely, but not entirely, in migration-drift equilibrium, with headwater populations harboring a signal of past colonizations and in some cases also recent population bottlenecks. Up- vs. downstream asymmetry in population structure was partly attributable to the effects of flow direction, but was enhanced by weirs prohibiting compensatory upstream migration. Estimators of migration showed strong correspondence, at least in relative terms, especially if pairwise F-ST was used as an indirect index of relative gene flow rather than being translated to Nm. Since true parameter values are unknown in natural systems, comparisons among estimators are important, both to determine confidence in estimates of migration and to validate the performance of different methods.

The process of recolonization after disturbance is crucial for the persistence and dynamics of patch-tracking metapopulations. We developed a model to compare the spatial distribution and spatial genetic structure of the epiphytic lichen Lobaria pulmonaria within the perimeter of two reconstructed 19th century disturbances with a nearby reference area without stand-level disturbance. Population genetic data suggested that after stand-replacing disturbance, each plot was colonized by one or a few genotypes only, which subsequently spread clonally within a local neighborhood. The model (cellular automaton) aimed at testing the validity of this interpretation and at assessing the relative importance of local dispersal of clonal propagules vs. long-distance dispersal of clonal and/or sexual diaspores. A reasonable model fit was reached for the empirical data on host tree distribution, lichen distribution, and tree- and plot-level genotype diversity of the lichen in the reference area. Although model calibration suggested a predominance of local dispersal of clonal propagules, a substantial contribution of immigration of non-local genotypes by long-distance dispersal was needed to reach the observed levels of genotype diversity. The model could not fully explain the high degree of clonality after stand-replacing disturbance, suggesting that the dispersal process itself may not be stationary but depend on the ecological conditions related to disturbance.

Spatial and temporal landscape patterns have long been recognized to influence biological processes, but these processes often operate at scales that are difficult to study by conventional means. Inferences from genetic markers can overcome some of these limitations. We used a landscape genetics approach to test hypotheses concerning landscape processes influencing the demography of Lahontan cutthroat trout in a complex stream network in the Great Basin desert of the western US. Predictions were tested with population- and individual-based analyses of microsatellite DNA variation, reflecting patterns of dispersal, population stability, and local effective population sizes. Complementary genetic inferences suggested samples from migratory corridors housed a mixture of fish from tributaries, as predicted based on assumed migratory life histories in those habitats. Also as predicted, populations presumed to have greater proportions of migratory fish or from physically connected, large, or high quality habitats had higher genetic variability and reduced genetic differentiation from other populations. Populations thought to contain largely non-migratory individuals generally showed the opposite pattern, suggesting behavioral isolation. Estimated effective sizes were small, and we identified significant and severe genetic bottlenecks in several populations that were isolated, recently founded, or that inhabit streams that desiccate frequently. Overall, this work suggested that Lahontan cutthroat trout populations in stream networks are affected by a combination of landscape and metapopulation processes. Results also demonstrated that genetic patterns can reveal unexpected processes, even within a system that is well studied from a conventional ecological perspective.

Several boll weevils, Anthonomus grandis Boheman, were captured in pheromone traps in 2004 near Tlabualilo, Durango, Mexico, an area where none had been reported for approximate to 10 yr. It is possible that they were from an endemic population normally too low in numbers to be detected but that increased in response to more favorable rainfall conditions in 2004. Alternatively, they may represent an influx of migrants or the immediate descendents of migrants. To identify the most likely origin of the boll weevils captured in this area, we characterized microsatellite variation of the Tlahualilo weevils and compared it with the variation from three other populations in northern Mexico and from one in southern Texas. Measures of gene flow and individual assignment tests suggest that the boll weevils captured near Tlabualilo were primarily from an endemic low-level population, but that this area also is receiving immigrants from a cotton growing region approximate to 200 km to the north, near Rosales, Chihuahua, which is currently under a boll weevil eradication program. Similarly, Rosales is receiving immigrants from Tlahualilo. This study shows that microsatellite markers and population assignment techniques will be practical tools for determining the most likely origins of boll weevils reintroduced to eradication zones in the United States and Mexico. Population assignment strategies based on genetic markers hold promise for replacing conventional, but spatially constrained, mark-recapture studies of insect dispersal. This relatively new and powerful analytical approach is widely used in conservation genetics and fisheries studies, but has been underused by entomologists.

Functional connectivity is a key factor for the persistence of many specialist species in fragmented landscapes. However, connectivity estimates have rarely been validated by the observation of dispersal movements. In this study, we estimated functional connectivity of a real landscape by modelling dispersal for the endangered natterjack toad (Bufo calamita) using cost distance. Cost distance allows the evaluation of `effective distances', which are distances corrected for the costs involved in moving between habitat patches in spatially explicit landscapes. We parameterized cost-distance models using the results of our previous experimental investigation of natterjack's movement behaviour. These model predictions (connectivity estimates from the GIS study) were then confronted to genetic-based dispersal rates between natterjack populations in the same landscape using Mantel tests. Dispersal rates between the populations were inferred from variation at six microsatellite loci. Based on these results, we conclude that matrix structure has a strong effect on dispersal rates. Moreover, we found that cost distances generated by habitat preferences explained dispersal rates better than did the Euclidian distances, or the connectivity estimate based on patch-specific resistances (patch viscosity). This study is a clear example of how landscape genetics can validate operational functional connectivity estimates.

Recent studies have focused on the relationship between the marine fauna of the eastern Atlantic and the Mediterranean Sea, but within the Atlantic, little is known about genetic relationships between populations of the Macaronesian islands. In this study, we tested whether the paleo-climatology and paleo-oceanography of the region could predict the genetic relationships among three eastern Atlantic populations (Azores, Madeira, and Canaries) of a damselfish, Chromis limbata, and compared our results with its Mediterranean and adjacent Atlantic sister species, Chromis chromis. We combined phylogeographic and coalescent approaches using the fast evolving mitochondrial control region gene. No population structure was found for the three archipelagos. The coalescence time estimated for C. limbata (0.857-1.17 Mya) was much greater than that estimated for C. chromis. We propose that this difference reflects differences in glaciating extents in the Northeastern Atlantic and the Mediterranean. Diversity indexes (Hd and genetic distances) together with historical demographic parameters of C. limbata (Theta and g) revealed a more stable population history when compared to C chromis. Our results suggest that the Macaronesian populations of C. limbata have probably been less affected by the last glaciation than the Mediterranean populations of C. chromis. Migration across the three archipelagos was estimated and a prevailing northwest trend was detected. This result supports the idea of a colonization of the Azores by warm water fish from Madeira or the westernmost Canary islands which acted as major glacial refugia for the tropical and subtropical marine fauna during the glaciations. (c) 2006 Elsevier Inc. All rights reserved.

We study the ancestral process of a sample from a subdivided population with stochastically varying subpopulation sizes. The sizes of the subpopulations change very rapidly (almost every generation) with respect to the coalescent time scale. For haploid populations of size N, one coalescence time unit corresponds to N generations. Coalescence and migration events occur on the same time scale. We show that. when the total population size tends to infinity. the structured coalescent is obtained, thus confirming the robustness of the coalescent. Many population structure models have been shown to converge to the structured coalescent (see Herbots (1997), Hudson (1998). Nordborg (2001), Nordborg and Krone (2002), and Notohara (1990)).

Most animal species show detectable genetic differentiation between populations, but the extent and pattern of this differentiation varies considerably between species. Some show gradual differentiation due to isolation by distance, some show chaotic patchiness, and some show relative uniformity over large distances with striking discontinuities over short distances. These varying patterns reflect both the dispersal powers of the organism and its population history. The evolution of locally adapted genotypes is facilitated in populations with restricted gene flow, and such co-adapted genotypes may then vary from population to population depending on local selective forces. Restocking and stock enhancement programmes need to be aware of the stock structure of the target species, as the introduction of genotypes unrepresentative of the augmented population can have negative effects. Swamping the native population with large numbers of genotypes from a few matings, even if derived from the native population, can also be detrimental. It follows that, wherever possible, restocking and stock enhancement programmes should use broodstock taken directly from the population to be enhanced, and that large numbers of broodstock should be used. If broodstock cannot be taken from the population to be enhanced, they should be taken from the genetically most similar population available. Restocking and stock enhancement programmes should be genetically monitored to determine their impacts and outcomes. Crown Copyright (c) 2006 Published by Elsevier B.V. All rights reserved.

Despite the considerable evidence showing that dispersal between habitat patches is often asymmetric, most of the metapopulation models assume symmetric dispersal. In this paper, we develop a Monte Carlo simulation model to quantify the effect of asymmetric dispersal on metapopulation persistence. Our results suggest that metapopulation extinctions are more likely when dispersal is asymmetric. Metapopulation viability in systems with symmetric dispersal mirrors results from a mean field approximation, where the system persists if the expected per patch colonization probability exceeds the expected per patch local extinction rate. For asymmetric cases, the mean field approximation underestimates the number of patches necessary for maintaining population persistence. If we use a model assuming symmetric dispersal when dispersal is actually asymmetric, the estimation of metapopulation persistence is wrong in more than 50% of the cases. Metapopulation viability depends on patch connectivity in symmetric systems, whereas in the asymmetric case the number of patches is more important. These results have important implications for managing spatially structured populations, when asymmetric dispersal may occur. Future metapopulation models should account for asymmetric dispersal, while empirical work is needed to quantify the patterns and the consequences of asymmetric dispersal in natural metapopulations.

We used mitochondrial DNA ( mtDNA) sequences to investigate the demographic history of the wood stork (Mycteria americana) populations in the Brazilian Pantanal. Sequences of 390/460 bp fragment of the mtDNA control region were analyzed in 62 wood stork specimens from 8 colonies using neutrality tests, phylogeographic, and coalescent analyses. Population expansion was supported by the significantly negative values of Tajima's (D = -2.071) and Fu's (Fs = -14.544) statistics and the unimodal pattern of mismatch distribution. Nested clade analyses indicated a historic range expansion event and recurrent gene flow that was restricted by isolation by distance as explanations for the haplotype distribution among the sampled colonies. High genetic diversity and the strictly unidirectional gene flow pattern emphasized the conservation importance of preserving the southern Pantanal colonies. Coalescence analyses suggested that northern and southern colonies diverged approximately 6,250 years before the present (YBP), and that their most recent common ancestor was approximately 18,900 YBP. Our results suggest that the contemporary wood stork Pantanal population originated from a more geographically limited founder population. Potential source populations may have occurred in the southern Pantanal or ancestry may reside in populations inhabiting the Brazilian central plateau or areas closer to the equatorial region.

Island species, particularly endemics, tend to have lower genetic diversity than their continental counterparts. The low genetic variability of endemic species and small populations has a direct impact on the evolutionary potential of those organisms to cope with changing environments. We studied the genetic population structure and morphological differentiation among island populations of the Galapagos Dove (Zenaida galapagoensis). Doves were sampled from five islands: Santa Fe, Santiago, Genovesa, Espanola, and Santa Cruz. Five microsatellite markers were used to determine genetic diversity, population structure, gene how, and effective population sizes. F-ST and R-ST values did not differ among populations; in general, populations with greater geographical separation were not more genetically distinct than those closer to one another, and estimated gene flow was high. There were no significant differences in allelic richness and gene diversity among populations. Although there was extensive morphological overlap among individuals from different island populations for both males and females, we found significant differences in overall body size only between populations on Santa Fe and Santa Cruz (males and females) and between Espahola and Santa Fe (males only). Significant differences in body size between populations undergoing high rates of gene flow indicate that differentiation may be due to either phenotypic plasticity or ecotypic differentiation. Based on the results of previously conducted disease surveys, we discuss the conservation implications for the Galapagos Dove and other endemics of the archipelago; we also discuss the possible effects of wind currents on gene flow.

information on the initial stages of dispersal and settlement are of great interest in understanding the dynamics of biological invasions and in designing management responses. A newly settled population of the Lessepsian rabbitfish migrant Siganus luridus, that arrived in Linosa Island (Sicily Strait) in 2000, offered a unique opportunity to examine the genetic variability of the early phase of invasion and the starting point to test genetic variation within and between colonist and source populations. Demographics and dynamic aspects of S. luridus in the Mediterranean were evaluated by using phylogeographic and demographic (coalescent) methods based on DNA sequences of the mitochondrial control region. Sequences from 95 S. luridus, 25 Siganus rivulatus, and one of Siganus (Lo) vulpinus and S. doliatus were used. Samples were collected in one locality in the Red Sea (Eilat) and three localities in the Mediterranean (Israel, Greece and Linosa, Italy). Data showed (for the first time in a Lessepsian migrant) a lowering of the genetic diversity of the invading population (Mediterranean) (haplotype diversity 0.879, nucleotide diversity 0.592) compared to the parental one (Red Sea) (haplotype diversity 0.978, nucleotide diversity 0.958). Within the Mediterranean populations, there was no pattern of regional separation and mitochondrial diversity appeared to be preserved during the Linosa colonization, with no traces of founder events. Such evidence agrees with the idea that Lessepsian migration involves many individuals from its earliest stages. (c) 2005 Elsevier B.V. All rights reserved.

We have added two software tools to our Suite of Nucleotide Analysis Programs (SNAP) for working with DNA sequences sampled from populations. SNAP Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map includes novel features such as recoding insertions or deletions, including or excluding variable sites that violate an infinite-sites model and the option of collapsing sequences with corresponding phenotypic information, important in testing for significant haplotype-phenotype associations. SNAP Combine merges multiple DNA sequence alignments into a single multiple alignment file. The resulting file can be the union or intersection of the input files. SNAP Combine currently reads from and writes to several sequence alignment file formats including both sequential and interleaved formats. Combine also keeps track of the start and end positions of each separate alignment file allowing the user to exclude variable sites or taxa, important in creating input files for multilocus analyses.

Microsatellites are frequently used to infer population structure and demographic history. Contrary to DNA sequence data, only very limited simulation software is currently available for microsatellites. The `ms-program' is an advanced computer simulation tool for sequence data under a broad range of demographic models. We report a PERL script that converts the output of the ms-program into microsatellite data. The ms2ms PERL script generates an output file that could be read by the microsatellite analyser software to calculate the desired summary statistics.

The historic processes which have led to the present-day patterns of genetic structure in the marine coastal fauna of the Northeast Atlantic are still poorly understood. While tectonic uplifts and changes in sea level may have caused large-scale vicariance, warmer conditions during glacial maxima may have allowed pockets of diversity to persist to a much wider extent than in the Northwestern Atlantic. The large-scale geographic distribution of deeply divergent lineages of the coastal polychaete tubeworms Pectinaria koreni (two clades) and Owenia fusiformis (three clades) were compared using a fragment of the mitochondrial cytochrome oxidase I gene (mtCOI). All lineages were present along the biogeographic transition zone on the north coast of Brittany (France) and we found evidence pointing towards congruence in the timing of cladogenic events between Pectinaria sp. (P. auricoma/P. belgica and P. koreni) and Owenia sp., suggesting a shared history of vicariant events. More conserved 16SrRNA sequences obtained from four species of Pectinariidae together with mtCOI sequences of P. koreni seem consistent with an initial establishment of pectinariids in the north, and a southward colonization of the Northeast Atlantic. Phylogeographic patterns in O. fusiformis were also consistent with a north/south pattern of lineage splitting and congruent levels of divergence were detected between lineages of both species. We observed signatures of both persistence in small northern glacial refugia, and of northwards range expansion from regions situated closer to the Mediterranean. However, whether the recolonization of the Northeast Atlantic by both species actually reflects separate interglacial periods is unclear with regards to the lack of molecular clock calibration in coastal polychaete species.

Locating birthplaces using genetic parentage determination can increase the precision and accuracy with which animal dispersal patterns are established. We re-analyse patterns of movement away from the birthplace as a function of time, sex and population density for a sample of 303 banner-tailed kangaroo rats, Dipodomys spectabilis. We located birth sites using a combination of likelihood-based parentage analysis with live-trapping of mothers during the breeding season. The results demonstrate that natal-breeding site distances are density dependent in this species; in particular, both sexes emigrate earlier in the year, and females disperse farther than males, at low population densities. Banner-tailed kangaroo rats were chosen as a study system because live-trapping easily detects maternal and offspring locations; nevertheless, parentage analysis reveals that some offspring evade early detection and move substantial distances before their first capture. In a few cases, the approach even detects dispersal out of the natal `deme' prior to first capture. Parentage analysis confirms the extreme philopatry of both sexes but indicates that prior estimates of median dispersal distance were too low. For D. spectabilis, more accurate location of individual birthplaces clarifies patterns of sex bias and density dependence in dispersal, and may resolve apparent discrepancies between direct and indirect estimates of dispersal distance. For species in which mothers can be more reliably trapped than juveniles, using offspring genotypes to locate parents is a novel way that genetic techniques can contribute to the analysis of animal dispersal.

The population genetic structure of the crimson snapper Lutjanus erythropterus in East Asia was examined with a 427-bp hypervariable portion of the mtDNA control region. A total of 262 samples were collected and 75 haplotypes were obtained. Neutrality tests (Tajima's and Fu's) suggested that Lutjanus erythropterus in East Asia had experienced a bottleneck followed by population expansion since the late Pleistocene. Despite the low phylogeographic structures in mtDNA haplotypes, a hierarchical examination of populations in 11 localities from four geographical regions using analysis of molecular variance (AMOVA) indicated significant genetic differentiation among regions (Phi(CT) = 0.08564, p < 0.01). Limited gene flow between the eastern region (including a locality in the western Pacific Ocean and two localities in the East Sea) and three geographic regions of the South China Sea largely contributed to the genetic subdivision. However, comparisons among three geographic regions of the South China Sea showed little to no genetic difference. Populations of Lutjanus erythropterus in East Asia are inferred to be divided into two major groups: an eastern group, including populations of the western Pacific Ocean and the East Sea, and a South China Sea group, consisting of populations from northern Malaysia to South China. The results suggest that fishery management should reflect the genetic differentiation and diversity in East Asia. (c) 2006 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.

The traditional view of the species as the fundamental unit of evolution has been challenged by observations that in heterogeneous environments, gene flow may be too restricted to overcome the effects of local selection. Whether a species evolves as a cohesive unit depends critically on the dynamic balance between homogenizing gene flow among populations and potentially disruptive local adaptation. To examine this evolutionary balance between “global” gene flow and local selection, we studied northern Californian populations of Helianthus exilis, the serpentine sunflower, within a mosaic of contrasting serpentine and nonserpentine areas that differ considerably in soil chemistry and water availability. Local adaptation to riparian and serpentine habitats was studied in Helianthus exilis along with an analysis of gene flow patterns among populations within these habitats. Local adaptation was assessed in H. exilis during 2002 and 2003 using reciprocal transplant experiments at multiple locations within serpentine and riparian habitats. Effects of competition and germination date on the expression of local adaptation were also examined within the reciprocal transplant experiments. Local adaptation was detected in both years at the local site level and at the level of habitat. The analysis of the transplanted populations indicated that the patterns of selection differed considerably between riparian and serpentine sites. Differential survivorship occurred in serpentine habitats, whereas selection on reproductive output predominated in riparian habitats. Local adaptation was expressed only in the absence of competition. Local adaptation in terms of survivorship was most strongly expressed in treatments with delayed seed germination. Microsatellite markers were used to quantify population genetic parameters and examine the patterns of gene flow among sampled populations. Analysis of molecular markers revealed a system of population patches that freely exchange genes with each other. Strong selection seems to maintain ecotypic variation within this endemic sunflower species, while extensive gene flow among populations prevents local speciation between serpentine and riparian ecotypes.

We expand a coalescent-based method that uses serially sampled genetic data from a subdivided population to incorporate changes to the number of demes and patterns of colonization. Often, when estimating population parameters or other parameters of interest from genetic data, the demographic structure and parameters are not constant over evolutionary time. In this paper, we develop a Bayesian Markov chain Monte Carlo method that allows for step changes in mutation, migration, and population sizes, as well as changing numbers of demes, where the times of these changes are also estimated. We show that in parameter ranges of interest, reliable estimates can often be obtained, including the historical times of parameter changes. However, posterior densities of migration rates can be quite diffuse and estimators somewhat biased, as reported by other authors.

Management interventions to halt the decline and restore productivity of coastal fisheries in developing countries are increasingly becoming spatially explicit and focused on local scales. As policies in these countries gravitate towards local management, knowledge of the extent to which the local management units are dependent or independent of others becomes essential to the success of any intervention. Defining resource boundaries and measuring connectivity in the marine environment, however, has not been easy. Asian developing countries, where the capability to use molecular genetic tools in fisheries and aquaculture has escalated in the last few years, are exploring the use of genetic markers as a means to obtain the elusive answers. The challenge is to test the potential of molecular methods and their usefulness to provide some indication of resource boundaries and connectivity among management units in the context of developing countries. The paper presents a brief summary of the available methods to determine connectivity using genetic markers and two examples where they have been applied in Southeast Asia. Recommendations for the more efficient conduct of the research based on the experiences from these projects are presented. (c) 2006 Elsevier B.V. All rights reserved.

Bigeye (Thunnus obesus) is a large, pelagic, and migratory species of tuna that inhabits tropical and temperate marine waters worldwide. Previous studies based on mitochondrial RFLP data have shown that bigeye tunas from the Atlantic Ocean are the most interesting from a genetic point of view. Two highly divergent mitochondrial haplotype clades (I and II) coexist in the Atlantic Ocean. One is almost exclusive of the Atlantic Ocean whereas the other is also found in the Indo-Pacific Ocean. Bigeye tuna from the Atlantic Ocean is currently managed as a single stock, although this assumption remains untested at the genetic level. Therefore, genetic diversity was determined at the mitochondrial control region to test the null hypothesis of no population structure in bigeye tuna from the Atlantic Ocean. A total of 331 specimens were sampled from four locations in the Atlantic Ocean (Canada, Azores, Canary Islands, and Gulf of Guinea), and one in the Indian and Pacific Oceans, respectively. The reconstructed neighbor-joining phylogeny confirmed the presence of Clades I and II throughout the Atlantic Ocean. No apparent latitudinal gradient of the proportions of both clades in the different collection sites was observed. Hierarchical AMOVA tests and pairwise phi(ST) comparisons involving Atlantic Ocean Clades I and II were consistent with a single stock of bigeye tuna in the Atlantic Ocean. Population genetic analyses considering phylogroups independently supported gene flow within Clade II throughout the Atlantic Ocean, and within Clade I between Atlantic and Indo-Pacific Oceans. The latter result suggests present uni-directional gene flow from the Indo-Pacific into the Atlantic Ocean. Moreover, mismatch analyses dated divergence of Clades I and II during the Pleistocene, as previously proposed. In addition, migration rates were estimated using coalescent methods, and showed a net migration from Atlantic Ocean feeding grounds towards the Gulf of Guinea, the best-known spawning ground of Atlantic bigeye tuna. (c) 2005 Elsevier Inc. All rights reserved.

Marine invertebrates with high larval dispersal capacity typically exhibit low degrees of population differentiation, which reflects both contemporary and historical processes. We sampled 346 individuals from seven populations of the lined shore crab, Pachygrapsus crassipes Randall, along the northeastern Pacific Coast and Korea during summer 2003. DNA sequence analysis of 613 bp of the mitochondrial COI gene showed that overall gene diversity (h) was high (0.92 +/- 0.01), whereas overall nucleotide diversity (pi) was low (0.009 +/- 0.005). A total of 154 mtDNA haplotypes were identified; however, 114 were present in only one individual. Analysis of molecular variance revealed significant genetic structuring at Point Conception, CA, USA, that is likely due to the oceanographic circulation patterns, which result in asymmetrical migration of haplotypes. However, genetic variation among eastern Pacific populations was generally low, probably because of high contemporary gene flow and recent common ancestry of haplotypes. Mismatch analysis and nested clade analysis suggested that the population history of this region is characterized by two contiguous northwards range expansions, which are congruent with Late Pleistocene glacial cycles. Highly significant genetic differentiation was detected between eastern Pacific populations and Korea, indicating transpacific gene flow is restricted. Time of divergence between the two transpacific lineages was estimated between 0.8 and 1.2 Myrs ago. The small, recently founded population of P. crassipes at Bamfield, BC, Canada, did not appear to have undergone a founder effect.

Geneticists seeking to understand HIV-1 evolution among human hosts generally assume that hosts represent a panmictic population. Social science research demonstrates that the network patterns over which HIV-1 spreads are highly nonrandom, but the effect of these patterns Oil the genetic diversity of HIV-1 and other sexually transmitted pathogens has yet to be thoroughly examined. In addition, interhost phylogenetic models rarely account explicitly for genetic diversity arising from intrahost dynamics. This study outlines a graph-theoretic framework (exponential random graph modeling, ERGN4) for the estimation, inference, and simulation of dynamic partnership networks. This approach is used to simulate HIV-1 transmission and evolution under eight mixing patterns resembling those observed in empirical human populations, while simultaneously incorporating intrahost viral diversity. Models of parametric growth fit panmictic Populations well, yielding estimates of total viral effective population oil the order of the product of infected host size an intrahost effective viral population size. Populations exhibiting patterns of nonrandom mixing differ more widely in estimates of effective population size they yield, however, and reconstructions of population dynamics call exhibit severe errors if panmixis is assumed. I discuss implications for HIV-1 phylogenetics and the potential for ERGM to provide a general framework for addressing these issues.

Genetic structure of the seagrass Zostera marina in a coastal lagoon with restricted water flow, and with heterogeneous water residence times and oceanographic characteristics, was assessed using 8 polymorphic microsatellite loci. Analyses of genetic differentiation (theta) and Bayesian clustering suggested that the Z. marina population in San Quintin Bay (SQB) is genetically substructured, with at least 4 genetically different groups; (1) West Head, (2) Mouth, (3) East Arm, and (4) East Head. The greatest theta value was observed between the most distant sites (theta = 0.095). The lowest values were found among sites closest to the mouth of the coastal lagoon (theta = 0.000 to 0.009). The maximum likelihood approach showed that the sites at the mouth have a mixed pattern of gene flow without a unidirectional pattern. In contrast, there was a clear pattern of asymmetrical gene flow from the mouth towards the West Head. These results suggested that the restriction of water flow at the heads, current pattern, and the distance between sites can reduce genetic flow and promote genetic differences within Z. marina meadows in small water embayments such as SQB. Though the population is genetically substructured and a 14% decline in cover has been detected, this study did not show evidence of a recent genetic bottleneck. In contrast, mouth sites have experienced a recent expansion in their population size, and also perhaps a recent influx of rare alleles from genetically distinct immigrants.

Divergent habitat preferences can contribute to speciation, as has been observed for host-plant preferences in phytophagous insects. Geographic variation in host preference can provide insight into the causes of preference evolution. For example, selection against maladaptive host-switching occurs only when multiple hosts are available in the local environment and can result in greater divergence in regions with multiple vs. a single host. Conversely, costs of finding a suitable host can select for preference even in populations using a single host. Some populations of Timema cristinae occur in regions with only one host-plant species present (in allopatry, surrounded by unsuitable hosts) whereas others occur in regions with two host-plant species adjacent to one another (in parapatry). Here, we use host choice and reciprocal-rearing experiments to document genetic divergence in host preference among 33 populations of T. cristinae. Populations feeding on Ceanothus exhibited a stronger preference for Ceanothus than did populations feeding on Adenostoma. Both allopatric and parapatric pairs of populations using the different hosts exhibited divergent host preferences, but the degree of divergence tended to be greater between allopatric pairs. Thus, gene flow between parapatric populations apparently constrains divergence. Host preferences led to levels of premating isolation between populations using alternate hosts that were comparable in magnitude to previously documented premating isolation caused by natural and sexual selection against migrants between hosts. Our findings demonstrate how gene flow and different forms of selection interact to determine the magnitude of reproductive isolation observed in nature.

We review commonly used population definitions under both the ecological paradigm (which emphasizes demographic cohesion) and the evolutionary paradigm (which emphasizes reproductive cohesion) and find that none are truly operational. We suggest several quantitative criteria that might be used to determine when groups of individuals are different enough to be considered `populations'. Units for these criteria are migration rate (m) for the ecological paradigm and migrants per generation (Nm) for the evolutionary paradigm. These criteria are then evaluated by applying analytical methods to simulated genetic data for a finite island model. Under the standard parameter set that includes L = 20 High mutation (microsatellite-like) loci and samples of S = 50 individuals from each of n = 4 subpopulations, power to detect departures from panmixia was very high (similar to 100%; P < 0.001) even with high gene flow (Nm = 25). A new method, comparing the number of correct population assignments with the random expectation, performed as well as a multilocus contingency test and warrants further consideration. Use of Low mutation (allozyme-like) markers reduced power more than did halving S or L. Under the standard parameter set, power to detect restricted gene flow below a certain level X (H-0: Nm < X) can also be high, provided that true Nm <= 0.5X. Developing the appropriate test criterion, however, requires assumptions about several key parameters that are difficult to estimate in most natural populations. Methods that cluster individuals without using a priori sampling information detected the true number of populations only under conditions of moderate or low gene flow (Nm <= 5), and power dropped sharply with smaller samples of loci and individuals. A simple algorithm based on a multilocus contingency test of allele frequencies in pairs of samples has high power to detect the true number of populations even with Nm = 25 but requires more rigorous statistical evaluation. The ecological paradigm remains challenging for evaluations using genetic markers, because the transition from demographic dependence to independence occurs in a region of high migration where genetic methods have relatively little power. Some recent theoretical developments and continued advances in computational power provide hope that this situation may change in the future.

Background: Molecular genetic approaches have much to offer population biology. Despite recent advances, convenient techniques to develop and screen highly-resolving markers can be limiting for some applications and taxa. We describe an improved PCR-based, cloning-free, nuclear marker development procedure, in which single-stranded conformation polymorphism ( SSCP) plays a central role. Sequence-variable alleles at putative nuclear loci are simultaneously identified and isolated from diploid tissues. Based on a multiple allele alignment, locus-specific primers are designed in conserved regions, minimizing `null' alleles. Using two undescribed endemic Australian Collembola as exemplars, we outline a comprehensive approach to generating and validating suites of codominant, sequence-yielding nuclear loci for previously unstudied invertebrates. Results: Six markers per species were developed without any baseline genetic information. After evaluating the characteristics of each new locus via SSCP pre-screening, population samples were genotyped on the basis of either DNA sequence, restriction site, or insertion/deletion variation, depending on which assay was deemed most appropriate. Polymorphism was generally high ( mean of nine alleles per locus), and the markers were capable of resolving population structuring over very fine spatial scales (< 100 km). SSCP coupled with targeted DNA sequencing was used to obtain genotypic, genic and genealogical information from six loci ( three per species). Phylogeographic analysis identified introns as being most informative. Conclusion: The comprehensive approach presented here feasibly overcomes technical hurdles of ( i) developing suitably polymorphic nuclear loci for non-model organisms, ( ii) physically isolating nuclear allele haplotypes from diploid tissues without cloning, and ( iii) genotyping population samples on the basis of nuclear DNA sequence variation.

Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of statistical and computational methods that infer haplotype phase from genotype data. Although a substantial number of such methods have been developed, they have focused principally on inference from unrelated individuals, and comparisons between methods have been rather limited. Here, we describe the extension of five leading algorithms for phase inference for handling father-mother-child trios. We performed a comprehensive assessment of the methods applied to both trios and to unrelated individuals, with a focus on genomic-scale problems, using both simulated data and data from the HapMap project. The most accurate algorithm was PHASE (v2.1). For this method, the percentages of genotypes whose phase was incorrectly inferred were 0.12%, 0.05%, and 0.16% for trios from simulated data, HapMap Centre d'Etude du Polymorphisme Humain (CEPH) trios, and HapMap Yoruban trios, respectively, and 5.2% and 5.9% for unrelated individuals in simulated data and the HapMap CEPH data, respectively. The other methods considered in this work had comparable but slightly worse error rates. The error rates for trios are similar to the levels of genotyping error and missing data expected. We thus conclude that all the methods considered will provide highly accurate estimates of haplotypes when applied to trio data sets. Running times differ substantially between methods. Although it is one of the slowest methods, PHASE (v2.1) was used to infer haplotypes for the 1 million-SNP HapMap data set. Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was similar to 0.8.

Volcanic islands represent excellent models with Which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galapagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in die Galapagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus genotyping method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals.

We used molecular methods and population genetic analyses to study the effects of chronic contaminant exposure in marsh frogs from Sumgayit, Azerbaijan. Marsh frogs inhabiting wetlands in Sumgayit are exposed to complex mixtures of chemical contaminants, including petroleum products, pesticides, heavy metals, and many other industrial chemicals. Previous results documented elevated estimates of genetic damage in marsh frogs front the two most heavily, contaminated sites. Based oil mitochondrial DNA (mtDNA) control region sequence data, the Sumgayit region has reduced levels of genetic diversity, likely due to environmental degradation. The Sumgayit region also acts as all ecological sink, with levels of gene flow into the region exceeding gene flow out of the region. Additionally, localized mtDNA heteroplasmy and diversity patterns suggest that one of the most severely contaminated sites in Sumgayit is acting as a source of new mutations resulting from an increased mutation rate. This Study provides an integrated method for assessing the cumulative population impacts of chronic contaminant exposure by Studying both population genetic and evolutionary effects.

The effective population Size (N-e) provides information on how fast genetic variation is being lost, or relatedness is increasing, in a population of interest. This parameter is often considered to be related to population viability. Genetic approaches offer several avenues for estimating N-e; recent developments have helped relax assumptions of closed populations and stable population sizes that have hindered the estimation of N-e in many wildlife Populations. The most promising areas of development are in the assessment of temporal changes in genetic composition for the estimation of contemporary N-e and the application of coalescent theory for estimation of historical N-e. Application of most estimators still requires making some questionable assumptions about wildlife populations. In general, these methods will be most beneficial when used in conjunction with Current and historical demographic information.

Three-spined sticklebacks (Gasterosteus aculeatus) are a powerful evolutionary model system due to the rapid and repeated phenotypic divergence of freshwater forms from a marine ancestor throughout the Northern Hemisphere. Many of these recently derived populations are found in overlapping habitats, yet are reproductively isolated from each other. This scenario provides excellent opportunities to investigate the mechanisms driving speciation in natural populations. Genetically distinguishing between such recently derived species, however, can create difficulties in exploring the ecological and genetic factors defining species boundaries, an essential component to our understanding of speciation. We overcame these limitations and increased the power of analyses by selecting highly discriminatory markers from the battery of genetic markers now available. Using species diagnostic molecular profiles, we quantified levels of hybridization and introgression within three sympatric species pairs of three-spined stickleback. Sticklebacks within Priest and Paxton lakes exhibit a low level of natural hybridization and provide support for the role of reinforcement in maintaining distinct species in sympatry. In contrast, our study provides further evidence for a continued breakdown of the Enos Lake species pair into a hybrid swarm, with biased introgression of the `limnetic' species into that of the `benthic'; a situation that highlights the delicate balance between persistence and breakdown of reproductive barriers between young species. A similar strategy utilizing the stickleback microsatellite resource can also be applied to answer an array of biological questions in other species' pair systems in this geographically widespread and phenotypically diverse model organism.

There is now increasing acceptance that divergence of phenotypic traits, and the genetic structuring that underlie such divergence, can occur in sympatry. Here we report the serendipitous discovery of a sympatric polymorphism in the upper Forth catchment, Scotland, in a species for which high levels of phenotypic variation have been reported previously, the Arctic charr, Salvelinus alpinus. Attempting to determine the proximate mechanisms through which this pattern of phenotypic variation is maintained, we examine the use of the available feeding resource and the genotypic and phenotypic structure of charr in this system. We show clear differences in head morphology between charr from three very closely connected lakes with no barrier to movement (Lochs Doine, Voil and Lubnaig) and also differences in muscle stable isotope signatures and in stomach contents. There were significant differences at 6 microsatelite loci (between Lubnaig and the other two lochs) and very low estimates of effective migration between populations. We conclude that, despite living in effective sympatry, strong genetic and phenotypic sub-structuring is likely maintained by very high levels of site fidelity, especially during spawning, resulting in functional allopatric divergence of phenotype.

We present a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates population genetic parameters from genetic data. LAMARC can co-estimate subpopulation Theta = 4N(e)mu, immigration rates, subpopulation exponential growth rates and overall recombination rate, or a user-specified subset of these parameters. It can perform either maximum-likelihood or Bayesian analysis, and accomodates nucleotide sequence, SNP, microsatellite or elecrophoretic data, with resolved or unresolved haplotypes. It is available as portable source code and executables for all three major platforms.

Studies of the genetic covariance between habitat preference and performance have reported conflicting outcomes ranging from no covariance to strong covariance. The causes of this variability remain unclear. Here we show that variation in the magnitude of genetic covariance can result from variability in migration regimes. Using data from walking stick insects and a mathematical model, we find that genetic covariance within populations between host plant preference and a trait affecting performance on different hosts ( cryptic color pattern) varies in magnitude predictably among populations according to migration regimes. Specifically, genetic covariance within populations is high in heterogeneous habitats where migration between populations locally adapted to different host plants generates nonrandom associations ( i. e., linkage disequilibrium) between alleles at color pattern and host preference loci. Conversely, genetic covariance is low in homogeneous habitats where a single host exists and migration between hosts does not occur. Our results show that habitat structure and patterns of migration can strongly affect the evolution and variability of genetic covariance within populations.

A computer simulation study has been made of the accuracy of estimates of Theta = 4N(e)mu from a sample from a single isolated population of finite size. The accuracies turn out to be well predicted by a formula developed by Fu and Li, who used optimistic assumptions. Their formulas are restated in terms of accuracy, defined here as the reciprocal of the squared coefficient of variation. This should be proportional to sample size when the entities sampled provide independent information. Using these formulas for accuracy, the sampling strategy for estimation of Theta can be investigated. Two models for cost have been used, a cost-per-base model and a cost-per-read model. The former would lead us to prefer to have a very large number of loci, each one base long. The latter, which is more realistic, causes us to prefer to have one read per locus and an optimum sample size which declines as costs of sampling organisms increase. For realistic values, the optimum sample size is 8 or fewer individuals. This is quite close to the results obtained by Pluzhnikov and Donnelly for a cost-per-base model, evaluating other estimators of Theta It can be understood by considering that the resources spent collecting larger samples prevent us from considering more loci. An examination of the efficiency of Watterson's estimator of Theta was also made, and it was found to be reasonably efficient when the number of mutants per generation in the sequence in the whole population is less than 2.5.

A central prediction of the geographic mosaic theory of coevolution is that coevolving interspecific interactions will show varying degrees of local maladaptation. According to the theory, much of this local maladaptation is driven by selection mosaics and spatially intermingled coevolutionary hot and cold spots, rather than a simple balance between gene flow and selection. Here I develop a genetic model of host-parasite coevolution that is sufficiently general to incorporate selection mosaics, coevolutionary hot and cold spots, and a diverse array of genetic systems of infection/resistance. Results from this model show that the selection mosaics experienced by the interacting species are an important determinant of the sign and magnitude of local maladaptation. In some cases, this effect may be stronger than a previously described effect of relative rates of parasite and host gene flow. These results provide the first theoretical evidence that selection mosaics and coevolutionary hot and cold spots per se determine the magnitude and sign of local maladaptation. At the same time, however, these results demonstrate that coevolution in a geographic mosaic can lead to virtually any pattern of local adaptation or local maladaptation. Consequently, empirical studies that describe only patterns of local adaptation or maladaptation do not provide evidence either for or against the theory.

Comparison of the performance and accuracy of different inference methods, such as maximum likelihood (ML) and Bayesian inference, is difficult because the inference methods are implemented in different programs, often written by different authors. Both methods were implemented in the program MIGRATE, that estimates population genetic parameters, such as population sizes and migration rates, using coalescence theory. Both inference methods use the same Markov chain Monte Carlo algorithm and differ from each other in only two aspects: parameter proposal distribution and maximization of the likelihood function. Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance. Motivation: The Markov chain Monte Carlo-based ML framework can fail on sparse data and can deliver non-conservative support intervals. A Bayesian framework with appropriate prior distribution is able to remedy some of these problems. Results: The program MIGRATE was extended to allow not only for ML(-) maximum likelihood estimation of population genetics parameters but also for using a Bayesian framework. Comparisons between the Bayesian approach and the ML approach are facilitated because both modes estimate the same parameters under the same population model and assumptions.

The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.

Comparisons across multiple taxa can often clarify the histories of biogeographic regions. In particular, historic barriers to movement should have affected multiple species and, thus, result in a pattern of concordant intraspecific genetic divisions among species. A striking example of such comparative phylogeography is the recent observation that populations of many small mammals and reptiles living on the Baja California peninsula have a large genetic break between northern and southern peninsular populations. In the present study, I demonstrate that five species of near-shore fishes living on the Baja coastline of the Gulf of California share this genetic pattern. The simplest explanation for this concordant genetic division within both terrestrial and marine vertebrates is that the Baja Peninsula was fragmented by a Plio-Pleistocene marine seaway and that this seaway posed a substantial barrier to movement for near-shore fishes. For some fish species, the signal of this vicariance in mtDNA has been eroded by gene flow and is not evident with classic, equilibrium measures of population structure. Yet, significant divisions are apparent in coalescent analyses that jointly estimate divergence with gene flow. The genetic divisions within Gulf of California fishes also coincide with recognized biogeographic regions based on fish community composition and several environmental factors. It is likely that adaptation to regional environments and present-day oceanographic circulation limit gene exchange between biogeographic regions and help maintain evidence of past vicariance.

Although many studies have documented the effect of glaciation on the evolutionary history of Northern Hemisphere flora and fauna, this study is the first to investigate how the indirect aridification of Africa caused by global cooling in response to glacial cycles at higher latitudes has influenced the evolutionary history of an African montane bird. Mitochondrial DNA sequences from the NADH 3 gene were collected from 283 individual Starred Robins (Pogonocichla stellata, Muscicapoidea). At least two major vicariant events, one that separated the Albertine Rift from all but the Kenyan Highlands around 1.3-1.2 Myrs BP, and another that separated the Kenyan Highlands from the northern Eastern Arc, and the northern Eastern Are from the south-central Eastern Arc between 0.9 and 0.8 Myrs BP appear to underlie much of the observed genetic diversity and structure within Starred Robin populations. These dates of divergence suggest a lack of recurrent gene flow; although the Albertine Rift and south-central Eastern Arc share haplotypes, based on coalescent analyses this can confidently be accounted for by ancestral polymorphism as opposed to recurrent gene flow. Taken collectively, strong evidence exists for recognition of four major ancestral populations: (1) Kenyan Highlands (subspecies keniensis), (2) Albertine Rift (ruwenzori), (3) northern Eastern Are (helleri), and (4) south-central Eastern Arc, Ufipa and the Malawi Rift (orientalis). The estimated divergence times cluster remarkably around one of the three estimated peaks of aridification in Africa during the Plio-Pleistocene centred on I Myrs BP. Further, time to most recent common ancestor (TMRCA) estimates (1.7-1.6 Myrs BP) of gene divergence between the Albertine Rift and the other montane highlands corresponds closely with a second estimated peak of aridification at about 1.7 Myrs BP. Collectively, these results suggest that aridification of Africa in response to glaciation at higher latitudes during the Pleistocene has had a profound influence on montane speciation in east and central Africa. (c) 2005 Elsevier Inc. All rights reserved.

To determine effects of pulp mill effluent on population genetic structure, redbreast sunfish (Lepomis auritus) were collected from several sites along the Pigeon River, NC, as well as from reference sites. Previous studies found effects on molecular, biochemical, physiological, population, and community level endpoints in these populations. The population genetic structure of these fish was determined using the randomly amplified polymorphic DNA (RAPD) technique. The level of genetic diversity was higher in the Pigeon River populations than in the reference populations. Genetic distances among populations could not be explained by drainage patterns and may have been altered by contaminant exposure. Phylogeographic analysis, maximum likelihood analysis, and assignment tests suggested that there were fewer emigrants and more immigrants in the contaminated sites than in the reference sites, suggesting that the contaminated sites may harbor “sinklike” populations. Finally, a “terminal branch amplitype” analysis (neighbor-joining and minimum-spanning trees) and maximum likelihood analysis indicated that there may be an elevated mutation rate in the polluted sites. Thus, the genetic diversity (within and among populations) in the Pigeon River populations may have been affected by altered gene flow and mutational processes as a result of pulp mill effluent discharge.

There is a need for biological information to support current stock designations of bottlenose dolphins (Tursiops truncatus) in the Gulf of Mexico. The existence of many inshore, resident “communities” raises questions as to the relationship these dolphins may hold with dolphins inhabiting neighboring inshore and coastal areas. In this study, population subdivision was examined among four resident, inshore bottlenose dolphin stocks (Sarasota Bay, FL, Tampa Bay, FL, Charlotte Harbor, FL and Matagorda Bay, TX) and one coastal stock (1-12 km offshore) in the Gulf of Mexico. Evidence of significant population structure among all areas was found on the basis of both mitochondrial DNA (mtDNA) control region sequence data and nine nuclear microsatellite loci. Estimates of relatedness showed no population contained a significantly high number of related individuals, while separate AMOVAs for males and females indicated that both sexes exhibit a significant level of site philopatry. Results presented here provide the first genetic evidence of population subdivision between the coastal Gulf of Mexico and adjacent inshore areas along the central west coast of Florida. Such strong genetic subdivision is surprising given the short geographical distance between many of these areas and the lack of obvious geographic barriers to prevent gene flow. These findings support the current, separate identification of stocks for bottlenose dolphins inhabiting the eastern coastal and inshore areas of the Gulf of Mexico.

The yellow lampmussel (Lampsilis cariosa) is a rare unionid species in need of conservation, as it is declining throughout most of its Atlantic slope range in North America. Because freshwater mussels rely on a fish host for dispersal of their larvae, barriers to the movement of hosts, such as habitat fragmentation by dams, may indirectly affect population genetic structure. We used microsatellite loci to assess genetic variation for L. cariosa within and among three river drainages in the northern part of its range, which emerged from glaciation only similar to 8-10 kya. Despite this relatively recent emergence, significant differences were observed among populations both within and among drainages, possibly because low effective population sizes meant that populations of these mussels achieved drift-migration equilibrium rapidly following glaciation. L. cariosa individuals could be assigned to their own drainages with 89.3% accuracy. Among-population differences were modest, however, in comparison to differences observed in another study of rare mussels south of the recently glaciated region. L. cariosa populations exhibited significant isolation by distance, but there was no additional variation explained by the number, size, or age of intervening dams. An understanding of mussel population genetic structure provides information, useful for conservation planning, on patterns of isolation and connectivity among populations.

We present an expanded data set of 50 unlinked autosomal noncoding regions, resequenced in samples of Hausa from Cameroon, Italians, and Chinese. We use these data to make inferences about human demographic history by using a technique that combines multiple aspects of genetic data, including levels of polymorphism, the allele frequency spectrum, and linkage disequilibrium. We explore an extensive range of demographic parameters and demonstrate that our method of combining multiple aspects of the data results in a significant reduction of the compatible parameter space. In agreement with previous reports, we find that the Hausa data are compatible with demographic equilibrium as well as a set of recent population expansion models. In contrast to the Hausa, when multiple aspects of the data are considered jointly, the non-Africans depart from an equilibrium model of constant population size and are compatible with a range of simple bottleneck models, including a 50-90% reduction in effective population size occurring some time after the appearance of modern humans in Africa 160,000-120,000 years ago.

Two general processes may influence gene flow among populations. One involves divergent selection, wherein the maladaptation of immigrants and hybrids impedes gene flow between ecological environments (i.e. ecological speciation). The other involves geographic features that limit dispersal. We determined the relative influence of these two processes in natural populations of Trinidadian guppies (Poecilia reticulata). If selection is important, gene flow should be reduced between different selective environments. If geography is important, gene flow should be impeded by geographic distance and physical barriers. We examined how genetic divergence, long-term gene flow, and contemporary dispersal within a watershed were influenced by waterfalls, geographic distance, predation, and habitat features. We found that waterfalls and geographic distance increased genetic divergence and reduced dispersal and long-term gene flow. Differences in predation or habitat features did not influence genetic divergence or gene flow. In contrast, differences in predation did appear to reduce contemporary dispersal. We suggest that the standard predictions of ecological speciation may be heavily nuanced by the mating behaviour and life history strategies of guppies.

Testing for simultaneous vicariance across comparative phylogeographic data sets is a notoriously difficult problem hindered by mutational variance, the coalescent variance, and variability across pairs of sister taxa in parameters that affect genetic divergence. We simulate vicariance to characterize the behaviour of several commonly used summary statistics across a range of divergence times, and to characterize this behaviour in comparative phylogeographic datasets having multiple taxon-pairs. We found Tajima's D to be relatively uncorrelated with other summary statistics across divergence times, and using simple hypothesis testing of simultaneous vicariance given variable population sizes, we counter-intuitively found that the variance across taxon pairs in Nei and Li's net nucleotide divergence (pi(net)), a common measure of population divergence, is often inferior to using the variance in Tajima's D across taxon pairs as a test statistic to distinguish ancient simultaneous vicariance from variable vicariance histories. The opposite and more intuitive pattern is found for testing more recent simultaneous vicariance, and overall we found that depending on the timing of vicariance, one of these two test statistics can achieve high statistical power for rejecting simultaneous vicariance, given a reasonable number of intron loci (> 5 loci, 400 bp) and a range of conditions. These results suggest that components of these two composite summary statistics should be used in future simulation-based methods which can simultaneously use a pool of summary statistics to test comparative the phylogeographic hypotheses we consider here.

Amanita muscaria sensu lato has a wide geographic distribution, occurring in Europe, Asia, Africa, Australia, New Zealand, and North, Central and South America. Previous phylogenetic work by others indicates three geographic clades (i.e. `Eurasian', `Eurasian-alpine' and `North American' groups) within A. muscaria. However, the historical dispersal patterns of A. muscaria remained unclear. In our project, we collected specimens from arctic, boreal and humid temperate regions in Alaska, and generated DNA sequence data from the protein-coding beta-tubulin gene and the internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA repeat. Homologous sequences from additional A. muscaria isolates were downloaded from GenBank. We conducted phylogenetic and nested clade analyses (NCA) to reveal the phylogeographic history of the species complex. Although phylogenetic analyses confirmed the existence of the three above-mentioned clades, representatives of all three groups were found to occur sympatrically in Alaska, suggesting that they represent cryptic phylogenetic species with partially overlapping geographic distributions rather than being allopatric populations. All phylogenetic species share at least two morphological varieties with other species, suggesting ancestral polymorphism in pileus and wart colour pre-dating their speciations. The ancestral population of A. muscaria likely evolved in the Siberian-Beringian region and underwent fragmentation as inferred from NCA and the coalescent analyses. The data suggest that these populations later evolved into species, expanded their range in North America and Eurasia. In addition to range expansions, populations of all three species remained in Beringia and adapted to the cooling climate.

We describe an importance-sampling method for approximating likelihoods of population parameters based on multiple summary statistics. In this first application, we address the demographic history of closely related members of the Drosophila pseudoobscura group. We base the maximum-likelihood estimation of the time since speciation and the effective population sizes of the extant and ancestral populations on the pattern of nucleotide variation at DPS2002, a noncoding region tightly linked to a paracentric inversion that strongly contributes to reproductive isolation. Consideration of summary statistics rather than entire nucleotide sequences permits a compact description of the genealogy of the sample. We use importance sampling first to propose a genealogical and mutational history consistent with the observed array of summary statistics and then to correct the likelihood with the exact probability of the history determined from a system of recursions. Analysis of a subset of the data, for which recursive computation of the exact likelihood was feasible, indicated close agreement between the approximate and exact likelihoods. Our results for the complete data set also compare well with those obtained through Metropolis-Hastings sampling of fully resolved genealogies of entire nucleotide sequences.

Humpback whales seasonally migrate long distances between tropical and polar regions. However, inter-oceanic exchange is rare and difficult to document. Using skin biopsy samples collected in the Indian Ocean and in the South Atlantic Ocean, and a genetic capture-recapture approach based on microsatellite genotyping, we were able to reveal the first direct genetic evidence of the inter-oceanic migration of a male humpback whale. This exceptional migration to wintering grounds of two different ocean basins questions traditional notions of fidelity to an ocean basin, and demonstrates how the behaviour of highly mobile species may be elucidated from combining genetics with long-term field studies. Our finding has implications for management of humpback whale populations, as well as for hypotheses concerning cultural transmission of behaviour.

The migratory locust Locusta migratoria L., which is widely distributed throughout the world, exhibits within- and between-population variation in cold tolerance. TO Understand physiological adaptation in populations, we studied the genetic basis of thermotolerance in Hainan (tropical) and Liaoning (temperate) populations and measured expression of Hsp70 and Hsp90 mRNA in both populations at low (0 degrees C) and high temperatures (40 degrees C). Phenotypic variation of thermotolerance is heritable. Heritable characteristics differed among different stages of locust egg development, as well as among different measures of thermotolerance. Nuclear genetic factors, rather than cytoplasmic factors, contribute to differences in cold tolerance between the tropical and temperate Populations of the migratory locust; for heat tolerance, maternal effects were involved in three stages of egg development. Expression of Hsp90 mRNA was induced in temperate Population after heat shock (40 degrees C x 12 h), whereas expression of Hsp70 and 90 was induced in tropical Population after cold shock (0 degrees C x 12 h). We suggest that thermotolerance of locust eggs has a complex genetic basis and heat shock proteins may be involved in differences of thermotolerance between locust populations. (c) 2005 Elsevier Ltd. All rights reserved.

Information on population connectivity throughout the annual cycle has become more crucial, because populations of many migratory birds are in decline. One such species is the American Woodcock (Scolopax minor), which inhabits early-successional forests in eastern North America. Although band recoveries have proved useful for dividing populations of this game bird species into an Eastern Region and Central Region for management purposes, these data do not provide enough detail to determine the breeding population of origin of birds recovered on stopover and wintering areas. To obtain more fine-scale data, we undertook a phylogeographic study of American Woodcock populations throughout their primary breeding range in the eastern United States and Canada using mitochondrial DNA (mtDNA) sequences from the hypervariable control region I (CRI) and ND6 gene. Despite high haplotype diversity, nucleotide diversity was low and there was no phylogeographic structure among American Woodcock populations across the species range, with birds from many states and provinces in both management regions sharing identical haplotypes. Results suggest recent or ongoing gene flow among populations, with asymmetric movement of birds between migration flyways. As has been demonstrated for several other avian species in North America, American Woodcock appear to have undergone a rapid population expansion following the late Pleistocene glacial retreat. Thus, a combination of historical demographic factors and recent or ongoing gene flow mask any population structure based on mtDNA that might accrue from philopatry to breeding areas observed in studies of marked birds.

Population genetic structure can be shaped by multiple ecological and evolutionary factors, but the genetic consequences of these factors for multiple species inhabiting the same environment remain unexplored. We used microsatellite markers to examine the population structures of two coexisting species of garter snake, Thamnophis elegans and Thamnophis sirtalis, to determine if shared landscape and biology imposed similar population genetic structures. These snakes inhabit a series of ponds, lakes and flooded meadows in northern California and tend to converge on prey type wherever they coexist. Both garter snakes had comparable effective population sizes and bidirectional migration rates (estimated using a maximum-likelihood method based on the coalescent) with low but significant levels of genetic differentiation (F-ST = 0.024 for T. elegans and 0.035 for T. sirtalis). Asymmetrical gene flow revealed large source populations for both species as well as potential sinks, suggesting frequent extinction-recolonization and metapopulation dynamics. In addition, we found a significant correlation between their genetic structures based on both pairwise F(ST)s for shared populations (P = 0.009) and for bidirectional migration rates (P = 0.024). Possible ecological and evolutionary factors influencing similarities and differences in genetic structure for the two species are discussed. Genetic measures of effective population size and migration rates obtained in this study are also compared with estimates obtained from mark-recapture data.

The desiccation of the Mediterranean Sea during the Messinian Salinity Crisis 6.0-5.3 million years ago (Ma), caused a major extinction of the marine ichthyofauna of the Mediterranean. This was followed by an abrupt replenishment of the Mediterranean from the Atlantic after the opening of the Strait of Gibraltar. In this study, we combined demographic and phylogeographic approaches using mitochondrial and nuclear DNA markers to test the alternative hypotheses of where (Atlantic or Mediterranean) and when ( before or after the Messinian Salinity Crisis) speciation occurred in the Mediterranean damselfish, Chromis chromis. The closely related geminate transisthmian pair Chromis multilineata and Chromis atrilobata was used as a way of obtaining an internally calibrated molecular clock. We estimated C. chromis speciation timing both by determining the time of divergence between C. chromis and its Atlantic sister species Chromis limbata (0.93-3.26 Ma depending on the molecular marker used, e. g. 1.23-1.39 Ma for the control region), and by determining the time of coalescence for C. chromis based on mitochondrial control region sequences (0.14-0.21 Ma). The time of speciation of C. chromis was always posterior to the replenishment of the Mediterranean basin, after the Messinian Salinity Crisis. Within the Mediterranean, C. chromis population structure and demographic characteristics revealed a genetic break at the Peloponnese, Greece, with directional and eastbound gene flow between western and eastern groups. The eastern group was found to be more recent and with a faster growing population ( coalescent time = 0.09-0.13 Ma, growth = 485.3) than the western group ( coalescent time = 0.13-0.20 Ma, growth = 325.6). Our data thus suggested a western origin of C. chromis, most likely within the Mediterranean. Low sea water levels during the glacial periods, the hydrographic regime of the Mediterranean and dispersal restriction during the short pelagic larval phase of C. chromis (18-19 days) have probably played an important role in C. chromis historical colonization.

There has been much recent interest in the extent to which marine planktonic larvae connect local populations demographically and genetically. Uncertainties about the true extent of larval dispersal have impeded our understanding of the ecology and evolution of marine species as well as our attempts to effectively manage marine populations. Because direct measurements of larval movements are difficult, genetic markers have often been used for indirect measurements of gene flow among marine populations. Here we examine data from allozymes, mitochondrial DNA sequences, and microsatellite length polymorphisms to assess the extent of gene flow among populations of the burrowing crustacean Callichirus islagrande. All three types of markers revealed a genetic break between populations separated by the Louisiana Chenier Plain. The extent of mitochondrial sequence divergence across this break indicates that the nominal species, C. islagrande, consists of at least two lineages that have been reproductively isolated for about a million years. Within the eastern lineage microsatellite allele frequencies were significantly heterogeneous among populations as little as 10 km apart. Maximum likelihood estimates of gene flow and effective population size based on a coalescent model for the microsatellite data indicated that local populations are nearly closed. A model-based clustering method identified four or five groups from the microsatellite data, although individuals sampled from each location generally consisted of mixtures of these groups. This suggests a mechanism that would lead to genetic differentiation of open populations: gene flow from different source populations that are themselves genetically distinct.

The well-documented Floridian Gulf/Atlantic marine genetic disjunction provides an influential example of presumed vicariant cladogenesis along a continental coastline for major elements of a diverse nearshore fauna. However, it is unclear if this disjunction represents a local anomaly for regionally distributed morphospecies, or if it is merely one of many such cryptic phylogenetic splits that underlay their assumed genetic cohesiveness. We aimed to place the previously characterized scorched mussel Gulf/Atlantic genetic disjunction into a regional phylogenetic perspective by incorporating genotypes of nominal conspecifics sampled throughout the Caribbean Basin as well as those of eastern Pacific potential geminate species. Our results show it to be one of multiple latent regional genetic disjunctions, involving five cryptic Caribbean species, that appear to be the product of a long history of regional cladogenesis. Disjunctions involving three stem lineages clearly predate formation of the Isthmus of Panama and of the Caribbean Sea, although four of the five cryptic species have within-basin sister relationships. Surprisingly, the Atlantic clade was also found to be widespread in the southern Caribbean, and ancestral demography calculations through time for Atlantic coast-specific genotypes are consistent with a northward range extension after the last glacial maximum. Our new data seriously undermine the hypothesis of a Floridian vicariant genesis and imply that the scorched mussel Gulf/Atlantic disjunction represents a case of geographic and temporal pseudocongruence. All five Caribbean Basin cryptic species exhibited an intriguing pattern of predominantly allopatric distribution characterized by distinct geographic areas of ecological dominance, often adjoining those of sister taxa. This pattern of distribution is consistent with allopatric speciation origins, coupled with restricted postspeciation range extensions. Several lines of indirect evidence favor the hypothesis that the predominantly allopatric distributions are maintained over evolutionary time scales, primarily by postrecruitment ecological filters rather than by oceanographic barriers to larval-mediated gene flow.

The present study reports the first population genetic analysis of Arapaima gigas, an important but critically over-exploited fish species of the Amazon basin. We sequenced two discontinuous mitochondrial DNA regions of 1204 base-pairs (bp) (NADH1 segment) and 1143 bp (ATPase segment) from 139 individuals of A. gigas representing eight localities spanning the Amazon basin from Iquitos, Peru to Macap, Brazil. We discovered 34 haplotypes separated by 44 segregating sites. The two most common haplotypes are shared among all populations and isolation-by-distance appears to be the most important population dynamic, although there is no significant association between geographical distance and genetic differentiation. Observed patterns of differentiation appear to be attributable largely to anthropogenic factors associated with over-exploitation. Greatest haplotypic diversity exists upstream of Manaus and in areas away from large centres of population. The female variance and inbreeding effective population sizes are approximately 150000 individuals and localities in the Amazon basin are connected by gene flow. Naturally low levels of population differentiation and relatively high between-population connectivity is encouraging for the conservation and management of A. gigas. If strategically placed biological reserves were created throughout the Amazon basin to act as sources of emigrants within a source-sink metapopulation model, we believe locally depleted populations can be re-populated and maintained by individuals immigrating from these reserves.

Invasions by exotic organisms have had devastating affects on aquatic ecosystems, both ecologically and economically. One striking example of a successful invader that has dramatically affected fish community structure in freshwater lakes of North America is the sea lamprey (Petromyzon marinus). We used eight microsatellite loci and multiple analytical techniques to examine competing hypotheses concerning the origins and colonization history of sea lamprey (n = 741). Analyses were based on replicated invasive populations from Lakes Erie, Huron, Michigan, and Superior, populations of unknown origins from Lakes Ontario, Champlain, and Cayuga, and populations of anadromous putative progenitor populations in North America and Europe. Populations in recently colonized lakes were each established by few colonists through a series of genetic bottlenecks which resulted in lower allelic diversity in more recently established populations. The spatial genetic structure of invasive populations differed from that of native populations on the Atlantic coast, reflecting founder events and connectivity of invaded habitats. Anadromous populations were found to be panmictic (theta(rho) = 0.002; 95% CI = -0.003 - 0.006; P > 0.05). In contrast, there was significant genetic differentiation between populations in the lower and upper Great Lakes (theta(rho) = 0.007; P < 0.05; 95% CI = 0.003 - 0.009). Populations in Lakes Ontario, Champlain, and Cayuga are native. Alternative models that describe different routes and timing of colonization of freshwater habitats were examined using coalescent-based analyses, and demonstrated that populations likely originated from natural migrations via the St Lawrence River.

Although most genetic estimates of contemporary effective population size (N-e) are based on models that assume N-e is constant, in real populations N-e changes (often dramatically) over time, and estimates (N-e) will be influenced by N-e in specific generations. In such cases, it is important to properly match N-e to the appropriate time periods (for example, in computing N-e/N ratios). Here I consider this problem for semelparous species with two life histories (discrete generations and variable age at maturity - the `salmon' model), for two different sampling plans, and for estimators based on single samples (linkage disequilibrium, heterozygote excess) and two samples (temporal method). Results include the following. Discrete generations: (i) Temporal samples from generations 0 and t estimate the harmonic mean N-e in generations 0 through t - 1 but do not provide information about N-e in generation t; (ii) Single samples provide an estimate of N-e in the parental generation, not the generation sampled; (iii) single-sample and temporal estimates never provide information about N-e in exactly the same generations; (iv) Recent bottlenecks can downwardly bias estimates based on linkage disequilibrium for several generations. Salmon model: (i) A pair of single-cohort (typically juvenile) samples from years 0 and t provide a temporal estimate of the harmonic mean of the effective numbers of breeders in the two parental years (N-b(0) and N-b(t)), but adult samples are more difficult to interpret because they are influenced by N-b in a number of previous years; (ii) For single-cohort samples, both one-sample and temporal methods provide estimates of N-b in the same years (contrast with results for discrete generation model); (iii) Residual linkage disequilibrium associated with past population size will not affect single-sample estimates of N-b as much as in the discrete generation model because the disequilibrium diffuses among different years of breeders. These results lead to some general conclusions about genetic estimates of N-e in iteroparous species with overlapping generations and identify areas in need of further research.

We present the first description of phylogeographic structure among Cuvier's beaked whales (Ziphius cavirostris) worldwide using mitochondrial DNA (mtDNA) control region sequences obtained from strandings (n = 70), incidental fisheries takes (n = 11), biopsy (n = 1), and whale-meat markets (n = 5). Over a 290-base pair fragment, 23 variable sites defined 33 unique haplotypes among the total of 87 samples. Nucleotide diversity at the control region was relatively low (pi = 1.27% +/- 0.723%) compared to wide-ranging baleen whales, but higher than strongly matrifocal sperm, pilot and killer whales. Phylogenetic reconstruction using maximum likelihood revealed four distinct haplotype groups, each of which displayed strong frequency differences among ocean basins, but no reciprocal monophyly or fixed character differences. Consistent with this phylogeographic pattern, an analysis of molecular variance showed high levels of differentiation among ocean basins (F-ST = 0.14, Phi(ST) = 0.42; P < 0.001). Estimated rates of female migration among ocean basins were low (generally <= 2 individuals per generation). Regional sample sizes were too small to detect subdivisions within oceans except in the North Atlantic, where the Mediterranean Sea (n = 12) was highly differentiated due to the presence of two private haplotypes. One market product purchased in South Korea grouped with other haplotypes found only in the North Atlantic, suggesting a violation of current agreements banning international trade in cetacean species. Together, these results demonstrate a high degree of isolation and low maternal gene flow among oceanic, and in some cases, regional populations of Cuvier's beaked whales. This has important implications for understanding the threats of human impact, including fisheries by-catch, direct hunting, and disturbance or mortality from anthropogenic sound.

In plant conservation, restoration (the augmentation or reestablishment of an extinct population or community) is a valuable tool to mitigate the loss of habitat. However, restoration efforts can result in the introduction of novel genes and genotypes into populations when plant materials used are not of local origin. This movement is potentially important because many plant species are subdivided into populations that are adapted to local environmental conditions. Here we focus on genetic concerns arising from ongoing restoration efforts, where often little is known about “How local is local?” (i.e., the geographic or environmental scale over which plant species are adapted). We review the major issues regarding gene flow and local adaptation in the restoration of natural plant populations. Finally, we offer some practical, commonsense guidelines for the consideration of genetic structure when restoring natural plant populations.

We analyzed sequences of two mitochondrial DNA gene regions (control region and ND2) from 186 specimens obtained from 17 Eurasian localities covering most of the distribution of the common rosefinch to assess phylogeographic structure. Populations possessed a high level of nucleotide diversity relative to many other Palearctic species, suggesting that rosefinch populations are relatively old and possess high effective sizes. Mismatch distributions suggested that many localities experienced past population expansions, which are older than those expected for post-Pleistocene climate warming and reforestation of Eurasia. Our Phi(st) analysis revealed that 12.4% of total genetic variation was distributed among localities owing in part to the existence of three incompletely isolated groups: southwestern (subspecies C e. kubanensis), northeastern (subspecies C e. grebnitskii), and northwestern (subspecies C e. erythrinus and C e. ferghanensis). The three groups are not reciprocally monophyletic which suggests that they were formed relatively recently. Gene flow among groups is restricted. Coalescence analysis indicated dispersal asymmetry. (c) 2005 Elsevier Inc. All rights reserved.

The effective population size (N-e) is an important parameter in ecology, evolutionary biology and conservation biology. It is, however, notoriously difficult to estimate, mainly because of the highly stochastic nature of the processes of inbreeding and genetic drift for which N-e is usually defined and measured, and because of the many factors (such as time and spatial scales, systematic forces) confounding such processes. Many methods have been developed in the past three decades to estimate the current, past and ancient effective population sizes using different information extracted from some genetic markers in a sample of individuals. This paper reviews the methodologies proposed for estimating N-e from genetic data using information on heterozygosity excess, linkage disequilibrium, temporal changes in allele frequency, and pattern and amount of genetic variation within and between populations. For each methodology, I describe mainly the logic and genetic model on which it is based, the data required and information used, the interpretation of the estimate obtained, some results from applications to simulated or empirical datasets and future developments that are needed.

We use genetic divergence at 16 microsatellite loci to investigate how geographical features of the Galapagos landscape structure island populations of Darwin's finches. We compare the three most genetically divergent groups of Darwin's finches comprising morphologically and ecologically similar allopatric populations: the cactus finches (Geospiza scandens and Geospiza conirostris), the sharp-beaked ground finches (Geospiza difficilis) and the warbler finches (Certhidea olivacea and Certhidea fusca). Evidence of reduced genetic diversity due to drift was limited to warbler finches on small, peripheral islands. Evidence of low levels of recent interisland migration was widespread throughout all three groups. The hypothesis of distance-limited dispersal received the strongest support in cactus and sharp-beaked ground finches as evidenced by patterns of isolation by distance, while warbler finches showed a weaker relationship. Support for the hypothesis that gene flow constrains morphological divergence was only found in one of eight comparisons within these groups. Among warbler finches, genetic divergence was relatively high while phenotypic divergence was low, implicating stabilizing selection rather than constraint due to gene flow. We conclude that the adaptive radiation of Darwin's finches has occurred in the presence of ongoing but low levels of gene flow caused by distance-dependent interisland dispersal. Gene flow does not constrain phenotypic divergence, but may augment genetic variation and facilitate evolution due to natural selection. Both microsatellites and mtDNA agree in that subsets of peripheral populations of two older groups are genetically more similar to other species that underwent dramatic morphological change. The apparent decoupling of morphological and molecular evolution may be accounted for by a modification of Lack ` s two-stage model of speciation: relative ecological stasis in allopatry followed by secondary contact, ecological interactions and asymmetric phenotypic divergence.

Black rhinoceros (Diceros bicornis) are one of the most endangered mammal species in Africa, with a population decline of more than 96% by the end of the last century. Habitat destruction and encroachment has resulted in fragmentation of the remaining populations. To assist in conservation management, baseline information is provided here on relative genetic diversity and population differentiation among the four remaining recognized subspecies. Using microsatellite data from nine loci and 121 black rhinoceros individuals, and comparing the results with those of other African species affected in similar ways, Diceros bicornis michaeli retained the most genetic diversity (heterozygosity 0.675) compared with Diceros bicornis minor (0.459) and Diceros bicornis bicornis (0.505), suggesting that the duration of the known bottlenecks in these populations has only had a limited impact on diversity. Comparable and moderate degrees of population differentiation were found between D. b. minor, D. b. bicornis and D. b. michaeli. Results from the single sample available of the most endangered subspecies, Diceros bicornis longipes, showed the least diversity of all individuals examined. This information should assist conservation management decisions, especially those affecting population viability assessments and selection of individuals for translocations, and will also facilitate subspecies identification for ex situ individuals of uncertain origin.

The glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree-nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well-supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.

An importance sampling algorithm for computing the likelihood of a sample of genes at loci under a stepwise mutation model in a subdivided population is developed. This allows maximum likelihood estimation of migration rates between subpopulations. The time to the most recent common ancestor of the sample can also be computed. The technique is illustrated by an analysis of a data set of Australian red fox populations. (c) 2005 Elsevier Inc. All rights reserved.

We used phylogenetic and phylogeographical methods to infer relationships among African ground squirrels of the genus Xerus. Using Bayesian, maximum-parsimony, nested clade and coalescent analyses of cytochrome b sequences, we inferred interspecific relationships, evaluated the specific distinctness of Cape (Xerus inauris) and mountain (Xerus princeps) ground squirrels, and tested hypotheses for historical patterns of gene flow within X. inauris. The inferred phylogeny supports the hypothesized existence of an `arid corridor' from the Horn of Africa to the Cape region. Although doubts have been raised regarding the specific distinctness of X. inauris and X. princeps, our analyses show that each represents a distinct well-supported, monophyletic lineage. Xerus inauris includes three major clades, two of which are geographically restricted. The distributions of X. inauris populations are concordant with divergences within and disjunctions between other taxa, which have been interpreted as results of Plio-Pleistocene climate cycles. Nested clade analysis, coalescent analyses, and analyses of genetic structure support allopatric fragmentation as the cause of the deep divergences within this species.

This article presents an efficient importance-sampling method for computing the likelihood of the effective size of a population under the coalescent model of Berthier et al. Previous computational approaches, using Markov chain Monte Carlo, required many minutes to several hours to analyze small data sets. The approach presented here is orders of magnitude faster and can provide an approximation to the likelihood curve, even for large data sets, in a matter of seconds. Additionally, confidence intervals on the estimated likelihood curve provide a useful estimate of the Monte Carlo error. Simulations show the importance sampling to be stable across a wide range of scenarios and show that the N-e estimator itself performs well. Further simulations show that the 95% confidence intervals around the N-e estimate are accurate. User-friendly software implementing the algorithm for Mac, Windows, and Unix/Linux is available for download. Applications of this computational framework to other problems are discussed.

The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

Recent theoretical and empirical studies of phylogeography and population structure indicate that many processes influence intraspecific evolutionary history. The present study represents the first examination of various forces influencing the spatial and temporal patterns of sequence variation in the freshwater Mexican banded spring snail, Mexipyrgus churinceanus. This snail occurs in one of the most critically endangered centres of freshwater endemism, the desert ecosystem of Cuatro Cienegas. From cytochrome b mtDNA sequence variation, there is strong evidence of long-term isolation of three regions, suggesting that these regions represent evolutionarily distinct lineages. Molecular clock estimates of clade age indicate a time to most recent common ancestor of approximately 2.5 million years ago (Ma). The three regions differ considerably in the historical and demographic forces affecting population structure. The western populations have extremely low mtDNA diversity consistent with a severe bottleneck dating to 50 000 years before present (BP). The nearby Rio Mesquites drainage is characterized by fragmentation events, restricted gene flow with isolation by distance, and higher levels of mtDNA polymorphism. These patterns are consistent with the long-term stability of this drainage along with habitat heterogeneity and brooding contributing to population isolation and restricted gene flow. Southeastern populations show evidence of range expansion and a strong influence of genetic drift. Migration rates between drainages indicate very little gene flow between drainages except for asymmetric migration from the Rio Mesquites into both western and southeastern drainages.

Complex population structure can result from either sex-biased gene flow or population overlap during migrations. Loggerhead turtles (Caretta caretta) have both traits, providing an instructive case history for wildlife management. Based on surveys of maternally inherited mtDNA, pelagic post-hatchlings show no population structure across the northern Atlantic (phi(ST) < 0.001, P = 0.919), subadults in coastal habitat show low structure among locations (phi(ST) = 0.01, P < 0.005), and nesting colonies along the southeastern coast of the United States have strong structure (phi(ST) = 0.42, P < 0.001). Thus the level of population structure increases through progressive life history stages. In contrast, a survey of biparentally inherited microsatellite DNA shows no significant population structure: R-ST < 0.001; F-ST = 0.002 (P > 0.05) across the same nesting colonies. These results indicate that loggerhead females home faithfully to their natal nesting colony, but males provide an avenue of gene flow between regional nesting colonies, probably via opportunistic mating in migratory corridors. As a result, all breeding populations in the southeastern United States have similar levels of microsatellite diversity (H-E = 0.70-0.89), whereas mtDNA haplotype diversity varies dramatically (h = 0.00-0.66). Under a conventional interpretation of the nuclear DNA data, the entire southeastern United States would be regarded as a single management unit, yet the mtDNA data indicate multiple isolated populations. This complex population structure mandates a different management strategy at each life stage. Perturbations to pelagic juveniles will have a diffuse impact on Atlantic nesting colonies, mortality of subadults will have a more focused impact on nearby breeding populations, and disturbances to adults will have pinpoint impact on corresponding breeding populations. These findings demonstrate that surveys of multiple life stages are desirable to resolve management units in migratory marine species.

Approximate Bayesian computation (ABC) is a highly flexible technique that allows the estimation of parameters under demographic models that are too complex to be handled by full-likelihood methods. We assess the utility of this method to estimate the parameters of range expansion in a two-dimensional stepping-stone model, using samples from either a single deme or multiple demes. A minor modification to the ABC procedure is introduced, which leads to an improvement in the accuracy of estimation. The method is then used to estimate the expansion time and migration rates for five natural common vole populations in Switzerland typed for a sex-linked marker and a nuclear marker. Estimates based on both markers suggest that expansion occurred < 10,000 years ago, after the most recent glaciation, and that migration rates are strongly male biased.

DNA sequences from five nuclear loci and data from three microsatellites were collected from 360 isolates representing 14 globally distributed populations of the plant pathogenic fungus Mycosphaerella graminicola. Haplotype networks were constructed for the five sequence loci and population subdivision was assessed using Hudson's permutation test. Migration estimates were calculated using six regional populations for both the sequence and microsatellite loci. While subdivision was detected among the six regional populations, significant gene flow was indicated among some of the populations. The European and Israeli populations contributed the majority of historical immigrants to the New World. Migration estimates for microsatellite loci were used to infer more recent migration events among specific New World populations. We conclude that gene flow was an important factor in determining the demographic history of Mycosphaerella graminicola.

Incomplete lineage sorting can genetically link populations long after they have diverged, and will exert a more powerful influence on larger populations. The effects of this stochastic process can easily be confounded with those of gene flow, potentially leading to inaccurate estimates of dispersal capabilities or erroneous designation of evolutionarily significant units (ESUs). We have used phylogenetic, population genetic, and coalescent methods to examine genetic structuring in large populations of a widely dispersing bat species and to test hypotheses concerning the influences of coalescent stochasticity vs. gene flow. The Mexican free-tailed bat, Tadarida brasiliensis mexicana, exhibits variation in both migratory tendency and route over its range. Observations of the species' migratory behaviour have led to the description of behaviourally and geographically defined migratory groups, with the prediction that these groups compose structured gene pools. Here, we used mtDNA sequence analyses coupled with existing information from allozyme, banding, and natural history studies to evaluate hypotheses regarding the relationship between migration and genetic structure. Analyses of molecular variance revealed no significant genetic structuring of behaviourally distinct migratory groups. Demographic analyses were consistent with population growth, although the timing of population expansion events differs between migratory and nonmigratory populations. Hypotheses concerning the role of gene flow vs. incomplete lineage sorting on these data are explored using coalescent simulations. Our study demonstrates the importance of accounting for coalescent stochasticity in formulating phylogeographical hypotheses, and indicates that analyses that do not take such processes into account can lead to false conclusions regarding a species' phylogeographical history.

Mountain Plover (Charadrius montanus) distribution and abundance have been reduced drastically in the past 30 years and the conversion of shortgrass prairie to agriculture has caused breeding populations to become geographically isolated. This, coupled with the fact that Mountain Plovers are thought to show fidelity to breeding grounds, leads to the prediction that the isolated breeding populations would be genetically distinct. This pattern, if observed, would have important management implications for a species at risk of extinction. Our study examined genetic variation at two mitochondrial regions for 20-30 individuals from each of four breeding sites. We found no evidence of significant population differentiation in the data from the control region or the ATPase 6/8 region. Nested-clade analysis revealed no relationship between haplotype phylogeny, and geography among the 47 control region haplotypes. In the ATPase 6/8 region, however, one of the two clades provided information suggesting that, historically, there has been continuous range expansion. Analysis of mismatch distributions and Tajima&PRIME; s D suggest that the Mountain Plover underwent a population expansion, following the Pleistocene glacial period. To explain the lack of detectable genetic differentiation among populations, despite their geographic isolation and fidelity to breeding locations, we speculate that there is sufficient female-mediated gene flow to homogenize gene pools among populations. Such gene flow might ensue if pair bonds are formed in mixed flocks on wintering grounds rather than on the summer breeding grounds.

The Variable Antshrike (Thamnophilus caerulescens) is arguably the most polytypic thamnophilid, with males ranging from almost entirely jet black to nearly white. The four subspecies that occur in Bolivia are strikingly divergent in male plumage: T. c. aspersiveuter (black with white-barred belly), T c. connectens (black back and bib with white belly), T c. dinellii (gray throat and back with rufous belly), and T c. paraguayeusis (light gray with white belly). To assess the genetic structure of those taxa in Bolivia, sequence variation at the mitochondrial cytochrome-b gene was screened in 126 individuals collected across transects spanning the plumage and vocal variation in the four forms. A 95-km-wide cline in haplotype frequencies from T. c. aspersiventer to T. c. dinellii was centered in the Serrania Cochabamba across an ecotone from humid to dry Andean foothill habitats. Thamnophilus caerulescens connectens is not a valid taxon, instead representing an introgressed population near the dinellii tail of the T c. aspersiventer-T. c. dinellii hybrid zone. Although direct contact between T. c. dinellii and T. c. paraguayensis remains undocumented, the mitochondrial data were consistent with introgression along a broad cline extending across most of southern Bolivia. Overall, the transitions in mitochondrial frequencies were remarkably concordant with clinal changes in vocalizations among those same populations (Isler et al. 2005). Both studies highlight the need for increased sampling, in both the geographic extent and number of individuals per population, to address adequately the potential for clinal variation between populations that are not isolated geographically. A more restricted sampling design in the present study might have led to the erroneous conclusion that T. c. aspersiventer, T c. dinellii, and T c. paraguayeusis have reciprocally monphyletic mitochondrial lineages, making them full species according to some species concepts.

We estimated genetic diversity in cave (hypogean) and surface (epigean) populations of the Mexican Tetra, Astyanax mexicanus, using RAPDs and microsatellites. By either measure, genetic diversity was significantly lower in hypogean than in epigean populations, although there was considerable variability in both classes. We examined three factors potentially influencing genetic diversity among hypogean populations: relative population size, cave isolation, and the presence of eyed fish in the cave. Of the three, only the presence of epigean forms within the caves correlated with increased genetic diversity in cave populations. This suggests that increased genetic diversity of A. mexicanus cave populations reflects introgression of alleles from surface populations. Estimation of migration rates among populations rising microsatellites supported this conclusion and also suggested that alleles can move among cave and surface populations more easily than from cave to cave.

We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.

Most phylogeographical studies of postglacial colonization focus on high latitude locations in the Northern Hemisphere. Here, we studied the phylogeographical structure of the red-necked snow finch Pyrgilauda ruficollis, an endemic species of the Tibetan plateau. We analysed 879 base pairs (bp) of the mitochondrial cytochrome b gene and 529 bp of the control region in 41 birds from four regional groups separated by mountain ranges. We detected 34 haplotypes, 31 of which occurred in a single individual and only three of which were shared among sampling sites within regional groups or among regional groups. Haplotype diversity was high (h = 0.94); nucleotide diversity was low (th = 0.00415) and genetic differentiation was virtually non-existent. Analyses of mismatch distributions and geographically nested clades yielded results consistent with contiguous range expansion, and the expansion times were estimated as 0.07-0.19 million years ago (Ma). Our results suggest that P. ruficollis colonized the Tibetan plateau after the extensive glacial period (0.5-0.175 Ma), expanding from the eastern margin towards the inner plateau. Thus, in contrast to many of the postglacial phylogeographical structures known at high latitudes, this colonization occurred without matrilineal population structuring. This might be due to the short glacial cycles typical of the Tibetan plateau, adaptation of P. ruficollis to cold conditions, or refugia and colonized habitat being semicontinuous and thus promoting population mixing.

Gene flow and drift shape the distribution of neutral genetic diversity in metapopulations, but their local rates are difficult to quantify. To identify gene flow between demes as distinct from individual migration, we present a modified Bayesian method to genetically test for descendants between an immigrant and a resident in a nonmigratory life stage. Applied to a metapopulation of pond-breeding European newts (Triturus cristatus, T. marmoratus) in western France, the evidence for gene flow was usually asymmetric and, for demes of known census size (N), translated into maximally seven reproducing immigrants. Temporal sampling also enabled the joint estimation of the effective demic population size (N-e) and the immigration rate m (including nonreproductive individuals). N-e ranged between 4.1 and 19.3 individuals, N-e/N ranged between 0.05 and 0.65 and always decreased with N; m was estimated as 0.19-0.63, and was possibly biased upwards. We discuss how genotypic data can reveal fine-scale demographic processes with important microevolutionary implications.

The aim of this study is to reveal gene flow between populations of the coral reef dwelling lionfish Pterois miles in the Gulf of Aqaba and northern Red Sea. Due to the fjord-like hydrography and topology of the Gulf of Aqaba, isolation of populations might be possible. Analysis of 5' mitochondrial control region sequences from 94 R miles specimens detected 32 polymorphic sites, yielding 38 haplotypes. Sequence divergence among different haplotypes ranged from 0.6% to 9.9% and genetic diversity was high (h = 0.85, pi = 1.9%). AMOVA indicates panmixia between the Gulf of Aqaba and northern Red Sea, but analysis of migration pattern shows an almost unidirectional migration originating from the Red Sea. (c) 2004 Elsevier B.V All rights reserved.

Motivation: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. Results: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework.

Two genetic consequences are often considered evidence of a founder effect: substantial loss in genetic diversity and rapid divergence between source and founder populations. Single-step founder events have been studied for these effects, but with mixed results, causing continued controversy over the role of founder events in divergence. Experiments of serial bottlenecks have shown losses of diversity, increased divergence, and rapid behavioural changes possibly leading to reproductive isolation between source and final populations. The few studies conducted on natural, sequentially founded systems show some evidence of these effects. We examined a natural vertebrate system of sequential colonization among northwestern song sparrows (Melospiza melodia). This system has an effectively linear distribution, it was probably colonized within the last 10 000 years, there are morphological and behavioural differences among populations, and the westernmost populations occur in atypical habitats for the species. Eight microsatellite loci from eight populations in Alaska and British Columbia (n = 205) showed stepwise loss of genetic diversity, genetic evidence for strong population bottlenecks, and increased population divergence. The endpoint population on Attu Island has extremely low diversity (H-E = 0.18). Our study shows that sequential bottlenecks or founder events can have powerful genetic effects in reducing diversity, possibly leading to rapid evolutionary divergence.

We used frequency-based and coalescent-based phylogeographic analysis of sea urchin (Strongylocentrolus droebachiensis) mitochondrial DNA (mtDNA) sequences and previously published microsatellite data to understand the relative influence of colonization and gene flow from older (north Pacific) and younger (northeast Atlantic) sea urchin populations on genetic variation in the northwest Atlantic. We found strong evidence of survival of northwestern Atlantic populations in local Pleistocene glacial refugia: most haplotypes were the same as or closely related to Pacific haplotypes, with deep gene genealogies that reflect divergence times within the northwestern Atlantic that are much older than the last glacial maximum. We detected gene flow across the North Atlantic in the form of haplotypes shared with or recently descended from European populations. We also found evidence of significant introgression of haplotypes from a closely related species (S. pallidus). The relative magnitude of gene flow estimated by coalescent methods (and the effective population size differences among oceanic regions) depended on the genetic marker used. In general, we found very small effective population size in the northeastern Atlantic and high trans-Arctic gene flow between the Pacific and northwestern Atlantic. Both analyses suggested significant back-migration to the Pacific. However, microsatellites more strongly reflected older Pacific migration (with similar effective population sizes across the Arctic), whereas mtDNA sequences appeared to be more sensitive to recent trans-Atlantic dispersal (with larger differences in effective population size). These differences across marker types might have several biological or methodological causes, and they suggest caution in interpretation of the results from a single locus or class of markers.

Fishes of the genus Prochilodus are ecologically and commercially important, ubiquitous constituents of large river biota in South America. Recent ecologic and demographic studies indicate that these fishes exist in large, stable populations with adult census numbers exceeding one million individuals. Abundance data present a stark contrast to very low levels of genetic diversity (Theta) and small effective population sizes (N-e) observed in a mitochondrial (nu) DNA dataset obtained for two species, Prochilodus mariae, and its putative sister taxon, Prochilodus rubrotaeniatus. Both species Occupy major river drainages (Orinoco, Essequibo, and Negro) of northeastern South America. Disparity between expectations based on current abundance and life history information and observed genetic data in these lineages could result from historical demographic bottlenecks, or alternatively, natural selection (i.e., a mtDNA selective sweep). To ascertain underlying processes that affect mtDNA diversity in these species we compared 0 and N-e estimates obtained from two, unlinked nuclear loci (calmodulin intron-4 and elongation factor-1 alpha intron-6) using an approach based on coalescent theory. Genetic diversity and N-e estimated from mtDNA and nuclear sequences were uniformly low in P. rubrotaeniatus from the Rio Negro, suggesting that this population has encountered a historical bottleneck. For all P. mariae populations, Theta and N-e based on nuclear sequences were comparable to expectations based on current adult census numbers and were significantly greater than mtDNA estimates, suggesting that a selective mtDNA sweep has occurred in this species. Comparative genetic analysis indicates that a suite of evolutionary processes involving historical demography and natural selection have influenced pattern, of genetic variation and speciation in this important Neotropical fish group.

The San Joaquin kit fox (Vulpes macrotis mutica) was once ubiquitous throughout California's San Joaquin Valley and its surrounds. However, most of its habitat has been lost to irrigated agriculture, urban development, and oil fields. The remaining foxes are concentrated in six areas, although there are several small pockets of foxes throughout the Valley. To help conserve kit foxes, we sought an ecological understanding of the level of genetic variation remaining in these locations and the extent of gene flow among them. We collected tissue from 317 kit foxes from 8 sites and estimated genetic variability in and gene flow among sites using data from 8 polymorphic, microsatellite markers. We found no differences in both observed and expected heterozygosity between locations using Bonferonni corrected paired t-tests. We found differences in mean number of alleles per locus, even after we used Monte Carlo simulations to adjust for sample size differences. Population subdivision was low among sites (F-st=0.043), yet a matrix of pairwise F-st values was correlated with a matrix of pairwise geographic distances. An assignment test classified only 45% of the individuals to the site where they were captured. Overall, these data suggest that kit fox dispersal between locations may still maintain genetic variation throughout most of the areas we sampled.

The renewed interest in the use of hybrid zones for studying speciation calls for the identification and study of hybrid zones across a wide range of organisms, especially in long-lived taxa for which it is often difficult to generate interpopulation variation through controlled crosses. Here, we report on the extent and direction of introgression between two members of the `model tree' genus Populus: Populus alba (white poplar) and Populus tremula (European aspen), across a large zone of sympatry located in the Danube valley. We genotyped 93 hybrid morphotypes and samples from four parental reference populations from within and outside the zone of sympatry for a genome-wide set of 20 nuclear microsatellites and eight plastid DNA restriction site polymorphisms. Our results indicate that introgression occurs preferentially from P. tremula to P. alba via P. tremula pollen. This unidirectional pattern is facilitated by high levels of pollen vs. seed dispersal in P. tremula (pollen/seed flow = 23.9) and by great ecological opportunity in the lowland floodplain forest in proximity to P. alba seed parents, which maintains gene flow in the direction of P. alba despite smaller effective population sizes (N-e) in this species (P. alba N(e)c. 500-550; P. tremula N(e)c. 550-700). Our results indicate that hybrid zones will be valuable tools for studying the genetic architecture of the barrier to gene flow between these two ecologically divergent Populus species.

The northern spotted owl (Strix occidentalis caurina) is a threatened subspecies and the California spotted owl (Strix occidentalis occidentalis) is a subspecies of special concern in the western United States. Concern for their continued viability has arisen because of habitat loss caused by timber harvesting. The taxonomic status of the northern subspecies has been the subject of continuing controversy. We investigated the phylogeographical and population genetic structure of northern and California spotted owls with special reference to their region of contact. Mitochondrial DNA (mtDNA) control region sequences confirmed the existence of two well-differentiated lineages connected by a narrow hybrid zone in a region of low population density in north central California. Maximum-likelihood estimates indicated bidirectional gene flow between the lineages but limited introgression outside the region of contact. The lengths of both the mtDNA hybrid zone and the reduced density patch were similar and slightly exceeded estimates of natal dispersal distances. This suggests that the two subspecies were in secondary contact in a hybrid zone trapped by a population density trough. Consequently, the zone of interaction is expected to be geographically stable. We discovered a third, rare clade of haplotypes, which we interpreted to be a result of incomplete lineage sorting; those haplotypes result in a paraphyletic northern spotted owl with respect to the California spotted owl. A congeneric species, the barred owl (Strix varia), occasionally hybridizes with spotted owls; our results indicated an upper bound for the frequency of barred owl mtDNA haplotypes in northern spotted owl populations of 3%.

Intraspecific phylogeographical patterns largely depend on the life history traits of a species. Especially species with a high degree of cold tolerance, limited requirements towards habitat preferences, and relatively low active dispersal capacities may have responded in a different way to the Pleistocene climatological fluctuations than the majority of taxa studied so far. To evaluate this possibility, we studied Arion fuscus (Muller, 1774), a common and widespread European terrestrial slug, from 88 locations (N = 964). Sequence variation was assessed for fragments of the mitochondrial 16S rDNA and COI genes by means of single-strand conformation polymorphisms (SSCP) and subsequent DNA sequencing. Additionally, eight allozyme loci were scored in 843 individuals. Phylogenetic analysis revealed the presence of two major evolutionary lineages, one in the Balkan region and another in the Alps and the rest of Europe. The sequence divergence between the two lineages was limited (3.3%), but gene flow between the regions was absent, suggesting that the two regions have been isolated since the late Pliocene or early Pleistocene. Allozyme differentiation among geographical regions and mitochondrial DNA (mtDNA) lineages was low. The geographical patterns observed in our data showed that (i) haplotype and nucleotide diversities are very low in northern Europe, suggesting that single haplotypes rapidly colonized large areas; (ii) recently expanded haplotype clades have restricted distribution ranges, suggesting that current gene flow is low; and (iii) genetic diversity in the Alps is much higher than in other regions and estimated past gene flow from the Eastern Alps to other regions was high, suggesting that this was a refugial zone during the Pleistocene. This full-range phylogeography suggests the existence of an alternative refugial zone, situated north of the refugial areas currently recognized in most other taxa.

Geographic variation in microsatellite allele frequencies was assessed at nine sites in two regional vocal dialects of the parrot Amazona auropalliata (yellow-naped amazon) to test for correspondence between dialects and population structure. There was no relationship between the genetic distances between individuals and their dialect membership. High rates of gene flow were estimated between vocal dialects based on genetic differentiation. In addition, 5.5% of pairs of individuals compared across the dialect boundary were estimated to be related at the level of half siblings, indicating that dispersal is ongoing. The number of effective migrants per generation between dialects estimated with the microsatellite data was roughly one-seventh the number estimated with mitochondrial control region sequence data from the same individuals, suggesting that gene flow may be female-biased. Together, these results suggest that the observed mosaic pattern of geographic variation in vocalizations is maintained by learning of local call types by immigrant birds after dispersal. We found no evidence that ongoing habitat fragmentation has contributed to cryptic population structure.

We show that the unstructured ancestral selection graph applies to part of the history of a sample from a population structured by restricted migration among subpopulations, or demes. The result holds in the limit as the number of demes tends to infinity with proportionately weak selection, and we have also made the assumptions of island-type migration and that demes are equivalent in size. After an instantaneous sample-size adjustment, this structured ancestral selection graph converges to an unstructured ancestral selection graph with a mutation parameter that depends inversely on the migration rate. In contrast, the selection parameter for the population is independent of the migration rate and is identical to the selection parameter in an unstructured population. We show analytically that estimators of the migration rate, based on pairwise sequence differences, derived under the assumption of neutrality should perform equally well in the presence of weak selection. We also modify an algorithm for simulating genealogies conditional on the frequencies of two selected alleles in a sample. This permits efficient simulation of stronger selection than was previously possible. Using this new algorithm, we simulate gene genealogies under the many-demes ancestral selection graph and identify some situations in which migration has a strong effect on the time to the most recent common ancestor of the sample. We find that a similar effect also increases the sensitivity of the genealogy to selection.

The Island Scrub-Jay (Aphelocoma insularis) is found on Santa Cruz Island, California, and is the only insular bird species in the continental United States. We typed seven microsatellite loci and sequenced a portion of the mitochondrial DNA control region of Island Scrub-Jays and their closest mainland relative, the Western Scrub-Jay ( Aphelocoma californica), to assess levels of variability and effective population size and to examine the evolutionary relationship between the two species. The estimated female effective population size, N-ef, of the Island Scrub-Jay was 1603 (90% confidence interval: 1481 - 1738) and was about 7.5% of the size of the mainland species. Island and Western Scrub-Jays have highly divergent control-region sequences, and the value of 3.14 +/- 0.09% sequence divergence between the two species suggests a divergence time of approximately 151,000 years ago. Because the four northern Channel Islands were joined as one large island as recently as 11,000 years ago, extinctions must have occurred on the three other northern Channel islands, Santa Rosa, San Miguel, and Anacapa, highlighting the vulnerability of the remaining population. We assessed the evolutionary significance of four island endemics, including the Island Scrub-Jay, based on both genetic and adaptive divergence. Our results show that the Island Scrub-Jay is a distinct species of high conservation value whose history and adaptive potential is not well predicted by study of other island vertebrates.

Recurrent glacial advances have shaped community histories across the planet. While biogeographic responses to glaciations likely varied with latitude, the consequences for temperate marine communities histories are less clear. By coalescent analyses of multiloci DNA sequence data (mitochondrial DNA control region, alpha-enolase intron, and alpha-tropomyosin intron) collected from a low-dispersing sister pair of rocky intertidal fishes commonly found from southeastern Alaska to California (Xiphister atropurpureus and X. mucosus), we uncover two very different responses to historical glaciations. A variety of methods that include a simulation analysis, coestimates of migration and divergence times, and estimates of minimum ages of populations sampled up and down the North American Pacific coast all strongly revealed a history of range persistence in X. atropurpureus and extreme range contraction and expansion from a southern refugium in X. mucosus. Furthermore, these conclusions are not sensitive to the independent estimates of the DNA substitution rates we obtain. While gene flow and dispersal are low in both species, the widely different histories are rather likely to have arisen from ecological differences such as diet breadth, generation time, and habitat specificity.

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using theta(ST) values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest theta(ST) (0.13-0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (theta(ST) = 0.04-0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Nino Southern Oscillation (ENSO) events along the Pacific coast.

A deep genetic cline between southern populations of the barnacle Balanus glandula (from about Monterey Bay southward) and northern populations (from northern California through Alaska) has recently been described. If this pattern is due to historical isolation and genetic drift, we expect it to have formed recently and represent a transient, nonequilibrium state. However, this cline appears to have formed well before the last glacial maximum. Our assays of sequence diversity at a region of mitochondrial cytochrome oxidase I, combined with coalescent estimators of the time of separation for these two regions, suggest that a late Pleistocene event more than 100 thousand years ago may be responsible for the initial separation. This suggests that either strong oceanographic mechanisms or natural selection have maintained the cline, because there has clearly been adequate time for this cline or polymorphism to resolve itself by genetic drift and migration. However, reliance on only a single mitochondrial marker for which the substitution rate has been estimated still limits the resolution of our analysis.

Models of speciation in African rain forests have stressed either the role of isolation or ecological gradients. Here we contrast patterns of morphological and genetic divergence in parapatric and allopatric populations of the Little Greenbul, Andropadus virens, within different and similar habitats. We sampled 263 individuals from 18 sites and four different habitat types in Upper and Lower Guinea. We show that despite relatively high rates of gene flow among populations, A. virens has undergone significant morphological divergence across the savanna-forest ecotone and mountain-forest boundaries. These data support a central component of the divergence-with-gene-flow model of speciation by suggesting that despite large amounts of gene flow, selection is sufficiently intense to cause morphological divergence. Despite evidence of isolation based on neutral genetic markers, we find little evidence of morphological divergence in fitness-related traits between hypothesized refugial areas. Although genetic evidence suggests populations in Upper and Lower Guinea have been isolated for over 2 million years, morphological divergence appears to be driven more by habitat differences than geographic isolation and suggests that selection in parapatry may be more important than geographic isolation in causing adaptive divergence in morphology.

Malaria control projects based on the introduction and spread of transgenes into mosquito populations depend on the extent of isolation between those populations. On the basis of the distribution of paracentric inversions, Anopheles gambiae has been subdivided into five subspecific chromosomal forms. Estimating gene flow between and within these forms of An. gambiae presents a number of challenges. We compared patterns of genetic divergence (AT) between sympatric populations of the Bamako and Mopti forms at five sites. We used microsatellite loci within the j inversion on chromosome 2, which is fixed in the Bamako form but absent in the Mopti form, and microsatellites on chromosome 3, a region void of inversions. Estimates of genetic diversity and F-sr's, suggest genetic exchanges between forms for the third chromosome but little for the j inversion. These results suggest a role for the inversion in speciation. Extensive gene flow within forms among sites resulted in populations clustering according to form despite substantial gene flow between forms. These patterns underscore the low levels of current gene flow between chromosomal forms in this area of sympatry. Introducing refractoriness genes in areas of the genome void of inversions may facilitate their spread within forms but their passage between forms may prove more difficult than previously thought.

Many species of sea turtles spend part of their life cycle gathered in large feeding aggregations that combine individuals from widely separated rookery populations. Biologists have applied methods of mixed-stock analysis to mitochondrial DNA samples from rookeries and mixed populations to estimate the contributions of different rookeries to the mixed stock. These methods are limited by the amount of genetic overlap between rookeries and fail to incorporate ecological covariates such as rookery size and location within major ocean currents that are strongly suspected to affect rookery contributions. A new hierarchical Bayesian model for rookery contributions incorporates these covariates (and potentially others) to draw stronger conclusions from existing data. Applying the model to various simple scenarios shows that, in some cases,: it can accurately estimate turtle origins even when turtles come from rookeries with high degrees of genetic overlap., Applying the model to more complex simulations shows that it performs well in a wide range of scenarios. Applying the model to existing data on green turtles (Chelonia mydas) narrows confidence intervals but does not change point estimates significantly. Applying it to loggerhead turtles (Caretta caretta) strengthens the dominance of the large rookery in south Florida, and brings estimates from a small data set on sea turtle strandings into line with those from rookery data. Used appropriately, hierarchical Bayesian methods offer great. potential for introducing multiple levels of variation and ecological covariates into ecological models.

Bathymetric gradients of biodiversity in the deep-sea benthos constitute a major class of large-scale biogeographic phenomena. They are typically portrayed and interpreted as variation in a diversity (the number of species recovered in individual samples) along depth transects. Here, we examine the depth ranges of deep-sea gastropods and bivalves in the eastern and western North Atlantic. This approach shows that the abyssal molluscan fauna largely represents deeper range extensions for a subset of bathyal species. Most abyssal species have larval dispersal, and adults live at densities that appear to be too low for successful reproduction. These patterns suggest a new explanation for abyssal biodiversity. For many species, bathyal and abyssal populations may form a source-sink system in which abyssal populations are regulated by a balance between chronic extinction arising from vulnerabilities to Allee effects and immigration from bathyal sources. An increased significance of source-sink dynamics with depth may be driven by the exponential decrease in organic carbon flux to the benthos with increasing depth and distance from productive coastal systems. The abyss, which is the largest marine benthic environment, may afford more limited ecological and evolutionary opportunity than the bathyal zone.

The reconstruction of population processes from DNA sequence variation requires the coordinated implementation of several coalescent-based methods, each bound by specific assumptions and limitations. In practice, the application of these coalescent-based methods for parameter estimation is difficult because they make strict assumptions that must be verified a priori and their parameter-rich nature makes the estimation of all model parameters very complex and computationally intensive. A further complication is their distribution as console applications that require the user to navigate through console menus or specify complex command-line arguments. To facilitate the implementation of these coalescent-based tools we developed SNAP Workbench, a Java program that manages and coordinates a series of programs. The workbench enhances population parameter estimation by ensuring that the assumptions and program limitations of each method are met and by providing a step-by-step methodology for examining population processes that integrates both summary-statistic methods and coalescent-based population genetic models.

Dispersal is a key ecological process linking metapopulation dynamics in the landscape to distribution patterns at larger spatial scales. In this study, we investigated the landscape occupancy and genetic population structure of a butterfly species, Melanargia galathea. Several, landscapes differing in composition and structure were sampled as well as populations at different spatial. scales. We found that M. galathea occupied 91.3 % of all habitat patches available within a particular landscape, probably due to a dominance of landscape scale processes such as rescue effect and recolonisation. A high level of genetic polymorphism within the sampled populations and a very low amount of genetic differentiation between populations was observed (G(st) = 0.034), characteristic of species with high dispersal capacity and/or high density. High dispersal rates ensured considerable gene mixing at the landscape scale while the influence of distance on dispersal success was detected at the regional and continental scales by a significant amount of isolation by distance. We also found that, at the landscape scale, the dispersal of this butterfly species was influenced by the spatial, distribution of its habitat patches. (C) 2004 Elsevier GmbH. All. rights reserved.

In 2004, the term `ghost population' was introduced to summarize the effect of unsampled subpopulations that exchange migrants with other subpopulations that have been sampled. Estimated long-term migration rates among populations sampled will be affected by ghost populations. Although it would be convenient to be able to define an apparent migration matrix among sampled populations that incorporate the exchange of migrants with ghost populations, no such matrix can be defined in a way that predicts all features of the coalescent process for the true migration matrix. This paper shows that if the underlying migration matrix is symmetric, it is possible to define an apparent migration matrix among sampled subpopulations that predicts the same within-population and between-population homozygosities among sampled populations as is predicted by the true migration matrix. Application of this method shows that there is no simple relationship between true and apparent migration rates, nor is there a way to place an upper bound on the effect of ghost populations. In general, ghost populations can create the appearance of migration between subpopulations that do not actually exchange migrants. Comparison with published results from the application of the program, MIGRATE, shows that the apparent migration rates inferred with that program in a three-subpopulation model differ from those based on pairwise homozygosities. The apparent migration matrix determined by the method described in this paper probably represents the upper bound on the effect of ghost populations.

Population structure and phylogeography of the pink-footed goose, Anser brachyrhynchus Baillon 1833, was studied using mtDNA control region sequences (221 bp) from 142 individuals. Present breeding areas of the species in Greenland, Iceland, and Svalbard were largely covered by ice during the late Pleistocene. In pairwise comparisons phi(ST) estimates showed significant differentiation among eastern and western populations, whereas sampling localities within both areas were not differentiated. The mtDNA data indicate that the populations have separated recently (less than 10 000 years ago) and present breeding areas were colonized from one refugial population. The levels of haplotype and nucleotide diversity were approximately five times higher for the eastern population compared to the western population and suggest that the latter was colonized by a subset of eastern birds. Time to the most recent common ancestor of the species is 32 000-46 000 years, i.e. the present mtDNA variation of the pink-footed goose has accumulated during the last 0.1 My. Estimates of the long-term female effective population size (5400-7700 for the eastern population) imply that the refugial population of the pink-footed goose has been large. Tundra habitats were more extensive in cold periods of the late Pleistocene than today and may have sustained population sizes that allowed the accumulation of extant genetic polymorphism. It is not probable that the postulated small refugial areas in the high latitudes had a significant role in maintaining this diversity.

We present a Bayesian statistical inference approach for simultaneously estimating mutation rate, papulation sizes, and migration rates in all island-structured population, using temporal and spatial sequence data. Markov chain Monte Carlo is used to collect samples front the posterior probability distribution. We demonstrate that this chain implementation successfully reaches equilibrium and recovers truth for simulated data. A real HIV DNA sequence data set with two demes, semen and blood, is used as an example to demonstrate the method by fitting asymmetric migration rates and different Population Sizes. This data set exhibits a bimodal joint posterior distribution, with modes favoring different preferred migration directions. This full data set was subsequently split temporally for further analysis. Qualitative behavior of one subset was similar to the bimodal distribution observed with the full data set. The temporally split data showed significant differences in the posterior distributions and estimates of parameter values over time.

Until a few hundred years ago, New Zealand hosted several species of flightless ratite birds, collectively known as the moa. We have used mitochondrial sequence data for Dinornis, the largest of the moa, and new coalescent approaches to estimate its population size prior to human arrival ca. 1000-6000 years BP. We show that, as little as 1000 years ago, Dinornis numbered between 300 000 and 1.4 million and that the standing population of all moa species was ca. 3-12 million. This estimate is an order of magnitude larger than the accepted population estimate (ca. 159 000) for all moa species at the arrival of humans and suggests that moa numbers had already declined prior to human settlement.

Given the recent interest in declining amphibian populations. it is surprising that there are so few data on genetic drift and gene flow in anuran species. We used seven microsatellite loci to investigate genetic structure and diversity at both large and small geographic scales, and to estimate gene flow In the Cascades frog, Rana cascadae. We sampled 18 sites in a hierarchical design (inter-population distances ranging from 1-670 km) to test for isolation by distance and to determine the geographic scale over which substantial gene flow occurs. Eleven of these sites were sampled as three fine-scale clusters of three. three, and five sites separated by pairwise distances of 1-23 km to estimate number of migrants exchanged per generation via F-ST and by a coalescent approach. We found R. cascadae exhibits a strong pattern of isolation by distance over the entire species range, and that there is a sharp drop in migrants exchanged between sites separated by greater than 10 km. These data, in conjunction with results of other recent studies, suggest that montane habitats promote unusually strong genetic isolation among frog populations. We discuss our results in light of future management and conservation of R. cascadae.

Quantifying dispersal, a fundamental biological process, is far from simple. Here, both direct and indirect methods were employed to estimate dispersal in an endangered butterfly species. A high and significant correlation between the dispersal patterns, generated by an inverse power function fitted to capture-mark-recapture (CMR) data on the one hand, and population genetic analyses on the other hand, was observed. Stepping-stone type movements were detected by both methods, evidence for the importance of connectivity in the studied metapopulation. These results are particularly relevant to those population and conservation biology studies where quantifying dispersal is essential for the elaboration of successful management actions.

Both the ability to generate DNA data and the variety of analytical methods for conservation genetics are expanding at an ever-increasing pace. Analytical approaches are now possible that were unthinkable even five years ago due to limitations in computational power or the availability of DNA data, and this has vastly expanded the accuracy and types of information that may be gained from population genetic data. Here we provide a guide to recently developed methods for population genetic analysis, including identification of population structure, quantification of gene flow, and inference of demographic history. We cover both allele-frequency and sequence-based approaches, with a special focus on methods relevant to conservation genetic applications. Although classical population genetic approaches such as F,,.,. (and its derivatives) have carried the field thus far, newer, more powerful, methods can infer much more from the data, rely on fewer assumptions, and are appropriate for conservation genetic management when precise estimates are needed.

Hierarchical genetic structure was examined in the three geographically-defined subspecies of spotted owl (Strix occidentalis) to define relationships among subspecies and quantify variation within and among regional and local populations. Sequences (522 bp) from domains I and II of the mitochondrial control region were analyzed for 213 individuals from 30 local breeding areas. Results confirmed significant differences between northern spotted owls and the other traditional geographically defined subspecies but did not provide support for subspecific level differences between California and Mexican spotted owls. Divergence times among subspecies estimated with a 936 bp portion of the cytochrome b gene dated Northern and California/Mexican spotted owl divergence time to 115,000-125,000 years ago, whereas California/Mexican spotted owl divergence was estimated at 15,000 years ago. Nested clade analyses indicated an association between California spotted owl and Mexican spotted owl haplotypes, implying historical contact between the two groups. Results also identified a number of individuals geographically classified as northern spotted owls (S. o. caurina) that contained haplotypes identified as California spotted owls (S. o. occidentalis). Among all northern spotted owls sampled (n = 131), 12.9% contained California spotted owl haplotypes. In the Klamath region, which is the contact zone between the two subspecies, 20.3% (n = 59) of owls were classified as California spotted owls. The Klamath region is a zone of hybridization and speciation for many other taxa as well. Analyses of population structure indicated gene flow among regions within geographically defined subspecies although there was significant differentiation among northern and southern regions of Mexican spotted owls. Among all areas examined, genetic diversity was not significantly reduced except in California spotted owls where the southern region consists of one haplotype. Our results indicate a stable contact zone between northern and California spotted owls, maintaining distinct subspecific haplotypes within their traditional ranges. This supports recovery efforts based on the traditional subspecies designation for the northern spotted owl. Further, although little variation was found between California and Mexican spotted owls, we suggest they should be managed separately because of current isolation between groups.

Nonequilibrium conditions due to either allopatry followed by secondary contact or recent range expansion can confound measurements of gene flow among populations in previously glaciated regions. We determined the scale at which gene flow can be estimated among breeding aggregations of bullfrogs (Rana catesbeiana) at the northern limit of their range in Ontario, Canada, using seven highly polymorphic DNA microsatellite loci. We first identified breeding aggregations that likely share a common history, determined from the pattern of allelic richness, factorial correspondence analysis, and a previously published mtDNA phylogeography, and then tested for regional equilibrium by evaluating the association between pairwise F-ST and geographic distance. Regional breeding aggregations in eastern Ontario separated by less than or equal to100 km were determined to be at or near equilibrium. High levels of gene flow were measured using traditional 1 statistics and likelihood estimates of Nm. Similarly high levels of recent migration (past one to three generations) were estimated among the breeding aggregations rising nonequilibrium methods. We also show that, in many cases, breeding aggregations separated by tip to tens of kilometers are not genetically distinct enough to be considered separate genetic populations. These results have important implications both for the identification of independent “populations” and in assessing the effect of scale in detecting patterns of genetic equilibrium and gene flow.

A maximum-likelihood method for demographic inference is applied to data sets consisting of the frequency spectrum of unlinked single-nucleotide polymorphisms (SNPs). We use simulation analyses to explore the effect of sample size and number of polymorphic sites on both the power to reject the null hypothesis of constant population size and the properties of two- and three-dimensional maximum-likelihood estimators (MLEs). Large amounts of data are required to produce accurate demographic inferences, particularly for scenarios of recent growth. Properties of the MLEs are highly dependent upon the demographic scenario, as estimates improve with a more ancient time of growth onset and smaller degree of growth. Severe episodes of growth lead to an upward bias in the estimates of the current population size, and that bias increases with the magnitude of growth. One data set of African origin supports a model of mild, ancient growth, and another is compatible with both constant population size and a variety of growth scenarios, rejecting greater than fivefold growth beginning >36,000 years ago. Analysis of a data set of European origin indicates a bottlenecked population history, with an 85% population reduction occurring similar to30,000 years ago.

1. Pest eradication is an important facet of conservation and ecological restoration and has been applied successfully to invasive rat species on offshore and oceanic islands. Successful eradication requires the definition of a target population that is of manageable size, with low recolonization risk. We applied a molecular genetic approach to the identification of populations suitable for eradication (eradication units) to provide a new tool to assist the management of brown rats Rattus norvegicus on South Georgia (Southern Ocean). 2. A single eradication attempt on South Georgia (4000 km(2)) would be an order of magnitude larger than any previously successful rat eradication programme (110 km(2)). However, rats are demarcated into glacially isolated populations, which could allow sequential eradication. We examined genetic variation at 18 nuclear microsatellite loci to identify gene flow between two glacially isolated rat populations. One population, Greene Peninsula (30 km(2)), was earmarked for an eradication trial. 3. Genetic diversity in 40 rats sampled from each population showed a pronounced level of genetic population differentiation, allowing individuals to be assigned to the correct population of origin. 4. Our study suggests limited or negligible gene flow between the populations and that glaciers, permanent ice and icy waters restrict rat dispersal on South Georgia. Such barriers define eradication units that, with due care, could be eradicated with low risk of recolonization, hence facilitating the removal of brown rats from South Georgia. 5. Synthesis and applications. We propose that the molecular definition of eradication units is a valuable approach to management as it (i) provides a temporal perspective to gene flow, which is important if dispersal events are rare; (ii) allows an eradication failure (i.e. surviving individuals) to be distinguished from a recolonization event, opening the way for adaptive management in the face of failure; and (iii) can aid the management of pest species in habitat continua by resolving meta-population dynamics, so guiding pest eradication/control strategies. This study further illustrates the developing array of applied ecological issues in which molecular techniques can help guide management.

Adult movement and natal dispersal data demonstrate that Northern Goshawks (Accipiter gentilis) are able to travel over long distances, suggesting a large functional population. However, these data are unable to determine whether these movements contribute to gene flow among adjacent breeding areas. We used eight microsatellite DNA loci and mitochondrial DNA control-region sequence data to assess population structure of Northern Goshawks breeding in Utah. Goshawks had moderate levels of genetic variation at microsatellite loci (observed heterozygosity = 50%), similar to levels found in other medium-sized, highly mobile birds. Overall estimates of interpopulation variance in microsatellite alleles (F-ST = 0.011) and mtDNA haplotypes (Phi(ST) = 0.126) were low and not significantly different from zero. Pairwise population comparisons using microsatellite markers revealed no differentiation among sampled sites, indicating that the functional population extends beyond Utah. However, pairwise population analyses of mtDNA uncovered a single case of differentiation between goshawks inhabiting Ashley National Forest, in northeastern Utah, and Dixie National Forest, in southwestern Utah. Low levels of population structuring observed in mtDNA between the two forests may be due to the smaller effective population size sampled by mtDNA, a cline of haplotypes across the West, or the presence of a contact zone between A. g. atricapillus and goshawks of southern Arizona and the Mexican Plateau.

How much of the variation in adaptive divergence can be explained by gene flow? The answer to this question should objectively reveal whether gene flow generally places a substantial constraint on evolutionary diversification. We studied multiple independent lake-stream population pairs of threespine stickleback (Gasterosteus aculeatus). For each pair, we quantified adaptive divergence based on morphological traits that have a genetic basis and are subject to divergent selection. We then estimated gene flow based on variation at five unlinked microsatellite loci. We found a consistent and significant pattern for morphological divergence to be positively correlated with genetic divergence and negatively correlated with gene flow. Statistical significance and the amount of variation explained varied within and among traits: 36.1-74. 1% for body depth and 11.8-5 1.7% for gill raker number. Variation within each trait was the result of differences among methods for estimating genetic divergence and gene flow. Variation among traits likely reflects different strengths of divergent selection. We conclude that gene flow has a substantial effect on adaptive divergence in nature but that the magnitude of this effect varies among traits. An alternative explanation is that cause and effect are reversed: adaptive divergence is instead constraining gene flow. This effect seems relatively unimportant for our system because genetic divergence and gene flow were not correlated with ecologically relevant habitat features of lakes (surface area) or streams (width, depth, flow, canopy openness).

The molecular clock hypothesis states that the rate of nucleotide substitution per generation is constant across lineages. If generation times were equal across lineages, samples obtained at the same calendar time would have experienced the same number of generations since their common ancestor. However, if sequences are not derived from contemporaneous samples, differences in the number of generations may be misinterpreted as variation in substitution rates and hence may lead to false rejection of the molecular clock hypothesis. A recent study has called into doubt the validity of clock-like evolution for HIV-1, using molecular sequences derived from noncontemporaneous samples. However, after separating their within-individual data according to sampling time, we found that what appeared to be nonclock-like behavior could be attributed, in most cases, to noncontemporaneous sampling, with contributions also likely to derive from recombination. Natural selection alone did not appear to obscure the clock-like evolution of HIV-1. (C) 2004 Elsevier Inc. All rights reserved.

Genetic variation was surveyed at nine microsatellite loci and the mitochondrial control region (868 bp) to test for the presence of genetic stock structure in young-of-the-year Atlantic bluefin tuna (Thunnus thynnus thynnus) from the Mediterranean Sea. Bluefin tuna were sampled over a period of 5 years from the Balearic and Tyrrhenian seas in the western basin of the Mediterranean Sea, and from the southern Ionian Sea in the eastern basin of the Mediterranean Sea. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences revealed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for both microsatellite markers and mitochondrial control region sequences (F-ST = 0.0023, P = 0.038 and Phi(ST) = 0.0233, P = 0.000, respectively). Significant genetic differentiation between the Tyrrhenian and Ionian collections was found for both microsatellite and mitochondrial markers (F-ST = 0.0087, P = 0.015 and Phi(ST) = 0.0367, P = 0.030, respectively). These results suggest the possibility of a genetically discrete population in the eastern basin of the Mediterranean Sea.

The Azorean bat Nyctalus azoreum is the only endemic mammal native to the remote archipelago of the Azores. It evolved from a continental ancestor related to the Leisler's bat Nyctalus leisleri and is considered threatened because of its restricted and highly fragmented distribution. We studied the genetic variability in 159 individuals from 14 colonies sampled throughout the archipelago. Sequences of the D-loop region revealed moderate but highly structured genetic variability. Half of the 15 distinct haplotypes were restricted to a single island, but the most common was found throughout the archipelago, suggesting a single colonization event followed by limited interisland female gene flow. All N. azoreum haplotypes were closely related and formed a star-like structure typical of expanded populations. The inferred age of demographic expansions was consistent with the arrival of founder animals during the Holocene, well before the first humans inhabited the Azores. Comparisons with a population of N. leisleri from continental Portugal confirmed not only that all N. azoreum lineages were unique to the archipelago, but also that the current levels of genetic diversity were surprisingly high for an insular species. Our data imply that the Azorean bat has a high conservation value. We argue that geographical patterns of genetic structuring indicate the existence of two management units.

Inferring the spatial expansion dynamics of invading species from molecular data is notoriously difficult due to the complexity of the processes involved. For these demographic scenarios, genetic data obtained from highly variable markers may be profitably combined with specific sampling schemes and information from other sources using a Bayesian approach. The geographic range of the introduced toad Bufo marinus is still expanding in eastern and northern Australia, in each case from isolates established around 1960. A large amount of demographic and historical information is available on both expansion areas. In each area, samples were collected along a transect representing populations of different ages and genotyped at 10 microsatellite loci. Five demographic models of expansion, differing in the dispersal pattern for migrants and founders and in the number of founders, were considered. Because the demographic history is complex, we used an approximate Bayesian method, based on a rejection-regression algorithm. to formally test the relative likelihoods of the five models of expansion and to infer demographic parameters. A stepwise migration-foundation model with founder events was statistically better supported than other four models in both expansion areas. Posterior distributions supported different dynamics of expansion in the studied areas. Populations in the eastern expansion area have a lower stable effective population size and have been founded by a smaller number of individuals than those in the northern expansion area. Once demographically stabilized, populations exchange a substantial number of effective migrants per generation in both expansion areas, and such exchanges are larger in northern than in eastern Australia. The effective number of migrants appears to be considerably lower than that of founders in both expansion areas. We found our inferences to be relatively robust to various assumptions on marker. demographic, and historical features. The method presented here is the only robust, model-based method available so far, which allows inferring complex population dynamics over a short time scale. It also provides the basis for investigating the interplay between population dynamics, drift, and selection in invasive species.

Glaciations and postglacial migrations are major factors responsible for the present patterns of genetic variation we see in natural populations in Europe. For ectomycorrhizal fungi, escape from refugia can only follow range expansion by their specific hosts. To infer phylogeographic relationships within Tuber melanosporum, sequences of internal transcribed spacers (ITS) and the 5.8S coding region of the ribosomal DNA repeat were obtained for 188 individuals sampled over the entire distribution of this species in France, and in north-western Italy and north-eastern Spain. Ten distinct ITS haplotypes were distinguished, mapped and treated using F- and N-ST-statistics and nested clade (NCA) analyses. They showed a significant genetic differentiation between regional populations. NCA revealed a geographical association of ITS haplotypes, an old fragmentation into two major groups of populations, which likely colonized regions on different sides of the French Central Massif. This re-colonization pattern is reminiscent of the one observed for host trees of the Perigord truffle, such as oaks and hazelnut trees. This suggests that host postglacial expansion was one of the major factors that shaped the mycobiont population structure.

The genetic variability of southern European populations of the marine amphipod Gammarus locusta (L.) was analyzed using randomly amplified polymorphic DNA (PCR-RAPD). We analyzed 4 populations along the Portuguese coast with 10 arbitrary primers, which produced a total of 114 interpretable bands. The average percentage of polymorphism was 77% and the within-population average similarity index was high (0.841). Between-population differentiation was low, as determined by Wright's fixation index, F-ST (0.074), analysis of molecular variance (AMOVA) Phi(ST) (0.048), and Nei's unbiased distances (mean 0.032). These results are consistent with those of previous allozyme analysis, which indicated that G. locusta has low intra- and inter-population genetic variability. Low between-population differentiation indicates that G. locusta has efficient dispersal mechanisms for an organism lacking larval stages and that disperses passively. Despite the low level of genetic differentiation it was still possible to detect some genetic subdivision. The Sado and Alvor populations clustered together consistently in dendograms based on several genetic distances, and AMOVA analysis indicated some level of differentiation between populations located to the north (Aveiro and Foz do Arelho) versus southern populations (Sado and Alvor), albeit this was very low (<1.5%). Analysis of migration patterns suggested that dispersal is unbalanced, occurring primarily from west coast populations to the south coast population of Alvor, with much less reciprocal dispersal. It would be worthwhile inspecting the significance of this unbalanced north-south flow, by determining whether populations located east of Alvor also exibit such unbalanced dispersal relative to west coast populations.

Marine protected areas (MPAs) have been heralded as the next important fisheries management tool. Predicted benefits include increased fish biomass, increased species diversity, and enhanced recruitment to the MPA itself, as well as to proximal areas. Whereas MPAs have in fact been shown to increase biomass and species diversity, evidence of enhanced recruitment has yet to be seen. If MPAs are significantly enhancing recruitment, one would expect to see the recruitment dominated by groups of siblings arising from highly productive females predicted to eventually reside in MPAs due to the protection afforded them. If occurring, such sibling-dominated recruitment could be identified by significantly fewer mtDNA haplotypes and significantly fewer singleton haplotypes in population samples of recruiting juveniles compared to adult populations. We investigated a new approach for potentially determining whether MPAs might be significantly enhancing recruitment to proximal areas of Santa Cruz and the Santa Catalina islands in the California Channel Islands, by seeking evidence of sibling-dominated juvenile recruitment in mitochondrial DNA haplotype data of the kelp bass Paralabrax clathratus. Our analyses found largely genetically mixed recruitment from the plankton, suggesting that recruitment to the sampled areas was not being measurably enhanced from point sources such as the nearby MPAs.

Variation in pigmentation is common in marine invertebrates, although few studies have shown the existence of genetic differentiation of chromatic forms in these organisms. We studied the genetic structure of a colonial ascidian with populations of different colour morphs in the northwestern Mediterranean. A fragment of the c oxidase subunit 1 (COI) mitochondrial gene was sequenced in seven populations of Pseudodistoma crucigaster belonging to three different colour morphs (orange, yellow and grey). Maximum likelihood analyses showed two well-supported clades separating the orange morph from the yellow-grey morphotypes. Genetic divergence between these clades was 2.12%, and gamma(ST) values between populations of the two clades were high (average 0.936), pointing to genetic isolation. Nested clade and coalescence analyses suggest that a past fragmentation event may explain the phylogeographical origin of these two clades. Non-neutral mtDNA evolution is observed in our data when comparing the two clades, showing a significant excess of nonsynonymous polymorphism within the yellow-grey morphotype using the McDonald-Kreitman test, which is interpreted as further support of reproductive isolation. We conclude that the two clades might represent separate species. We compare the population genetic differentiation found with that estimated for other colonial and solitary ascidian species, and relate it to larval dispersal capabilities and other life-history traits.

The volcanic island of Tenerife (Canary archipelago) was formerly covered at 600-1200 m above sea level on most of its northern side by a cloud forest holding much of the endemic insect fauna. In the most significant surviving patches of this laurel forest at the eastern and western tips of the island occur two forest-specialist, closely related species of Eutrichopus (Coleoptera, Carabidae); here we present data on mitochondrial DNA variation among populations of these species. In total, 116 individuals from 16 localities were sampled and a 638 bp fragment of the cytochrome oxidase subunit II gene was sequenced, obtaining evidence for two distinct evolutionary lineages, in accordance with morphological and biogeographical data. Volcanic events at similar to0.7 Ma might be responsible for vicariance and the fragmentation of the geographical range of an ancestral species, causing the establishment of two matrilineal lineages. Using nested clade and historical demography analyses we infer past cycles of demographic bottlenecks followed by population expansion, mostly in agreement with the geological timescale of volcanic events. Recent trends, however, refer to fragmentation of the cloud forest due to human intervention.

The lesser white-fronted goose is a sub-Arctic species with a currently fragmented breeding range, which extends from Fennoscandia to easternmost Siberia. The population started to decline at the beginning of the last century and, with a current world population estimate of 25,000 individuals, it is the most threatened of the Palearctic goose species. Of these, only 30 - 50 pairs breed in Fennoscandia. A fragment of the control region of mtDNA was sequenced from 110 individuals from four breeding, one staging and two wintering areas to study geographic subdivisions and gene flow. Sequences defined 15 mtDNA haplotypes that were assigned to two mtDNA lineages. Both the mtDNA lineages were found from all sampled localities indicating a common ancestry and/or some level of gene flow. Analyses of molecular variance showed significant structuring among populations (phi(ST) 0.220, P< 0.001). The results presented here together with ecological data indicate that the lesser white-fronted goose is fragmented into three distinctive subpopulations, and thus, the conservation status of the species should be reconsidered.

In the past several decades, the development of novel molecular techniques and the advent of noninvasive DNA sampling, coupled with the ease and speed with which molecular analyses can now be performed, have made it possible for primatologists to directly examine the fitness effects of individual behavior and to explore how variation in behavior and social systems influences primate population genetic structure. This review describes the theoretical connections between individual behavior and primate social systems on the one hand and population genetic structure on the other, discusses the kinds of molecular markers typically employed in genetic studies of primates, and summarizes what primatologists have learned from molecular studies over the past few decades about dispersal patterns, mating systems, reproductive strategies, and the influence of kinship on social behavior. Several important conclusions can be drawn from this overview. First, genetic data confirm that, in many species, male dominance rank and fitness are positively related, at least over the short term, though this relationship need not simply be a reflection of male-male contest competition over mates. More importantly, genetic research reveals the significance of female choice in determining male reproductive success, and documents the efficacy of alternative mating tactics among males. Second, genetic data suggest that the presumed importance of kinship in structuring primate social relationships needs to be evaluated further, at least for some taxa such as chimpanzees in which demographic factors may be more important than relatedness. I conclude this paper by offering several suggestions of additional ways in which molecular techniques might be employed in behavioral and ecological studies of primates (e.g., for conducting,”molecular censuses” of unhabituated populations, for studying disease and host-parasite interactions, or for tracking seed fate in studies of seed dispersal) and by providing a brief introduction to the burgeoning field of nonhuman primate behavioral genetics. (C) 2003 Wiley-Liss, Inc.

The 8-10 million European Roma/Gypsies are a founder population of common origins that has subsequently split into multiple socially divergent and geographically dispersed Gypsy groups. Unlike other founder populations, whose genealogy has been extensively documented, the demographic history of the Gypsies is not fully understood and, given the lack of written records, has to be inferred from current genetic data. In this study, we have used five disease loci harboring private Gypsy mutations to examine some missing historical parameters and current structure. We analyzed the frequency distribution of the five mutations in 832-1,363 unrelated controls, representing 14 Gypsy populations, and the diversification of chromosomal haplotypes in 501 members of affected families. Sharing of mutations and high carrier rates supported a strong founder effect, and the identity of the congenital myasthenia 1267delG mutation in Gypsy and Indian/Pakistani chromosomes provided the best evidence yet of the Indian origins of the Gypsies. However, dramatic differences in mutation frequencies and haplotype divergence and very limited haplotype sharing pointed to strong internal differentiation and characterized the Gypsies as a founder population comprising multiple subisolates. Using disease haplotype coalescence times at the different loci, we estimated that the entire Gypsy population was founded similar to32-40 generations ago, with secondary and tertiary founder events occurring similar to16-25 generations ago. The existence of multiple subisolates, with endogamy maintained to the present day, suggests a general approach to complex disorders in which initial gene mapping could be performed in large families from a single Gypsy group, whereas fine mapping would rely on the informed sampling of the divergent subisolates and searching for the shared genomic region that displays the strongest linkage disequilibrium with the disease.

Evolutionary processes can be strongly affected by landscape features. In vagile carnivores that disperse widely, however, genetic structure has been found to be minimal. Using microsatellite DNA primers developed for other mustelids, we found that populations of a vagile forest carnivore, the fisher (Martes pennanti), exhibit high genetic structure (F-ST = 0.45, SE = 0.07) and limited gene flow (Nm < 1) within a > 1,600-km narrow strip of forested habitat; that genetic diversity decreases from core to periphery; and that populations do not show an equilibrium pattern of isolation-by-distance. Genetic structure was greater at the periphery than at the core of the distribution and our data fit a I-dimensional model of stepping-stone range expansion. Multiple lines of paleontological and genetic evidence suggest that the fisher recently (<5,000 years ago) expanded into the mountain forests of the Pacific coast. The reduced dimensionality of the distribution of the fisher in western coastal forests appears to have contributed to the high levels of structure and decreasing diversity from north to south. These effects were likely exacerbated by human-caused changes to the environment. The low genetic diversity and high genetic structure of populations in the southern Sierra Nevada suggest that populations in this part of the geographic range are vulnerable to extinction.

Reconstructing ancestral geographic origins is critical for understanding the long-term evolution of a species. Bayesian methods have been proposed to test biogeographic hypotheses while accommodating uncertainty in phylogenetic reconstruction. However, the problem that certain taxa may have a disproportionate influence on conclusions has not been addressed. Here, we infer the geographic origin of Drosophila simulans using 2014 bp of the period locus from 63 lines collected from 18 countries. We also analyze two previously published datasets, alcohol dehydrogenase related and NADH.-ubiquinone reductase 75 kDa subunit precursor. Phylogenetic inferences of all three loci support Madagascar as the geographic origin of D. simulans. Our phylogenetic conclusions are robust to taxon resampling and to the potentially confounding effects of recombination. To test our phylogenetically derived hypothesis we develop a randomization test of the population genetics prediction that sequences from the geographic origin should contain more genetic polymorphism than those from derived populations. We find that the Madagascar population has elevated genetic polymorphism relative to non-Madagascar sequences. These data are corroborated by mitochondrial DNA sequence data. (C) 2004 Elsevier Inc. All rights reserved.

HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics and epidemic history of HIV-1 group 0 from viral gene sequence data and evaluate the effect of variable evolutionary rates and recombination on our estimates. First, model selection tools were used to specify suitable evolutionary and coalescent models for HIV group O. Second, divergence times and population genetic parameters were estimated in a Bayesian framework using Markov chain Monte Carlo sampling, under both strict and relaxed molecular clock methods. Our results date the origin of the group 0 radiation to around 1920 (1890-1940), a time frame similar to that estimated for HIV-1 group M. However, group 0 infections, which remain almost wholly restricted to Cameroon, show a slower rate of exponential growth during the twentieth century, explaining their lower current prevalence. To explore the effect of recombination, the Bayesian framework is extended to incorporate multiple unlinked loci. Although recombination can bias estimates of the time to the most recent common ancestor, this effect does not appear to be important for HIV-1 group O. In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.

Genetic, ethnographic, and historical evidence suggests that the Hindu castes have been highly endogamous for several thousand years and that, when movement between castes does occur, it typically consists of females joining castes of higher social status. However, little is known about migration rates in these populations or the extent to which migration occurs between caste groups of low, middle, and high social status. To investigate these aspects of migration, we analyzed the largest collection of genetic markers collected to date in Hindu caste populations. These data included 45 newly typed autosomal short tandem repeat polymorphisms (STRPs), 411 bp of mitochondrial DNA sequence, and 43 Y-chromosomal single-nucleotide polymorphisms that were assayed in more than 200 individuals of known caste status sampled in Andrah Pradesh, in South India. Application of recently developed likelihood-based analyses to this dataset enabled us to obtain genetically derived estimates of intercaste migration rates. STRPs indicated migration rates of 1-2% per generation between high-, middle-, and low-status caste groups. We also found support for the hypothesis that rates of gene flow differ between maternally and paternally inherited genes. Migration rates were substantially higher in maternally than in paternally inherited markers. In addition, while prevailing patterns of migration involved movement between castes of similar rank, paternally inherited markers in the low-status castes were most likely to move into high-status castes. Our findings support earlier evidence that the caste system has been a significant, long-term source of population structuring in South Indian Hindu populations, and that patterns of migration differ between males and females.

The Eastern Spot-billed Duck (Anas zonorhyncha) historically was rare in the southern Russian Far East. However, during the last 60-70 years, its breeding range in East Asia has expanded northwest; Eastern Spot-billed Ducks are breeding increasingly within the range of Mallards (A. platyrhynchos). We collected 120 Eastern Spot-billed Ducks and Mallards from Primorye, Russia, and sequenced 666-667 base pairs (bp) of the maternally inherited mitochondrial DNA (mtDNA) control region and 255 bp of the ornithine decarboxylase intron six (ODC6). Control region and ODC-6 allele sequences revealed two divergent groups of haplotypes and alleles that differ by 1.5% and 2.0%, respectively, and correspond to Avise et al.'s (1990) group A and B mtDNA haplotypes. Group A mtDNA haplotypes occurred in 22 Eastern Spot-billed Ducks and 78 Asian Mallards, and group B haplotypes occurred in 14 Eastern Spot-billed Ducks and 4 Asian Mallards. Moreover, the group B haplotypes that we observed predominantly in Eastern Spot-billed Ducks (i.e. group SB) were monophyletic and diverged by 2-16 substitutions from group B haplotypes previously sequenced from 241 Mottled (A. fulvigula), American Black (A. rubripes), and Mexican ducks (A. diazi), and from North American Mallards. In contrast, type 1 and 2 ODC-6 allele frequencies for Eastern Spot-billed Ducks and Mallards did not differ, but heterozygosity for the former was greater than expected under Hardy-Weinberg equilibrium. Our analysis is the first to document the existence of two divergent haplotype and allele lineages (group A and B, type I and 2) in Asian mallard species and suggests that Eastern Spot-billed Ducks are more closely related to North America's Mottled, American Black, and Mexican ducks than they are to Mallards, which occur sympatrically in East Asia. Our data are consistent with the hypothesis that Eastern Spot-billed Ducks and Mallards have hybridized extensively in the Russian Far East. If so, apparent differences in group A and B mtDNA haplotype ratios, effective populations sizes, and migration rates indicate that many more male Eastern Spot-billed Ducks mated with female Mallards and more Eastern Spot-billed Ducks received ODC-6 alleles from Mallards than vice versa. We hypothesize that those differences reflect strong female natal-site fidelity and high levels of male dispersal, and that Mallards significantly outnumber Eastern Spot-billed Ducks in Primorye. Excess heterozygosity in Eastern Spot-billed Ducks (and in Mallards to a lesser extent) is probably maintained by ongoing emigration of Eastern Spot-billed Ducks and Mallards from areas of allopatry outside the Primorye region, where Eastern Spot-billed Ducks and Mallards are predicted to possesses genotypic frequencies historically diagnostic of each species.

Historical reconstruction of the population dynamics of whales before, during and after exploitation is crucial to marine ecological restoration and for the consideration of future commercial whaling. Population dynamic models used by the International Whaling Commission require historical catch records, estimates of intrinsic rates of increase and current abundance, all of which are subject to considerable uncertainty. Population genetic parameters can be used for independent estimates of historical demography, but also have large uncertainty, particularly for rates of mutational substitution and gene flow. At present, demographic and genetic estimates of pre-exploitation abundance differ by an order of magnitude and, consequently, suggest vastly different baselines for judging recovery. Here, we review these two approaches and suggest the need for a synthetic analytical framework to evaluate uncertainty in key parameters. Such a framework could have broad application to modelling both historical and contemporary population dynamics in other exploited species.

The genetic study of diverging, closely related Populations is required for basic questions on demography and speciation, as well as for biodiversity and conservation research. However, it is often unclear whether divergence is due Simply to separation or whether populations have also experienced gene flow. These questions can be addressed with a full model of population separation with gene flow, by applying a Markov chain Monte Carlo method for estimating the posterior probability distribution of model parameters. We have generalized this method and made it applicable to data from multiple unlinked loci. These loci can vary in their modes of inheritance, and inheritance scalars can be implemented either as constants or as parameters to be estimated. By treating inheritance scalars as parameters it is also possible to address variation among loci in the impact via linkage of recurrent selective sweeps or background selection. These methods are applied to a large multilocus data set from Drosophila pseudoobscura and D. persimilis. The species are estimated to have diverged similar to500,000 years ago. Several loci have nonzero estimates of gene flow since the initial separation of the species, with considerable variation in gene flow estimates among loci, in both directions between the species.

Phylogenetic analyses of complete mitochondrial cytochrome b sequences support the monophyly of pocket gopher (Thomomys bottae) populations from the 1000 km length of the Baja California peninsula of Mexico, relative to other geographical segments of the species range in western North America. The Baja California peninsula is an area that encompasses considerable ecomorphological and infraspecific diversity within this pocket gopher species. However, detailed population analyses encompassing 35 localities distributed over the southern half of the peninsula reveal only trivial phylogeographical structure. Rather, most of the 72 unique 500-base pair haplotypes examined from 142 individuals is restricted to single populations, although a few haplotypes are shared broadly across geography. Individual populations are typically comprised of haplotype sets from different branches in a network of relationships. Analysis of molecular variance (AMOVA) indicates that approximately half of the total pool of variation is contained among individuals within local populations, and that only about 25% can be explained by the regional subdivisions of current subspecies distributions or physiographic realms. A hypothesized historical vicariant event that has been causally linked to the phylogeographical structure of other, codistributed species has had little influence on these pocket gopher populations, explaining only 13% of the total variation. The temporal depth, estimated by coalescence parameters, of the haplotype lineage in Baja California is relatively recent, approximately 300 000 generations; both the mismatch distribution of pairwise comparisons and a significantly positive exponential growth estimate support a recent history of expanding populations; but current, or recent past, migration estimates have remained small, are largely unidirectional from north to south, and weak isolation by distance is present. All data suggest that pocket gophers have relatively recently invaded the southern half of peninsular Baja California, with the genetic signature of expansion still evident but with sufficient time having lapsed to result in a weak isolation by distance pattern. The geographical assemblage of sampled populations thus appears as a meta-population, with limited gene flow contrasting with random haplotype loss due to drift in small, localized populations.

Patterns of geographic variation in phenotype or genotype may provide evidence for natural selection. Here, we compare phenotypic variation in color, allele frequencies of a pigmentation gene (the melanocortin-1 receptor, Mc1r), and patterns of neutral mitochondrial DNA (mtDNA) variation in rock pocket mice (Chaetodipus intermedius) across a habitat gradient in southern Arizona. Pocket mice inhabiting volcanic lava have dark coats with unbanded, uniformly melanic hairs, whereas mice from nearby light-colored granitic rocks have light coats with banded hairs. This color polymorphism is a presumed adaptation to avoid predation. Previous work has demonstrated that two Mc1r alleles, D and d, differ by four amino acids, and are responsible for the color polymorphism: DD and Dd genotypes are melanic whereas dd genotypes are light colored. To determine the frequency of the two Mc1r allelic classes across the dark-colored lava and neighboring light-colored granite, we sequenced the Mc1r gene in 175 individuals from a 35-km transect in the Pinacate lava region. We also sequenced two neutral mtDNA genes, COIII and ND3, in the same individuals. We found a strong correlation between Mc1r allele frequency and habitat color and no correlation between mtDNA markers and habitat color. Using estimates of migration from mtDNA haplotypes between dark- and light-colored sampling sites and Mc1r allele frequencies at each site, we estimated selection coefficients against mismatched Mc1r alleles, assuming a simple model of migration-selection balance. Habitat-dependent selection appears strong but asymmetric: selection is stronger against light mice on dark rock than against melanic mice on light rock. Together these results suggest that natural selection acts to match pocket mouse coat color to substrate color, despite high levels of gene flow between light and melanic populations.

Since the completion of the human genome sequencing project, the discovery and characterization of human genetic variation is a principal focus for future research. Comparative studies across ethnically diverse human populations and across human and nonhuman primate species is important for reconstructing human evolutionary history and for understanding the genetic basis of human disease. In this review, we summarize data on patterns of human genetic diversity and the evolutionary forces (mutation, genetic drift, migration, and selection) that have shaped these patterns of variation across both human populations and the genome. African population samples typically have higher levels of genetic diversity, a complex population substructure, and low levels of linkage disequilibrium (LD) relative to non-African populations. We discuss these differences and their implications for mapping disease genes and for understanding how population and genomic diversity have been important in the evolution, differentiation, and adaptation of humans.

Though the rock ptarmigan, Lagopus mutus (Montin, 1776), is a relatively common breeding bird in arctic regions worldwide, several Nearctic insular populations have become extinct or threatened in the past 250 years. In this study, we use patterns of DNA sequence variation in the mitochondrial control region and a nuclear intron (GAPDH) to reexamine the evolutionary history of Nearctic rock ptarmigan populations as a basis for conservation and management. The extent of genetic diversity within currently recognized subspecies varies widely, with many nonmigratory insular subspecies genetically invariant and continental subspecies moderately diverse. Our analyses suggest at least six evolutionarily significant units (ESUs) in the Nearctic and Iceland, four of which correspond to recognized subspecies: Lagopus mutus evermanni (Elliot, 1896) on Attu I., Alaska, Lagopus mutus welchi (Brewster, 1885) on Newfoundland, Lagopus mutus rupestris (Gmelin, 1789) in the Canadian Arctic, and Lagopus mutus islandorum (Faber, 1822) on Iceland. A fifth ESU comprises three central Aleutian subspecies. The remaining subspecies of the Aleutian archipelago, along with Lagopus mutus nelsoni (Stejneger, 1884) of mainland Alaska and Lagopus mutus captus (Peters, 1934) of Ellesmere I., Nunavut, constitute a sixth ESU, which we further subdivide into three management units based on patterns of genetic substructuring and geographic barriers to immigration.

Microsatellite analysis and computer simulations strongly suggested that a culvert, i.e. a connection between two river stretches by a narrow tube underneath an artificial channel, was not a migration barrier for the endangered bullhead Cottus gobio. (C) 2004 The Fisheries Society of the British Isles.

Genetic differentiation among populations of the South African scrub hare Lepus saxalilis was examined using hypervariable mitochondrial DNA control region I (CR-I) sequences. Neighbour-joining analysis revealed a pattern that did not correspond to the current subspecies delineations. The CR-I sequence data delimit scrub hares into three major maternal lineages. The three phylogenetic assemblages exhibited different geographical distributions. AMOVA analyses and exact tests for population differentiation confirmed this phylogeographic partitioning. One lineage (SW) was confined to the south-western Cape, the second lineage (N) was exclusively found in the northern part of South Africa and in the neighbouring Countries, and the third lineage (C) was predominant in the central parts of South Africa. This spatial distribution did not coincide with the ranges of the 10 described Subspecies covered by our sampling regime. The lineages C and N overlapped in an area including eastern parts of South Africa and Southern Namibia. The presence of both lineages in that area of overlap was interpreted as the result of secondary contact due to recent range expansions after the two lineages had undergone a population restriction approximately 18 000 years ago. Analyses of contemporary gene flow disclosed an exchange of migrants between N and C, which was biased towards a movement from C to N. The SW group represents a very distinct evolutionary lineage that has been isolated for more than 45 000 years. It does not exchange female migrants with the other two groups. Mismatch distribution analyses indicated sudden Population size expansions in the history of all three populations.

Evidence is mounting that evolutionary change can occur rapidly and may be an important means by which species escape extinction in the face of global change. Consequently, biologists need to incorporate evolutionary thinking into management decisions in conservation and restoration ecology. Here, we review the genetic and demographic properties that influence the ability of populations to adapt to rapidly changing selective pressures. To illustrate how evolutionary thinking can influence conservation and restoration strategies, we compare the potential of two California plant communities (vernal pools and blue oak woodlands) to evolve in response to global change. We then suggest ways in which restoration biologists can manipulate the genetic architecture of target populations to increase their ability to adapt to changing conditions. While there may not be any universal rules regarding the adaptive potential of species, an understanding of the various processes involved in microevolution will increase the short- and long-term success of conservation and restoration efforts.

Patterns of intraspecific genetic variation result from interactions among both historical and contemporary evolutionary processes. Traditionally, population geneticists have used methods such as F-statistics, pairwise isolation by distance models, spatial autocorrelation and coalescent models to analyse this variation and to gain insight about causal evolutionary processes. Here we introduce a novel approach (Population Graphs) that focuses on the analysis of marker-based population genetic data within a graph theoretic framework. This method can be used to estimate traditional population genetic summary statistics, but its primary focus is on characterizing the complex topology resulting from historical and contemporary genetic interactions among populations. We introduce the application of Population Graphs by examining the range-wide population genetic structure of a Sonoran Desert cactus (Lophocereus schottii). With this data set, we evaluate hypotheses regarding historical vicariance, isolation by distance, population-level assignment and the importance of specific populations to species-wide genetic connectivity. We close by discussing the applicability of Population Graphs for addressing a wide range of population genetic and phylogeographical problems.

Population genetic structures of the mackerel (Scomber scombrus) and chub mackerel (Scomber japonicus) were studied in the Mediterranean Sea. Fragments of 272 bp (S. scomber) and 387 bp (S. japonicus) of the 5'-end of the mitochondrial control region were sequenced from spawning individuals collected off the coasts of Greece, Italy, Spain, and Portugal. High levels of mitochondrial control region haplotypic diversity (>0.98) were found for both Scomber species. Nucleotide diversity was higher in the mackerel (0.022) than in the chub mackerel (0.017). Global F-ST values were also higher and significant in the mackerel (0.024, P<0.0001) as opposed to the chub mackerel (0.003, P>0.05). Molecular variance analyses showed differential genetic structuring for these two closely related species. There is extensive gene flow between Mediterranean Sea and Atlantic Ocean populations of chub mackerel, which are organized into a larger panmictic unit. In contrast, Mediterranean Sea populations of mackerel show some degree of genetic differentiation and are structured along an east-west axis. The analysed eastern Mediterranean Sea mackerel populations (Greece, Italy) are clearly separated from that of the western Mediterranean Sea (Barcelona), which forms a panmictic unit with eastern Atlantic Ocean populations. The genetic structures of both species showed asymmetric migration patterns and indicated population expansion.

Orissa, on the east coast of India, is one of the three mass nesting sites in the world for olive ridley turtles (Lepidochelys olivacea). This population is currently under threat as a result of fishery-related mortality; more than 100 000 olive ridleys have been counted dead in the last 10 years in Orissa. In general, the globally distributed olive ridley turtle has received significantly less conservation attention than its congener, the Kemp's ridley turtle (L. kempi), because the latter is recognized as a distinct species consisting of a single endangered population. Our study of mitochondrial DNA haplotypes suggests that the ridley population on the east coast of India is panmictic, but distinct from all other populations including Sri Lanka. About 96% of the Indian population consisted of a distinct `K' clade with haplotypes not found in any other population. Nested clade analysis and conventional analysis both supported range expansions and/or long-distance colonization from the Indian Ocean clades to other oceanic basins, which suggested that these are the ancestral source for contemporary global populations of olive ridley turtles. These data support the distinctiveness of the Indian Ocean ridleys, suggesting that conservation prioritization should be based on appropriate data and not solely on species designations.

We investigated the genetic population structure and species status of a relatively sedentary bird that is a permanent resident of western North American forests, the blue grouse (Dendragapus obscurus). Phylogenetic analysis of complete mitochondrial control region DNA sequences resulted in the identification of three basal clades of haplotypes that were largely congruent with well-known biogeographical regions. These clades corresponded to the parapatric sooty (D. o. fuliginosus) and dusky (D. o. obscurus) subspecies groups of blue grouse plus a previously unrecognized division between northern and southern dusky grouse populations; the latter does not correspond closely to any currently recognized subspecies boundary. Approximately 66% of the total genetic variation was distributed among these three regions. Maximum likelihood estimates of gene flow between the regions were low or asymmetric; gene flow has been insufficient to prevent genetic divergence between dusky and sooty grouse. Estimates of gene flow among populations within sooty grouse were large except across the Columbia River valley. Among populations of dusky grouse, estimates of gene flow were heterogeneous and asymmetrical, reflecting large-scale fragmentation of the distribution due to landscape features and associated vegetation. Genetic, morphological and behavioural evidence suggest that sooty and dusky grouse are species-level taxa; the specific status of a third clade remains ambiguous.

Stephens and Donnelly (2000) constructed an efficient sequential importance-sampling proposal distribution on coalescent histories of a sample of genes for computing the likelihood of a type configuration of genes in the sample. In the current paper a characterization of their importance-sampling proposal distribution is given in terms of the diffusion-process generator describing the distribution of the population gene frequencies. This characterization leads to a new technique for constructing importance-sampling algorithms in a much more general framework when the distribution of population gene frequencies follows a diffusion process, by approximating the generator of the process.

De Iorio and Griffiths (2004) developed a new method of constructing sequential importance-sampling proposal distributions on coalescent histories of a sample of genes for computing the likelihood of a type configuration of genes in the sample by simulation. The method is based on approximating the diffusion-process generator describing the distribution of population gene frequencies, leading to an approximate sample distribution and finally to importance-sampling proposal distributions. This paper applies that method to construct an importance-sampling algorithm for computing the likelihood of samples of genes in subdivided population models. The importance-sampling technique of Stephens and Donnelly (2000) is thus extended to models with a Markov chain mutation mechanism between gene types and migration of genes between subpopulations. An algorithm for computing the likelihood of a sample configuration of genes from a subdivided population in an infinitely-many-alleles model of mutation is derived, extending Ewens's (1972) sampling formula in a single population. Likelihood calculation and ancestral inference in gene trees constructed from DNA sequences under the infinitely-many-sites model are also studied. The Griffiths-Tavare method of likelihood calculation in gene trees of Bahlo and Griffiths (2000) is improved for subdivided populations.

Genealogy-based methods were used to estimate migration of the fungal virus Cryphonectria hypovirus I between vegetative compatibility types of the host fungus, Cryphonectria parasitica, as a means of estimating horizontal transmission within two host populations. Vegetative incompatibility is a self/non-self recognition system that inhibits virus transmission under laboratory conditions but its effect. on transmission in nature has not been clearly demonstrated. Recombination within and among different loci in the virus,genome restricted the genealogical analyses to haplotypes with common initiation and recombinational histories. The existence of recombination necessitated that we also Use genealogical approaches that can take advantage of both the imitation and recombinational histories of the sample. Virus migration between populations was significantly restricted. In contrast, estimates of migration between vegetative compatibility types were relatively high within populations despite previous evidence that transmission in the laboratory was restricted. The discordance between laboratory estimates and migration estimates from natural populations highlights the challenges in estimating pathogen transmission rates. Genealogical analyses inferred migration patterns throughout the entire coalescent history of one viral region in natural populations and not just recent patterns of migration or laboratory transmission. This application of genealogical analyses provides markedly stronger inferences on overall transmission rates than laboratory estimates do.

We examined the effects of habitat fragmentation of the white-starred robin Pogonocichla stellata metapopulation in the Taita Hills archipelago, a hotspot for biodiversity which was fragmented similar to40 years ago. Using seven microsatellite markers, we analysed the robin's genetic structure and tested for equilibrium between migration and drift (testing the probability of decreased dispersal) as well as between mutation and drift (test for recent reduction in effective population size, i.e. bottlenecks). This metapopulation was found to retain relatively high levels of genetic variability (H-E between 0.63 and 0.71) and to be in migration-drift equilibrium, suggesting that increased isolation between fragments did not have much effect on the dispersal between them. Furthermore, this equilibrium test greatly enhanced the interpretation of parameters (e.g. F-ST) assumed to have reached an equilibrium value. In contrast to previous findings on the related and sympatric Taita thrush Turdus helleri (which is critically endangered), there were no indications for recent bottlenecks in any of the robin subpopulations. This difference can be attributed to the higher dispersal capacity of the robin compared with the thrush (deduced from both the genetic and capture-recapture data). Our results stress the importance of sustained dispersal for species conservation.

We examined polymorphism at seven microsatellite loci among sea trout (Salmo trutta) (n = 846) collected from three areas in the Limfjord (Denmark). We then assessed their potential population source by comparing, using a mixed stock analysis (MSA) Bayesian framework, their genetic composition to that of brown trout collected from 32 tributaries pooled into nine geographical regions (n = 3801) and two hatcheries (n = 222) used for stocking. For each of the three regional sea trout groups (western, central and eastern Limfjord, n = 91, n = 426, n = 329, respectively), MSA was conducted with (i) all individuals in the group, (ii) with the subset of spawning sea trout only and (iii) with the subset of foraging, nonspawning individuals only, a subset that consisted primarily of sea trout caught during their first year at sea. For all three regional sea trout groups, a higher proportion of individuals (regardless of whether they were foraging or spawning) appear to have originated from the rivers that drain locally, than from the rivers that drain in other parts of the Limfjord. This suggests (1) that sea trout, at least during their first year at sea, undertake limited migrations within the Limfjord system and (2) that sea trout on their spawning run were caught close to their natal rivers. The proportion of sea trout of hatchery origin varied widely among all three Limfjord areas and broadly reflected regional stocking histories, with high proportions of sea trout of domestic origin in the east (39.3%), where stocking with domestic trout was practised intensely at the time of sampling, and in the west (57.2%), where a programme of coastal stocking of post smolts took place over several years in the early 1990s. In contrast, in the central Limfjord, where stocking with domestic trout was largely abandoned in the early 1990s, the proportion of sea trout of domestic origin was only 8.5%. Interestingly, for all three regional sea trout groups, virtually no sea trout of hatchery origin were found among the spawning individuals, which were on average larger than the nonspawning sea trout. These results suggest that stocked domestic brown trout that become anadromous experience high mortality at sea and are therefore largely absent among the larger, spawning individuals. We conclude that sea trout of domestic origin exhibit much reduced ability to reproduce and are unlikely to contribute significantly to the local gene pool largely because of a relatively high mortality at sea before the onset of maturity.

Western European populations of red-crested pochard (Netta rufina) are characterized by low size and high fragmentation, which accentuate their sensitivity to hunting. Uncertainties regarding the demographic trends of these populations highlight the need for pertinent hunting regulations. This requires identification of the limits of the populations under exploitation, i.e. delimiting a management unit. We used the left domain of the mitochondrial control region and seven nuclear loci (four microsatellites and three introns) to assess the level of genetic structure and demographic independence between the fragmented Western European and the large Central Asian populations. The second objective was to investigate the colonization history of the Western European populations. This study demonstrated that the Western European populations of red-crested pochard constitute a separate demographic conservation unit relative to the Asian population as a result of very low female dispersal (mitochondrial DNA: Phi(ST) = 0.152). A morphometric analysis further suggested that Central Asian and Western European specimens of both sexes originate from different pools of individuals. Male dispersal seems higher than female dispersal, as suggested by the lack of clear genetic structure for the nuclear markers at this continental scale. Genetic data, in conjunction with historical demographic data, indicate that the current Western European populations probably originate from a recent colonization from Central Asia. As numbers of red-crested pochards in Western Europe cannot be efficiently supplemented by immigration from the larger Asian populations, a management plan regulating the harvest in Western Europe is required.

Over the last decade, a number of new methods of population genetic analysis based on likelihood have been introduced. This review describes and explains the general statistical techniques that have recently been used, and discusses the underlying population genetic models. Experimental papers that use these methods to infer human demographic and phylogeographic history are reviewed. It appears that the use of likelihood has hitherto had little impact in the field of human population genetics, which is still primarily driven by more traditional approaches. However, with the current uncertainty about the effects of natural selection, population structure and ascertainment of single-nucleotide polymorphism markers, it is suggested that likelihood-based methods may have a greater impact in the future.

Brownian motions on coalescent structures have a biological relevance, either as an approximation of the stepwise mutation model for microsatellites, or as a model of spatial evolution considering the locations of individuals at successive generations. We discuss estimation procedures for the dispersal parameter of a Brownian motion defined on coalescent trees. First, we consider the mean square distance unbiased estimator and compute its variance. In a second approach, we introduce a phylogenetic estimator. Given the UPGMA topology, the likelihood of the parameter is computed thanks to a new dynamical programming method. By a proper correction, an unbiased estimator is derived from the pseudomaximum of the likelihood. The last approach consists of computing the likelihood by a Markov chain Monte Carlo sampling method. In the one-dimensional Brownian motion, this method seems less reliable than pseudomaximum-likelihood. (C) 2004 Elsevier Inc. All rights reserved.

Human immunodeficiency virus type I (HIV-1) has high replication and mutation rates that generate large census populations and high levels of genetic variation. We examined the roles of natural selection, population growth, random genetic drift, and recombination in shaping the variation in 1509 C2-V5 env sequences derived from nine men with chronic HIV-1 infection. These sequences were obtained from clinical visits that reflect the first 6-13.7 years of infection. Pairwise comparisons of nonsynonymous and synonymous distances, Tajima's D test, Fu and Li's D* test, and a test of recurrent mutation revealed evidence for episodes of nonneutral evolution in a total of 22 out of 145 blood samples, representing six of the nine individuals. Using three coalescent-based maximum-likelihood estimators, we found viral effective population sizes in all nine individuals to be similar to10(3). We also show that a previous estimate of the effective population Size Of similar to10(5) based on rare haplotype frequencies decreases to similar to10(3) upon correcting a biased sampling procedure. We conclude that the genetic variation in these data sets can be explained by a predominance of random genetic drift of neutral mutations with brief episodes of natural selection that were frequently masked by recombination.

Three coalescent-based methods allowed us to infer some aspects of the history of three Bulgarian Gypsies populations belonging to the Vlax linguistic group: the Lom, Rudari and Kalderas. We used several kinds of genetic markers: HV1 sequences of the maternally inherited mitochondrial genome and microsatellites of the paternally inherited Y chromosome and of the biparentally inherited chromosome 8. This allowed us to infer several parameters for men and women: the splitting order of the populations and the ages of the splitting events, the growth rate in each population and the migration rates between populations. Altogether, they enabled us to infer a demographic scenario that could explain the genetic diversity of Vlax Roma: recent splits occurring after the arrival in Europe, asymmetric migration flows especially for males and unequal growth rates. This represents a considerable contribution to the Vlax Roma history in comparison with the inferences from classical population genetics.

Allelic variation at hypervariable, nuclear-encoded loci and mitochondrial (mt)DNA was studied among three geographic samples (40 individuals) of the critically endangered Cape Fear shiner, Notropis mekistocholas. Genetic variation, as measured by allelic richness and gene (microsatellite) or nucleon (mtDNA) diversity, was similar to that in other fish species. Homogeneity tests of allele and genotype distributions and analysis of molecular variance (AMOVA) at nuclear-encoded loci revealed significant genetic heterogeneity among localities. No differences in mtDNA allele (haplotype) frequencies were detected. The ratio of the number of microsatellite alleles to the range in allele size suggested that significant reductions in effective size have occurred at two of the three localities. Long-term (inbreeding) effective population size differed among the samples and ranged from similar to1,300 to similar to3,000. Collectively, these results indicate that (i) Cape Fear shiners at these localities are not genetically impoverished, (ii) separate populations of Cape Fear shiners may exist in the Cape Fear drainage, (iii) recent reduction in effective size may have occurred in two of the three localities. and (iv) ancestral populations of Cape Fear shiners may have been of sufficient effective size to offset extinction due to genetic factors.

Bayesian statistics allow scientists to easily incorporate prior knowledge into their data analysis. Nonetheless, the sheer amount of computational power that is required for Bayesian statistical analyses has previously limited their use in genetics. These computational constraints have now largely been overcome and the underlying advantages of Bayesian approaches are putting them at the forefront of genetic data analysis in an increasing number of areas.

The endemic Hawaiian grouper, Epinephelus quernus, is a commercially important species experiencing intense fishing pressure in part of its distributional range. We examined population genetic structure with 398 base pairs of the mitochondrial control region across a large portion of the range of E. quernus, spanning approximately 2000 km of the Hawaiian archipelago. Examination of genetic diversity shows that Gardner Island, situated midway along the island chain, harbours the most diverse haplotypes. F-statistics and Bayesian estimates of migration also reveal the mid-archipelago as genetically differentiated, where the first significant break among adjacent pairs of populations lies between the islands of Nihoa and Necker. Most island comparisons beyond Necker and Gardner to the northwest and among the lower five islands to the south-east show little to no genetic differences. Evidence of historical population expansion across the islands was also found by Maximum Likelihood analyses. The results suggest that management should be structured to reflect the genetic differentiation and diversity in the mid-archipelago, the patterns of which may be associated with oceanic current patterns. (C) 2004 The Linnean Society of London,

We have examined the population genetic structure in a collection of nine isolates of the parasitic lungworm Dictyocaulus viviparus. Eight of the isolates were sampled from cattle in geographically separated farms throughout south-central Sweden, and one isolate was a laboratory strain that has been maintained in experimentally infected calves for almost four decades. A total of 72 worms were examined, with eight individual worms from the same individual host representing each isolate. The genetic variation as revealed by amplified fragment length polymorphism analysis using four selective primer combinations was high. Depending on the primer combination a total of 66-79 restriction fragments were amplified, with 26-44 peaks of similar complexity from each of the isolates. The heterozygosity within populations was relatively small, as were the population mutation and immigration rates, which seemed to be in neutral equilibrium. The genetic diversity was therefore reasonably well structured in the field; and the laboratory isolate was quite distinct from the field samples. There was no relationship between the patterns of genetic diversity and the geographical proximity of the farms. The estimates of heterozygosity were much larger and more consistent than those previously estimated for this nematode species using mitochondrial sequencing, and the genetic structuring was thus much less pronounced and the gene flow greater. We attribute these differences in estimation to the broader sampling of loci available using amplified fragment length polymorphism markers, which may therefore constitute a superior technique for the study of patterns of lungworm diversity. Furthemore, the data estimating gene flow for D. viviparus was less than previously reported for closely related species in North America. This might be related to different rates of movements of infected hosts. It seems likely that lungworm infections are rather persistent on different farms, and the sudden outbreaks of disease that can be observed with host movements are most likely to be related to the introduction of susceptible stock. (C) 2003 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

We propose a method of analysing genetic data to obtain separate estimates of the size (N-p) and migration rate (m(p)) for the sampled populations, without precise prior knowledge of mutation rates at each locus (mu(L)). The effects of migration and mutation can be distinguished because high migration has the effect of reducing genetic differentiation across all loci, whereas a high mutation rate will only affect the locus in question. The method also takes account of any differences between the spectra of immigrant alleles and of new mutant alleles. If the genetic data come from a range of population sizes, and the loci have a range of mutation rates, it is possible to estimate the relative sizes of the different N-p values, and likewise the m(p) and the mu(L). Microsatellite loci may also be particularly appropriate because loci with a high mutation rate can reach mutation-drift-migration equilibrium more quickly, and because the spectra of mutants arriving in a population can be particularly distinct from the immigrants. We demonstrate this principle using a microsatellite data set from Mauritian skinks. The method identifies low gene flow between a putative new species and populations of its sister species, whereas the differentiation of two other populations is attributed to small population size. These distinct interpretations were not readily apparent from conventional measures of genetic differentiation and gene diversity. When the method is evaluated using simulated data sets, it correctly distinguishes low gene flow from small population size. Loci that are not at mutation-migration-drift equilibrium can distort the parameter estimates slightly. We discuss strategies for detecting and overcoming this effect.

Current estimators of gene flow come in two methods; those that estimate parameters assuming that the populations investigated are a small random sample of a large number of populations and those that assume that all populations were sampled. Maximum likelihood or Bayesian approaches that estimate the migration rates and population sizes directly using coalescent theory can easily accommodate datasets that contain a population that has no data, a so-called `ghost' population. This manipulation allows us to explore the effects of missing populations on the estimation of population sizes and migration rates between two specific populations. The biases of the inferred population parameters depend on the magnitude of the migration rate from the unknown populations. The effects on the population sizes are larger than the effects on the migration rates. The more immigrants from the unknown populations that are arriving in the sample populations the larger the estimated population sizes. Taking into account a ghost population improves or at least does not harm the estimation of population sizes. Estimates of the scaled migration rate M (migration rate per generation divided by the mutation rate per generation) are fairly robust as long as migration rates from the unknown populations are not huge. The inclusion of a ghost population does not improve the estimation of the migration rate M; when the migration rates are estimated as the number of immigrants Nm then a ghost population improves the estimates because of its effect on population size estimation. It seems that for `real world' analyses one should carefully choose which populations to sample, but there is no need to sample every population in the neighbourhood of a population of interest.

A plethora of statistical models have recently been developed to estimate components of population genetic history. Very few of these methods, however, have been adequately evaluated for their performance in accurately estimating population genetic parameters of interest. In this paper, we continue a research program of evaluation of population genetic methods through computer simulation. Specifically, we examine the software MIGRATEE-N 1.6.8 and test the accuracy of this software to estimate genetic diversity (Theta), migration rates, and confidence intervals. We simulated nucleotide sequence data under a neutral coalescent model with lengths of 500 bp and 1000 bp, and with three different per site Theta values of (0.00025, 0.0025, 0.025) crossed with four different migration rates (0.0000025, 0.025, 0.25, 2.5) to construct 1000 evolutionary trees per-combination per-sequence-length. We found that while MIGRATEE-N 1.6.8 performs reasonably well in estimating genetic diversity (Theta), it does poorly at estimating migration rates and the confidence intervals associated with them. We recommend researchers use this software with caution under conditions similar to those used in this evaluation.

We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and theta(B); (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Information Criterion (DIC) as a model choice criterion for determining whether there is evidence for inbreeding within populations or genetic differentiation among populations; and (iv) use of samples from the posterior distributions for f and theta(B) derived from different data sets to determine whether the estimates are consistent with one another. We illustrate each of these extensions by applying them to data derived from previous alloyzme and random amplified polymorphic DNA surveys of an endangered orchid, Platanthera leucophaea, and we conclude that differences in theta(B) from the two data sets may represent differences in the underlying mutational processes.

Population differentiation often reflects a balance between divergent natural selection and the opportunity for homogenizing gene flow to erode the effects of selection. However, during ecological speciation, trait divergence results in reproductive isolation and becomes a cause, rather than a consequence, of reductions in gene flow. To assess both the causes and the reproductive consequences of morphological differentiation, we examined morphological divergence and sexual isolation among 17 populations of Timema cristinae walking-sticks. Individuals from populations adapted to using Adenostoma as a host plant tended to exhibit smaller overall body size, wide heads, and short legs relative to individuals using Ceonothus as a host. However, there was also significant variation in morphology among populations within host-plant species. Mean trait values for each single population could be reliably predicted based upon host-plant used and the potential for homogenizing gene flow, inferred from the size of the neighboring population using the alternate host and mitochondrial DNA estimates of gene flow. Morphology did not influence the probability of copulation in between-population mating trials. Thus, morphological divergence is facilitated by reductions in gene flow, but does not cause reductions in gene flow via the evolution of sexual isolation. Combined with rearing data indicating that size and shape have a partial genetic basis, evidence for parallel origins of the host-associated forms, and inferences from functional morphology, these results indicate that morphological divergence in T. cristinae reflects a balance between the effects of host-specific natural selection and gene flow. Our findings illustrate how data on mating preferences can help determine the causal associations between trait divergence and levels of gene flow.

Little is known about what controls effective sizes and migration rates among parasite populations. Such data are important given the medical, veterinary, and economic (e.g., fisheries) impacts of many parasites. The autogenic-allogenic hypothesis, which describes ecological patterns of parasite distribution, provided the foundation on which we studied the effects of life cycles on the distribution of genetic variation within and among parasite populations. The hypothesis states that parasites cycling only in freshwater hosts (autogenic life cycle) will be more limited in their dispersal ability among aquatic habitats than parasites cycling through freshwater and terrestrial hosts (allogenic life cycle). By extending this hypothesis to the level of intraspecific genetic variation, we examined the effects of host dispersal on parasite gene flow. Our a priori prediction was that for a given geographic range, autogenic parasites would have lower gene flow among subpopulations. We compared intraspecific mitochondrial DNA variation for three described species of trematodes that infect salmonid fishes. As predicted, autogenic species had much more highly structured populations and much lower gene flow among subpopulations than an allogenic species sampled from the same locations. In addition, a cryptic species was identified for one of the autogenic trematodes. These results show how variation in life cycles can shape parasite evolution by predisposing them to vastly different genetic structures. Thus, we propose that knowledge of parasite life cycles will help predict important evolutionary processes such as speciation, coevolution, and the spread of drug resistance.

Phylogeography and intraspecific genetic variation Were studied in prochilodontids endemic to the Orinoco, Essequibo and Amazon River basins of northern South America. Portions of two,protein-encoding mitochondrial (mt) DNA genes, ND4 and COI, were examined using single-strand conformational polymorphisms (SSCPs) and nucleotide sequencing. Phylogeographic analysis indicated that the geographically widespread Prochilodus rubrotaeniatus is paraphyletic, with individuals from the Orinoco sharing most recent common ancestry with co-occurring Prochilodus mariae. A second Prochilodus rubrotaeniatus clade was composed of haplotypes found in the Rio Cuyuni (Essequibo Basin) and tributaries of the Rio Negro (Amazon Basin). Intraspecific genetic analysis suggested that a complex set of processes have influenced patterns of genetic variation in prochilodontid lineages. Prochilodus rubrotaeniatus is monomorphic at both loci in the Rio Negro and probably recently colonized this basin from the Rio Essequibo. Only two of 55 P. mariae exhibited variant haplotypes, and both had resulted from non-synonymous changes in the ND4 region. These observations were counter to neutral expectation and consistent with the action of natural selection on the mitochondrion. Overall, these analyses implicate vicariance, demography and selection for driving diversification of prochilodontids in northern South America. (C) 2004 The Fisheries Society of the British Isles.

The antagonistic pleiotropy theory of senescence postulates genes or traits that have opposite effects on early-life and late-life performances. Because selection is generally weaker late in life, genes or traits that improve early-life performance but impair late-life performance should come to predominate. Variation in the strength of age-specific selection should then generate adaptive variation in senescence. We demonstrate this mechanism by comparing early and late breeders within a population of semelparous capital-breeding sockeye salmon (Oncorhynchus nerka). We show that early breeders (but not late breeders) are under strong selection for a long reproductive lifespan (RLS), which facilitates defence of their nests against disturbance by later females. Accordingly, early females invest less energy in egg production while reserving more for nest defence. Variation along this reproductive trade-off causes delayed or slower senescence in early females (average RLS of 26 days) than in late females (reproductive lifespan of 12 days). We use microsatellites to confirm that gene flow is sufficiently limited between early and late breeders to allow adaptive divergence in response to selection. Because reproductive trade-offs should be almost universal and selection acting on them should typically vary in time and space, the mechanism described herein may explain much of the natural variation in senescence.

We used both direct (mark-recapture) and indirect (microsatellite analysis) methodologies to investigate dispersal between two putative populations of brook charr (Salvelinus fontinalis) in Freshwater River, Cape Race, Newfoundland, Canada. Over a 5-year study period, mark-recapture data revealed some movement by fish, but the proportion of recaptured fish migrating from one population area to another was low (0-4.1%). Additionally, during sampling periods in the spawning seasons, no fish was found in the alternate population area to that of its first capture. Despite this pattern of limited movement, microsatellite analysis based on sixteen polymorphic loci provided no evidence of genetic differentiation. Indirect estimates of dispersal parameters varied greatly between different methods of analysis. While use of a coalescent-based model yielded estimated migration rates congruent with the results of the mark-recapture study, other methods resulted in much higher estimates of migration between the populations. In particular, the lack of genetic differentiation coupled with likely violations of the assumed island model prevented generation of meaningful estimates of dispersal using Fst. The disparities between migration rates estimated from the mark-recapture work and from the different indirect methods highlight the difficulties of using indirect methods to estimate dispersal on an ecological timescale. However, mark-recapture methods can fail to detect historical or episodic movement that is important in an evolutionary context, and we therefore argue that a combination of direct and indirect methods can provide a more complete picture of dispersal than either approach alone.

Background: The study of organisms with restricted dispersal abilities and presence in the fossil record is particularly adequate to understand the impact of climate changes on the distribution and genetic structure of species. Trochoidea geyeri (Soos 1926) is a land snail restricted to a patchy, insular distribution in Germany and France. Fossil evidence suggests that current populations of T. geyeri are relicts of a much more widespread distribution during more favourable climatic periods in the Pleistocene. Results: Phylogeographic analysis of the mitochondrial 16S rDNA and nuclear ITS-1 sequence variation was used to infer the history of the remnant populations of T. geyeri. Nested clade analysis for both loci suggested that the origin of the species is in the Provence from where it expanded its range first to Southwest France and subsequently from there to Germany. Estimated divergence times predating the last glacial maximum between 25-17 ka implied that the colonization of the northern part of the current species range occurred during the Pleistocene. Conclusion: We conclude that T. geyeri could quite successfully persist in cryptic refugia during major climatic changes in the past, despite of a restricted capacity of individuals to actively avoid unfavourable conditions.

The phylogeographical patterns of a small marine fish, the common goby, Pomatoschistus microps, were assessed at 12 sites along the northeastern Atlantic coasts and the western Mediterranean Sea. A combination of two genetic markers was employed: cellulose acetate allozyme electrophoresis (CAGE) and sequence analysis of a 289 bp fragment of the mitochondrial locus cytochrome b. Both markers were congruent in revealing significant differences between samples (global F-ST = 0.247 for the allozymes and Phi(ST) = 0.437 for the mitochondrial DNA data) and a pattern of isolation-by-distance. Phylogeographical analyses yielded a shallow branching structure with four groups. Three of those were confined to the Atlantic basin and showed a star-like pattern. The fourth group contained a central haplotype occurring at the edges of the species' distribution, accompanied by a few more rare variants, which were restricted to the Mediterranean Sea. A genetic break was observed around the British Isles, with distinct haplotypes dominating at either side of the English Channel. A significantly negative correlation between the degree of genetic diversity and latitude was recorded both for mitochondrial DNA (mtDNA) and allozymes in the Atlantic basin. Gene flow analysis suggested that recolonization of the North Sea and the coasts of western Scotland and Ireland may have taken place from a glacial refugium in the Southern Bight of the North Sea. These results are discussed in the perspective of possible postglacial migration routes of marine fish along the northeastern Atlantic coasts.

In the newly emerging field of statistical phylogeography, consideration of the stochastic nature of genetic processes and explicit reference to theoretical expectations under various models has dramatically transformed how historical processes are studied. Rather than being restricted to ad hoc explanations for observed patterns of genetic variation, assessments about the underlying evolutionary processes are now based on statistical tests of various hypotheses, as well as estimates of the parameters specified by the models. A wide range of demographical and biogeographical processes can be accommodated by these new analytical approaches, providing biologically more realistic models. Because of these advances, statistical phylogeography can provide unprecedented insights about a species' history, including decisive information about the factors that shape patterns of genetic variation, species distributions, and speciation. However, to improve our understanding of such processes, a critical examination and appreciation of the inherent difficulties of historical inference and challenges specific to testing phylogeographical hypotheses are essential. As the field of statistical phylogeography continues to take shape many difficulties have been resolved. Nonetheless, careful attention to the complexities of testing historical hypotheses and further theoretical developments are essential to improving the accuracy of our conclusions about a species' history.

Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to Mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter Theta to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of Theta, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

Long-distance dispersal (LDD) includes events in which propagules arrive, but do not necessarily establish, at a site far removed from their origin. Although important in a variety of ecological contexts, the system-specific nature of LDD makes “far removed” difficult to quantify, partly, but not exclusively, because of inherent uncertainty typically involved with the highly stochastic LDD processes. We critically review the main methods employed in studies of dispersal, in order to facilitate the evaluation of their pertinence to specific aspects of LDD research. Using a novel classification framework, we identify six main methodological groups: biogeographical; Eulerian and Lagrangian movement/redistributional; short-term and long-term genetic analyses; and modeling. We briefly discuss the strengths and weaknesses of the most promising methods available for estimation of LDD, illustrating them with examples from current studies. The rarity of LDD events will continue to make collecting, analyzing, and interpreting the necessary data difficult, and a simple and comprehensive definition of LDD will remain elusive. However, considerable advances have been made in some methodological areas, such as miniaturization of tracking devices, elaboration of stable isotope and genetic analyses, and refinement of mechanistic models. Combinations of methods are increasingly used to provide improved insight on LDD from multiple angles. However, human activities substantially increase the variety of long-distance transport avenues, making the estimation of LDD even more challenging.

The houbara bustard, Chlamydotis undulata, is a declining cryptic desert bird whose range extends from North Africa to Central Asia. Three subspecies are currently recognized by geographical distribution and morphology: C.u.fuertaventurae, C.u.undulata and C.u.macqueenii. We have sequenced 854 bp of mitochondrial control region from 73 birds to describe their population genetic structure with a particular sampling focus on the connectivity between C.u.fuertaventurae and C.u.undulata along the Atlantic seaboard of North Africa. Nucleotide and haplotypic diversity varied among the subspecies being highest in C.u.undulata, lowest in C.u.fuertaventurae and intermediate in C.u.macqueenii. C.u.fuertaventurae and C.u.undulata are paraphyletic and an average nucleotide divergence of 2.08% splits the later from C.u.macqueenii. We estimate that C.u.fuertaventurae and C.u.undulata split from C.u.macqueenii approximately 430 000 years ago. C.u.fuertaventurae and C.u.undulata are weakly differentiated (F-ST = 0.27, N-m = 1.3), indicative of a recent shared history. Archaeological evidence indicates that houbara bustards have been present on the Canary Islands for 130-170 000 years. However, our genetic data point to a more recent separation of C.u.fuertaventurae and C.u.undulata at around 20-25 000 years. Concordant archaeological, climatic opportunities for colonization and genetic data point to a scenario of: (i) initial colonization of the Canary Islands about 130 000 years ago; (ii) a period of secondary contact 19-30 000 years ago homogenizing any pre-existing genetic structure followed by; (iii) a period of relative isolation that persists today.

Unravelling relationships between dispersal and population structure requires considering the impacts of assumption violations of indirect gene flow models in a given system. We combined temporal, individual and coalescent-based analyses of microsatellite DNA variation to explore the general hypothesis that unequal effective population size (N-e), asymmetric gene flow (m) and nonrandom (sex-biased) individual dispersal had an important effect on spatiotemporal population structuring in lake-dwelling brook charr (Salvelinus fontinalis). This integrative examination shed light on the dichotomous structuring observed between an outlet and three tributary-spawning populations and their potential for adaptive divergence. It revealed further that finer tributary population structuring incongruent with drainage structure has been shaped by asymmetric m from one population with a large N-e towards two populations of smaller N-e. Gene flow among the tributaries was also mediated mainly by male-biased dispersal. However, longer distance dispersal from tributaries to the outflow was female-biased. Spatially dependent sex-biased dispersal may have contributed therefore to gene flow at different levels of population structuring. Our results demonstrate how dispersal and population structure may interrelate to produce spatial variation in intraspecific diversity, and are therefore relevant for conservation programmes seeking to define conservation units or predict recolonization rates of extirpated populations.

European grayling populations in Bavaria have shown steady declines during the last 10-20 years. In order to provide guidelines for conservation strategies and future management programs, we investigated the genetic structure of 15 grayling populations originating from three major Central European drainages (the Danube, the Elbe and the Rhine/Main) using 20 microsatellite loci. Genetic divergence between the three drainage systems was substantial as illustrated by highly significant heterogeneity of genotype frequencies, high number of drainage-specific private alleles, high between-drainage F-ST values, high assignment success of individuals to their drainage of origin and the high bootstrap support for the genetic distance based drainage-specific population clusters. In agreement with earlier studies, microsatellites revealed relatively low levels of intrapopulational genetic diversity in comparison to the overall level of variation across populations. Maximum likelihood methods using the coalescent approach revealed that the proportion of common ancestors was generally high in native populations and that the estimates of N-e were correlated with the genetic diversity parameters in all drainages. The number of effective immigrants per generation (N(e)m) was less than one for all pairwise comparisons of populations within the drainages, indicating restricted interpopulational gene flow. Based on these findings we recommend a drainage and sub-drainage specific conservation of grayling populations in order to preserve their overall genetic diversity and integrity. For large-scale stocking actions to supplement declining or to restore extinct populations, creation of separate broodstocks for major conservation units (ESUs and MUs) is warranted.

Islands are considered to be natural laboratories in which to examine evolution because of the implicit assumption that limited gene flow allows tests of evolutionary processes in isolated replicates(1). Here we show that this well-accepted idea requires re-examination. Island inundation during hurricanes can have devastating effects on lizard populations in the Bahamas(2,3). After severe storms, islands may be recolonized by overwater dispersal of lizards from neighbouring islands(3). High levels of gene flow may homogenize genes responsible for divergence, and are widely viewed as a constraining force on evolution(4,5). Ultimately, the magnitude of gene flow determines the extent to which populations diverge from one another, and whether or not they eventually form new species(6,7). We show that patterns of gene flow among island populations of Anolis lizards are best explained by prevailing ocean currents, and that over-water dispersal has evolutionary consequences. Across islands, divergence in fitness-related morphology decreases with increasing gene flow(5). Results suggest that over-water dispersal after hurricanes constrains adaptive diversification in Anolis lizards, and that it may have an important but previously undocumented role in this classical example of adaptive radiation.

Orchids of the genus Ophrys (Orchidaceae) are pollinated by male bees and wasps through sexual deception. The Ophrys sphegodes group encompasses several closely related species that differ slightly in floral morphology and are pollinated by different solitary bee species. Populations representing different species of the O. sphegodes group often flower simultaneously in sympatry. To test whether gene flow across the species boundaries occurs in these sympatric populations, or whether they are reproductively isolated, we examined the distribution of genetic variation within and among populations and species of this group. We collected at each of five different localities in southern France and Italy two sympatric, co-flowering Ophrys populations, representing six Ophrys species in total. The six microsatellite loci surveyed were highly variable. Genetic differentiation among geographically distant populations of the same species was lower than differentiation among sympatric populations of different species. However, the strength of genetic differentiation among species was among the lowest reported for orchids. Genotype assignment tests and marker-based estimates of gene flow revealed that gene flow across species boundaries occurred and may account for the low observed differentiation among species. These results suggest that sexual deceit pollination in Ophrys may be less specific than thought, or that rare mistakes occur.

The availability of new genetic technologies has positioned the field of biological control as a test bed for theories in evolutionary biology and for understanding practical aspects of the release of genetically manipulated material. Purposeful introductions of pathogens, parasites, predators and herbivores, when considered as replicated semi-natural field experiments, show the unpredictable nature of biological colonization. The characteristics of organisms and their environments that determine this variation in the establishment and success of biological control can now be explored using genetic tools. Lessons from studies of classical biological control can help inform researchers and policy makers about the risks that are associated with the release of genetically modified organisms, particularly with respect to long-term evolutionary changes.

Population viability has often been assessed by census of reproducing adults. Recently this method has been called into question and estimation of the effective population size (N-e) proposed as a complementary method to determine population health. We examined genetic diversity in five populations of chinook salmon (Oncorhynchus tshawytscha) from the upper Fraser River watershed (British Columbia, Canada) at 11 microsatellite loci over 20 years using DNA extracted from archived scale samples. We tested for changes in genetic diversity, calculated the ratio of the number of alleles to the range in allele size to give the statistic M, calculated N-e from the temporal change in allele frequency, used the maximum likelihood method to calculate effective population size (N-e M), calculated the harmonic mean of population size, and compared these statistics to annual census estimates. Over the last two decades population size has increased in all five populations of chinook examined; however, N-e calculated for each population was low (81-691) and decreasing over the time interval measured. Values of N-e M were low, but substantially higher than N-e calculated using the temporal method. The calculated values for M were generally low (M < 0.70), indicating recent population reductions for all five populations. Large-scale historic barriers to migration and development activities do not appear to account for the low values of N-e; however, available spawning area is positively correlated with N-e. Both N-e and M estimates indicate that these populations are potentially susceptible to inbreeding effects and may lack the ability to respond adaptively to stochastic events. Our findings question the practice of relying exclusively on census estimates for interpreting population health and show the importance of determining genetic diversity within populations.

Molecular and geological evidence indicates that the emergence of the Isthmus of Panama influenced the historical biogeography of the Neotropics in a complex, staggered manner dating back at least 9 Myr BP. To assess the influence of Isthmus formation on the biogeography of the harlequin beetle-riding pseudoscorpion, Cordylochernes scorpioides, we analysed mitochondrial COI sequence data from 71 individuals from 13 locations in Panama and northern South America. Parsimony and likelihood-based phylogenies identified deep divergence between South American and Panamanian clades. In contrast to low haplotype diversity in South America, the Panamanian Cordylochernes clade is comprised of three highly divergent lineages: one clade consisting predominantly of individuals from central Panama (PAN A), and two sister clades (PAN B1 and PAN B2) of western Panamanian pseudoscorpions. Breeding experiments demonstrated a strictly maternal mode of inheritance, indicating that our analyses were not confounded by nuclear-mitochondrial pseudogenes. Haplotype diversity is striking in western Atlantic Panama, where all three Panamanian clades can occur in a single host tree. This sympatry points to the existence of a cryptic species hybrid zone in western Panama, a conclusion supported by interclade crosses and coalescence-based migration rates. Molecular clock estimates yield a divergence time of approximate to3 Myr between the central and western Panamanian clades. Taken together, these results are consistent with a recent model in which a transitory proto-Isthmus enabled an early wave of colonization out of South America at the close of the Miocene, followed by sea level rise, inundation of the terrestrial corridor and then a second wave of colonization that occurred when the Isthmus was completed approximate to3 Myr bp.

Asymmetrical gene flow is an important, but rarely examined genetic parameter. Here, we develop a new Method for detecting departures from symmetrical migration between two populations using microsatellite data that are based on the difference in the proportion of private alleles. Application of this approach to data collected from wild-caught Drosophila melanogaster along a latitudinal body-size cline in eastern Australia revealed that asymmetrical gene flow could be detected, but was uncommon, nonlocalized, and occurred in both directions. We also show that, in contrast to the findings of a previous study, there is good evidence to suggest that the cline experiences significant levels of gene flow between populations.

The genetic structure of populations of the true armyworm, Pseudaletia unipuncta (Haworth) (Lepidoptera: Noctuidae), in the Azores archipelago was studied using polyacrylamide-gel electrophoresis. Four enzyme systems (aldehyde oxidase, esterase, phosphoglucomutase, and phosphoglucose isomerase) were examined in six populations from islands in the Azores (Santa Maria, Sao Miguel, Terceira, Pico, Faial, Flores) and compared with those from populations from mainland Portugal and Canada. The North American and European populations are not clearly separated from the Azorean ones. Similarly, studies of different enzyme systems (aldehyde oxidase, esterase, malic enzyme, sorbitol dehydrogenase, manose-6-phosphate isomerase, and phosphoglucomutase) over 2 years (1997 and 1998) at different times of the year (spring, summer, and autumn) and at three different altitudes (0, 250, and 500 m above sea level) on three different islands (Santa Maria, Sao Miguel, and Faial) uncovered no distinct differences. These results, obtained from classically used loci, suggest that there is still some gene flow between sites or that island populations have not been isolated for sufficient time to have diverged from founder populations.

A class of two-sex population models is considered with N females and equal number N of males constituting each generation. Reproduction is assumed to undergo three stages: 1) random mating, 2) exchangeable reproduction, 3) random sex assignment. Treating individuals as pairs of genes at a certain locus we introduce the diploid ancestral process (the past genealogical tree) for n such genes sampled in the current generation. Neither mutation nor selection are assumed. A convergence criterium for the diploid ancestral process is proved as N goes to infinity while n remains unchanged. Conditions are specified when the limiting process (coalescent) is the Kingman coalescent and situations are discussed when the coalescent allows for multiple mergers of ancestral lines.

Recent years have seen a resurgence of interest in the process of speciation but few studies have elucidated the mechanisms either driving or constraining the evolution of reproductive isolation. In theory, the direct effects of reinforcing selection for increased mating discrimination where interbreeding produces hybrid offspring with low fitness and the indirect effects of adaptation to different environments can both promote speciation. Conversely, high levels of homogenizing gene flow can counteract the forces of selection. We demonstrate the opposing effects of reinforcing selection and gene flow in Timema cristinae walking-stick insects. The magnitude of female mating discrimination against males from other populations is greatest when migration rates between populations adapted to alternate host plants are high enough to allow the evolution of reinforcement, but low enough to prevent gene flow from eroding adaptive divergence in mate choice. Moreover, reproductive isolation is strongest under the combined effects of reinforcement and adaptation to alternate host plants. Our findings demonstrate the joint effects of reinforcement, ecological adaptation and gene flow on progress towards speciation in the wild.

Mutations arise in a single individual and at a single point in time and space. The geographic distribution of mutations reflects both historical population size and frequency of migration. We employ coalescence-based methods to coestimate effective population size, frequency of migration, and level of recombination compatible with observed genealogical relationships in sequence data from nine nuclear genes in wild barley (Hordeum vulgare ssp. spontaneum), a highly self-fertilizing grass species. In self-fertilizing plants, gamete dispersal is severely limited; dissemination occurs primarily through seed dispersal. Also, heterozygosity is greatly reduced, which renders recombination less effective at randomizing genetic variation and causes larger portions of the genome to trace a similar history. Despite these predicted effects of this mating system, the majority of loci show evidence of recombination. Levels of nucleotide variation and the patterns of geographic distribution of mutations in wild barley are highly heterogeneous across loci. Two of the nine sampled loci maintain highly diverged, geographic region-specific suites of mutations. Two additional loci include region-specific haplotypes with a much shallower coalescence. Despite inbreeding, sessile growth habit, and the observation of geographic structure at almost half of sampled loci, parametric estimates of migration suggest that seed dispersal is sufficient for migration across the approximate to3,500-km range of the species. Recurrent migration is also evident based on the geographic distribution of mutational variation at some loci. At one locus a single haplotype has spread rapidly enough to occur, unmodified by mutation, across the range of the species.

The effective population sizes of ancestral as well as modern species are important parameters ill models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology, of the species free is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method call handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be similar to20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

The availability of nucleotide and amino acid sequences sampled at different points in time has fostered the development of new statistical methods that exploit this temporal dimension. Such sequences enable us to observe evolution in action and to estimate the rate and magnitude of evolutionary processes through time. Populations for which such studies are possible measurably evolving populations (MEPs) - are characterized by sufficiently long or numerous sampled sequences and a fast mutation rate relative to the available range of sequence sampling times. The impact of sequences sampled through time has been most apparent in the disciplines of RNA viral evolution and ancient DNA, where they enable us to estimate divergence times without paleontological calibrations, and to analyze temporal changes in population size, population structure and substitution rates. Thus, MEPs could increase our understanding of evolutionary processes in diverse organisms, from viruses to vertebrates.

This paper studies the speciation of two land snail species in south-east France. By using two mitochondrial and one nuclear gene, the species are shown to be sister species within the larger clade of western European Candidula species. The species never occurred syntopically, but a narrow contact zone population was identified. Recent range expansions inferred from phylogeographical methods indicated that the present day distributions are not limited by the colonization capacity of the species. Analysis of environmental variables suggested distribution along an ecotone. The gastropod community is also correlated to this gradient. Morphometric shell analysis showed that the divergence between the sister species is a result of desiccation-resistant shell characters. We therefore conclude that the cause for the ecological speciation is most probably the establishment of the Mediterranean climate approximate to 3.2 mya. A model of ecological speciation with a moving ecotone is put forward. (C) 2003 The Linnean Society of London.

I genotyped lek-mating Long-tailed Manakins (Chiroxiphia linearis) at Monteverde and Santa Rosa, Costa Rica, 115 km apart. Cavalli-Sforza distance was 0.04, D-LR was 0.18, and R-ST and theta were both 0.02. Bayesian clustering analysis indicated that both populations were part of a single cluster rather than from distinct clusters. I present a binomial test for probability of allelic absence as a function of sample size. Genotypic likelihood tests assigned 50% of Monteverde birds to Santa Rosa, versus 26% of Santa Rosa birds to Monteverde. Two lines of evidence supported the idea of asymmetric gene flow up the elevational gradient from Santa Rosa to Monteverde. Low differentiation at this spatial scale, despite intense sexual selection, suggests that sexual selection alone is unlikely to promote rapid divergence leading to speciation. Reduced gene flow, produced by geographic barriers or behavioral factors, may also be required.

This article introduces a new general method for genealogical inference that samples independent genealogical histories using importance sampling (IS) and then samples other parameters with Markov chain Monte Carlo (MCMC). It is then possible to more easily utilize the advantages of importance sampling in a fully Bayesian framework. The method is applied to the problem of estimating recent changes in effective population size from temporally spaced gene frequency data. The method gives the posterior distribution of effective population size at the time of the oldest sample and at the time of the most recent sample, assuming a model of exponential growth or decline during the interval. The effect of changes in number of alleles, number of loci, and sample size on the accuracy of the method is described using test simulations, and it is concluded that these have an approximately equivalent effect. The method is used on three example data sets and problems in interpreting the posterior densities are highlighted and discussed.

Mitochondrial DNA sequence data for 295 individuals of the marine bivalve Macoma balthica (L.) were collected from 10 sites across the European distribution, and from Alaska. The data were used to infer population subdivision history and estimate current levels of gene flow. Inferred historical biogeography was expected to be congruent with colonization of the Atlantic Ocean from the Pacific Ocean after the opening of the Bering Strait 3.5 Ma. In addition, the last glacial maximum, about 18 000 years ago, was expected to have been responsible for most of the present-day distribution of molecular variation within Europe, because the area must have been recolonized after confinement to France and the south of the British Isles during the last glacial maximum. Current gene flow was hypothesized to be high, because the larvae of M. balthica spend 2-5 weeks drifting in the water column. The geographical distribution of one highly diverged haplotype clade was found to be disjunct and was encountered exclusively in samples from the Baltic Sea and Alaska. A molecular clock calibration for marine bivalve cytochrome-c -oxidase I dates this clade as having split off from the other haplotypes 9.8-39 Ma. Multiple colonizations of the Atlantic Ocean from the Pacific by M. balthica may explain the strong differences found between Baltic Sea and other European populations of this species. The sympatric occurrence of the highly diverged mitochondrial lineages in western parts of the Baltic Sea points to secondary admixture. With the use of coalescent analysis, population divergence times for French vs. other non-Baltic European populations ('Atlantic population assemblage') were estimated at a minimum of about 110 000 years ago, well before the last glacial maximum 18 000 years ago. Signatures of population divergence of M. balthica that appear to have originated during the Pleistocene have thus survived the last glacial maximum. Some of the populations within the Atlantic assemblage are currently isolated, while others appear to be connected by gene flow. Apparently, populations of this species can remain highly subdivided in spite of the potential for high gene flow, implying that their population and evolutionary dynamics can be independent.

Within populations, the stochastic effect of genetic drift and deterministic effect of natural selection are potentially weakened or altered by gene flow among populations. The influence of gene flow on Lake Erie populations of the common garter snake has been of particular interest because of a discontinuous colour pattern polymorphism (striped vs. melanistic) that is a target of natural selection. We reassessed the relative contributions of gene flow and genetic drift using genetic data and population size estimates. We compared all combinations of two marker systems and two analytical approaches to the estimation of gene flow rates: allozymes (data previously published), microsatellite DNA (new data), the island model (F-ST-based approach), and a coalescence-based approach. For the coalescence approach, mutation rates and sampling effects were also investigated. While the two markers produced similar results, gene flow based on F-ST was considerably higher (Nm > 4) than that from the coalescence-based method (Nm < 1). Estimates of gene flow are likely to be inflated by lack of migration-drift equilibrium and changing population size. Potentially low rates of gene flow (Nm < 1), small population size at some sites, and positive correlations of number of microsatellite DNA alleles and island size and between M, mean ratio of number of alleles to range in allele size, and island size suggest that in addition to selection, random genetic drift may influence colour pattern frequencies. (C) 2003 The Linnean Society of London.

It is well known that hunting dramatically reduced all baleen whale populations, yet reliable estimates of former whale abundances are elusive. Based on coalescent models for mitochondrial DNA sequence variation, the genetic diversity of North Atlantic whales suggests population sizes of approximately 240,000 humpback, 360,000 fin, and 265,000 minke whales. Estimates for fin and humpback whales are far greater than those previously calculated for prewhaling populations and 6 to 20 times higher than present-day population estimates. Such discrepancies suggest the need for a quantitative reevaluation of historical whale populations and a fundamental revision in our conception of the natural state of the oceans.

Natural populations, including those of humans, have complex geographies and histories. Studying how they evolve is difficult, but it is possible with population-based DNA sequence data. However, the study of structured populations is divided by two distinct schools of thought and analysis. The phylogeographic approach is fundamentally graphical and begins with a gene-tree estimate. By contrast, the more traditional approach of using summary statistics is fundamentally mathematical. Both approaches have limitations, but there is promise in newer probabilistic methods that offer the flexibility and data exploitation of the phylogeographic approach in an explicitly model-based mathematical framework.

We used mitochondrial DNA data to infer phylogenies for 28 samples of gall-inducing Tamalia aphids from 12 host-plant species, and for 17 samples of Tamalia inquilinus , aphid `inquilines' that obligately inhabit galls of the gall inducers and do not form their own galls. Our phylogenetic analyses indicate that the inquilines are monophyletic and closely related to their host aphids. Tamalia coweni aphids from different host plants were, with one exception, very closely related to one another. By contrast, the T. inquilinus aphids were strongly genetically differentiated among most of their host plants. Comparison of branch lengths between the T. coweni clade and the T. inquilinus clade indicates that the T. inquilinus lineage evolves 2.5-3 times faster for the cytochrome oxidase I gene. These results demonstrate that: (1) Tamalia inquilines originated from their gall-inducing hosts, (2) communal (multi-female) gall induction apparently facilitated the origin of inquilinism, (3) diversification of the inquilines has involved rapid speciation along host-plant lines, or the rapid evolution of host-plant races, and (4) the inquilines have undergone accelerated molecular evolution relative to their hosts, probably due to reduced effective population sizes. Our findings provide insight into the behavioural causes and evolutionary consequences of transitions from resource generation to resource exploitation.

1. Fishes can often rebound numerically and distributionally from short-term (i.e. seasonal) drought, yet their capacity to recover from decades or centuries of drought is less apparent. An exceedingly warm and dry period swept the intermontane west of North America ca. 7500 years BP, concomitant with an abrupt extinction of >35 mammal species. Were larger fishes in mainstem rivers also impacted by this drought? 2. The Colorado River Basin encompasses seven states in western North America and drains 600 000 km(2) . Its endemic mainstem fish community is ancient (i.e. Miocene) but depauperate. 3. We evaluated one widely distributed candidate species (flannelmouth sucker, Catostomus latipinnis ) for basin-wide genetic and geographic structure at three fast-evolving mitochondrial (mt) DNA genes, ND2 with 589 bp and ATPase 8 and 6 with 642 bp. It is hypothesized that a concomitant signature would be present in the mtDNA of this species, if indeed it had been seriously bottlenecked by post-Pleistocene drought. A total of 352 individuals were sequenced from 24 populations (4-40 individuals/population; average of 14.7). 4. Only 49 unique haplotypes were found, 53% of which represented single individuals. Haplotype diversity was high (0.905 +/- 0.007) whereas nucleotide diversity was low (0.002 +/- 0.000). 5. A significant and positive geographical cline (P < 0.001) in nucleotide diversity was observed as sampling locations progressed upstream from southwest to northeast. These results divided the Colorado River Basin into three reaches: the lower reach with six populations and 83 individuals; the upper reach with seven populations and 83 individuals; and the middle reach with 11 populations and 186 individuals. An analysis of molecular variance (amova) revealed that 81.5% of the total genetic variation was within populations, 16% among populations within reaches and 2.5% among reaches. Only the last was significant. Populations from the three reaches diverged from one another by 3400-11 000 years BP. Haplotype distribution suggested populations in the upper Colorado River are expanding. 6. The lack of genetic variation and recent coalescence of lineages in C. latipinnis are unusual given its fossil history, broad geographical sampling, the rapid rate of mtDNA evolution and the number (and evolutionary rate) of the genes examined. The most parsimonious explanation for these data is a rapid expansion following a recent period of low effective population size at the end of the Pleistocene. 7. The intense drought is suggested at the end of the Pleistocene (late-to-mid-Holocene), severely impacted not only large mammals but also larger fishes in western North American rivers. These perspectives have important implications for management of endangered and threatened species in this region.

Life history variation and genetic differentiation were analysed in sockeye salmon in Klukshu River, Yukon Canada over 7 years (1994-2000). Sockeye salmon return to the Klukshu River in two distinct runs, with a small `early run' in June-August, and a larger `late run' in August-September. A maximum likelihood test for clusters indicated that the return frequency distribution was bimodal in all the years analysed. Life history differences (fork length, sex ratio, age at maturity, fresh- and saltwater residency times) were found between the early and late runs; however, inconsistent patterns suggest that environmental effects outweigh, or strongly interact with, genetic effects for the life history characters evaluated. Analysis of variation at eight microsatellite loci showed that the early and late runs are genetically differentiated in all years examined (exact test). F-ST estimates between runs within years were significantly greater than zero (range: 0.018-0.041) for all years except one (0.004). The genetic variance explained by early vs. late runs (2.27%) was twice the variance among years (1.16%) based on analysis of molecular variance. Our neighbour-joining tree showed early and late runs generally clustering separately, indicating higher gene flow among the early or late run fish across years relative to between-run gene flow. Two years did not fit the general clustering pattern; although the early and late runs in 1995 and 2000 were genetically differentiated, they clustered separately from the rest of the groups. We cannot offer a definitive explanation for these anomalies; however, an analysis of possible cryptic population structure in early and late runs indicated that at least a few fish strayed between the runs in each year, and the highest rate of mixing was in 1995 and 2000. Our data indicate that the runs are at least partially reproductively isolated as a result of temporal and/or spatial isolating mechanisms. Such reproductive isolation has important implications for conservation and management of the Klukshu sockeye salmon, and make them an evolutionarily interesting group because of parallels with incipient speciation.

We develop a flexible class of Metropolis-Hastings algorithms for drawing inferences about population histories and mutation rates from deoxyribonucleic acid (DNA) sequence data. Match probabilities for use in forensic identification are also obtained, which is particularly useful for mitochondrial DNA profiles. Our data augmentation approach, in which the ancestral DNA data are inferred at each node of the genealogical tree, simplifies likelihood calculations and permits a wide class of mutation models to be employed, so that many different types of DNA sequence data can be analysed within our framework. Moreover, simpler likelihood calculations imply greater freedom for generating tree proposals, so that algorithms with good mixing properties can be implemented. We incorporate the effects of demography by means of simple mechanisms for changes in population size and structure, and we estimate the corresponding demographic parameters, but we do not here allow for the effects of either recombination or selection. We illustrate our methods by application to four human DNA data sets, consisting of DNA sequences, short tandem repeat loci, single-nucleotide polymorphism sites and insertion sites. Two of the data sets are drawn from the male-specific Y-chromosome, one from maternally inherited mitochondrial DNA and one from the beta-globin locus on chromosome 11.

1 We used genetic markers to study gene flow of the riparian pioneer tree species Populus nigra along the Drome river (France). This dioecious species is supposed to have more efficient dispersal mechanisms for pollen (wind) and seeds (wind and water) than other trees. 2 Seedlings belonging to the same reproduction /migration event were sampled in 22 riparian forest fragments along the river and their genetic diversity assessed through six nuclear microsatellites. 3 We found a high level of diversity and significant differentiation among populations. The significant isolation by distance allowed us to reject the infinite island model of migration. 4 Gene flow parameters were higher in the upper, mountainous part than in the alluvial plain downstream. There was no accumulation of diversity downstream, indicating migration rates were symmetrical upstream and downstream. This was confirmed by computing individual migration parameters between adjacent populations. 5 The results are discussed with regard to the dispersal mechanisms of seeds and pollen. The discrepancy between potential gene flow and effective gene flow is interpreted as an effect of fragmentation, due to the alteration of the natural dynamics of the riparian ecosystem rather than to physical barriers.

Among tuco-tucos, Ctenomys rionegrensis is especially amenable to the study of the forces driving population differentiation because of the restricted geographic range it occupies in Uruguay. Within this limited area, the Rio Negro tuco-tuco is limited to sandy soils. It nonetheless exhibits remarkable variation in pelage color, including melanic, agouti, and dark-backed individuals. Two hypotheses have been put forth to explain this pattern: (1) local differentiation and fixation of alternative pelage types by genetic drift under limited gene flow; or (2) fixation by natural selection that may take place even in the presence of gene flow. A previous allozyme study rejected the genetic drift hypothesis on the basis of high inferred levels of migration. New estimates of gene flow from microsatellites and mitochondrial cytochrome b sequences were obtained for C. rionegrensis populations to further test these hypotheses. Much lower levels of gene flow were estimated with these more sensitive markers. Microsatellite-based estimates of gene flow are close to zero and may come closest to estimating current levels of migration. A lack of equilibrium between migration and genetic drift is also strongly suggested by the absence of an isolation-by-distance pattern found in all three genetic datasets. The microsatellite genotype data show that the species is strongly structured geographically, with subpopulations constituting distinct genetic entities. If current levels of gene flow are very low, as indicated by the new data, the local fixation of alternative alleles, including those responsible for pelage color polymorphism, is possible by drift alone. A scenario is thus proposed in which the species expanded in the recent past from a more restricted geographic range and has subsequently differentiated in near isolation, with genetic drift possibly playing a primary role in overall genetic differentiation. The local fixation of pelage color types could also be due to drift, but selection on this trait cannot be ruled out without direct analysis.

Using properties of moment stationarity we develop exact expressions for the mean and covariance of allele frequencies at a single locus for a set of populations subject to drift, mutation, and migration. Some general results can be obtained even for arbitrary mutation and migration matrices, for example: (1) Under quite general conditions, the mean vector depends only on mutation rates, not on migration rates or the number of populations. (2) Allele frequencies covary among all pairs of populations connected by migration. As a result, the drift, mutation, migration process is not ergodic when any finite number of populations is exchanging genes. In addition, we provide closed-form expressions for the mean and covariance of allele frequencies in Wright's finite-island model of migration under several simple models of mutation, and we show that the correlation in allele frequencies among populations can be very large for realistic rates of mutation unless an enormous number of populations are exchanging genes. As a result, the traditional diffusion approximation provides a poor approximation of the stationary distribution of allele frequencies among populations. Finally, we discuss some implications of our results for measures of population structure based on Wright's F-statistics. (C) 2003 Elsevier Science (USA). All rights reserved.

In vivo virologic compartments are cell types or tissues between which there is a restriction of virus flow, while virologic reservoirs are cell types or tissues in which there is a relative restriction of replication. The distinction between reservoirs and compartments is important because therapies that would be effective against a reservoir may not be effective against viruses produced by a given compartment, and vice versa. For example, the use of cytokines to “flush out” long-lived infected cells in patients on highly active antiretroviral therapy (T. W. Chun, D. Engel, M. M. Berrey, T. Shea, L. Corey, and A. S. Fauci, Proc. Natl. Acad. Sci. USA 95:8869-8873, 1998) may be successful for a latent reservoir but may not impact a compartment in which virus continues to replicate because of poor drug penetration. Here, we suggest phylogenetic criteria to illustrate, define, and differentiate between reservoirs and compartments. We then apply these criteria to the analysis of simulated and actual human immunodeficiency virus type 1 sequence data sets. We report that existing statistical methods work quite well at detecting viral compartments, and we learn from simulations that viral divergence from a calculated most recent common ancestor is a strong predictor of viral reservoirs.

Geographic patterns of genetic diversity depend on a species' demographic properties in a given habitat, which may change over time. The rates at which patterns of diversity respond to changes in demographic properties and approach equilibrium are therefore pivotal in our understanding of spatial patterns of diversity. The brook charr Salvelinus fontinalis is a coastal fish exhibiting limited marine movements, such that a stable one-dimensional isolation-by distance (IBD) pattern should be observed over the whole range. Its range, however, recently shifted northward such that northern populations may still be in the process of reaching equilibrium. We investigated variation in IBD patterns, genetic divergence, and allelic richness at six microsatellite markers in 2087 anadromous brook chart from 59 rivers along the most likely postglacial colonization route. We observed a decrease in allelic richness, together with an increase in differentiation and a decrease in IBD in the most recently colonized northern populations, as expected following recent colonization. Contrary to expectation, however, similar patterns were also observed at the southernmost part of the range, despite the fact that these populations are not considered to be newly colonized. We propose that the loss of dispersal capabilities associated with anadromy may have caused the southernmost populations to evolve relatively independently of one another. This study thus demonstrated that changes in a species' geographic range and dispersal capabilities may contribute to shaping geographic patterns of genetic diversity.

A new Bayesian method that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations is presented. The method also estimates the posterior probability distributions of individual immigrant ancestries, population allele frequencies, population inbreeding coefficients, and other parameters of potential interest. The method is implemented in a computer program that relies on Markov chain Monte Carlo techniques to carry out the estimation of posterior probabilities. The program can be used with allozyme, microsatellite, RFLP, SNP, and other kinds of genotype data. We relax several assumptions of early methods for detecting recent immigrants, using genotype data; most significantly, we allow genotype frequencies to deviate from Hardy Weinberg equilibrium proportions within populations. The program is demonstrated by applying it to two recently published microsatellite data sets for populations of the plant species Centaurea corymbosa and the gray wolf species Canis lupus. A computer simulation study suggests that the program can provide highly accurate estimates of migration rates and individual migrant ancestries, given sufficient genetic differentiation among populations and sufficient numbers of marker loci.

The neutral island model forms the basis for several estimation models that relate patterns of genetic structure to microevolutionary processes. Estimates of gene flow are often based on this model and may be biased when the model's assumptions are violated. An appropriate test for violations is to compare F (ST) scores for individual loci to a null distribution based on the average F (ST) taken over multiple loci. A parametric bootstrap method is described here based on Wright's beta-distribution to generate null distributions of F (ST) for each locus. These null distributions account for error introduced by sampling populations, individuals and loci, and also biological sources of error, including variable alleles/locus and inbreeding. Confidence limits can be obtained directly from these distributions. Significant deviations from the island model may be the result of selection, deviations from the island model's migration pattern, nonequilibrium conditions, or other deviations from island-model assumptions. Only strong biases are likely to be detected because of the inherently large sampling variation of F (ST) . Nevertheless, a coefficient, Nb , describing bias in the spread of the beta-distribution in units comparable to the gene flow parameter, Nm , can be obtained for each locus. In samples from populations of the butterfly Coenonympha tullia , the loci Idh-1, Mdh-1, Pgi and Pgm showed significantly lower F (ST) than expected.

In molecular ecology the analysis of large microsatellite data sets is becoming increasingly popular. Here we introduce a new software tool, which is specifically designed to facilitate the analysis of large microsatellite data sets. All common microsatellite summary statistics and distances can be calculated. Furthermore, the MICROSATELLITE ANALYSER (MSA) software offers an improved method to deal with inbred samples (such as Drosophila isofemale lines). Executables are available for Windows and Macintosh computers.

Many bryophyte species have distributions that span multiple continents. The hypotheses historically advanced to explain such distributions rely on either long-distance spore dispersal or slow rates of morphological evolution following ancient continental vicariance events. We use phylogenetic analyses of DNA sequence variation at three chloroplast loci (atpB-rbcL spacer, rps4 gene, and trnL intron and 3' spacer) to examine these two hypotheses in the trans-Antarctic moss Pyrrhobryum mnioides. We find: (1) reciprocal monophyly of Australasian and South American populations, indicating a lack of intercontinental dispersal; (2) shared-haplotypes between Australia and New Zealand, suggesting recent or ongoing migration across the Tasman Sea; and (3) reciprocal monophyly among Patagonian and neotropical populations, suggesting no recent migration along the Andes. These results corroborate experimental work suggesting that spore features may be critical determinants of species range. We use the mid-Miocene development of the Atacama Desert, 14 million years ago, to calibrate a molecular clock for the tree. The age of the trans-Antarctic disjunction is estimated to be 80 million years ago, consistent with Gondwanan vicariance, making it among the most ancient documented cases of cryptic speciation. These data are in accord with niche conservatism, but whether the morphological stasis is a product of stabilizing selection or phylogenetic constraint is unknown.

To investigate the evolutionary and biogeographical history of Peromyscus keeni and P. maniculatus within the coastal forest ecosystem of the Pacific Northwest of North America, we sampled 128 individuals from 43 localities from southeastern Alaska through Oregon. We analysed mitochondrial DNA variation using DNA sequence data from the mitochondrial cytochrome-b (cyt-b ) gene and control region, and we found two distinct clades consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt-b and 0.0396 for the control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. We also examined the historical demography of the two clades using stepwise and exponential expansion models, both of which indicated recent rapid population growth. Furthermore, using the program migrate we found evidence of migration from populations north of the Fraser River (British Columbia) to the south in both clades. This study demonstrates the utility of these model-based demographic methods in illuminating the evolutionary and biogegographic history of natural systems.

In the past, moment and likelihood methods have been developed to estimate the effective population size (N-e) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of Ne if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of N-e and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of N-e, respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both N-e and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers.

At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide polymorphism (SNP) marker map has been constructed. Many of the SNPs on this map, however, were identified by sampling a small number of chromosomes from a single population, and inferences drawn from studies using such SNPs may be influenced by ascertainment bias (AB). Through extensive simulations, we have found that AB is a potentially significant problem in estimating and comparing LD within and between populations. Specifically, the magnitude of AB is a function of the SNP discovery strategy, number of chromosomes used for SNP discovery, population genetic characteristics of the particular genomic region considered, amount of gene flow between populations, and demographic history of the populations. We demonstrate that a balanced SNP discovery strategy (where equal numbers of chromosomes are sampled from multiple subpopulations) is the optimal study design for generating broadly applicable SNP resources. Finally, we validate our theoretical predictions by comparing our results to publicly available data from ten genes sequenced in 24 African American and 23 European American individuals.

We explored the impact of phylogeny shape on the results of interspecific statistical analyses incorporating phylogenetic information. In most phylogenetic comparative methods (PCMs), the phylogeny can be represented as a relationship matrix, and the hierarchical nature of interspecific phylogenies translates into a distinctive blocklike matrix that can be described by its eigenvectors (topology) and eigenvalues (branch lengths). Thus, differences in the eigenvectors and eigenvalues of different relationship matrices can be used to gauge the impact of possible phylogeny errors by comparing the actual phylogeny used in a PCM analysis with a second phylogenetic hypothesis that may be more accurate. For example, we can use the sum of inverse eigenvalues as a rough index to compare the impact of phylogenies with different branch lengths. Topological differences are better described by the eigenvectors. In general, phylogeny errors that involve deep splits in the phylogeny (e.g., moving a taxon across the base of the phylogeny) are likely to have much greater impact than will those involving small perturbations in the fine structure near the tips. Small perturbations, however, may have more of an impact if the phylogeny structure is highly dependent (with many recent splits near the tips of the tree). Unfortunately, the impact of any phylogeny difference on the results of a PCM depends on the details of the data being considered. Recommendations regarding the choice, design, and statistical power of interspecific analyses are also made.

We report here a simulation study examining the effect of a recent spatial expansion on the pattern of molecular diversity within a deme. We first simulate a range expansion in a virtual world consisting in a two-dimensional array of demes exchanging a given proportion of migrants (m) with their neighbors. The recorded demographic and migration histories are then used under a coalescent approach to generate the genetic diversity in a sample of genes. We find that the shape of the gene genealogies and the overall pattern of diversity within demes depend not only on the age of the expansion but also on the level of gene flow between neighboring demes, as measured by the product Nm, where N is the size of a deme. For small Nm values (< approximately 20 migrants sent outwards per generation), a substantial proportion of coalescent events occur early in the genealogy, whereas with larger levels of gene flow, most coalescent events occur around the time of the onset of the spatial expansion. Gene genealogies are star shaped, and mismatch distributions are unimodal after a range expansion for large Nm values. In contrast, gene genealogies present a mixture of both very short and very long branch lengths, and mismatch distributions are multimodal for small Nm values. It follows that statistics used in tests of selective neutrality like Tajima's D statistic or Fu's F-S statistic will show very significant negative values after a spatial expansion only in demes with high Nm values. In the context of human evolution, this difference could explain very simply the fact that analyses of samples of mitochondrial DNA sequences reveal multimodal mismatch distributions in hunter-gatherers and unimodal distributions in post-Neolithic populations. Indeed, the current simulations show that a recent increase in deme size (resulting in a larger Nm value) is sufficient to prevent recent coalescent events and thus lead to unimodal mismatch distributions, even if deme sizes (and therefore Nm values) were previously much smaller. The fact that molecular diversity within deme is so dependent on recent levels of gene flow suggests that it should be possible to estimate Nm values from samples drawn from a single deme.

Using eight microsatellite loci and a variety of analytical methods, we estimated genetic effective size (N-e) of an abundant and long-lived marine fish species, the red drum (Sciaenops ocellatus), in the northern Gulf of Mexico (Gulf). The ratio N-e/N, where short-term variance N-e was estimated via the temporal method from shifts in allele-frequency data over four cohorts and where N reflected a current estimate of adult census size in the northern Gulf, was similar to0.001. In an idealized population, this ratio should approximate unity. The extraordinarily low value of N-e/N appears to arise from high variance in individual reproductive success and perhaps more importantly from variance in productivity of critical spawning and nursery habitats located in spatially discrete bays and estuaries throughout the northern Gulf. An estimate of N, based on a coalescent approach, which measures long-term, inbreeding effective size, was four orders of magnitude lower than the estimate of current census size, suggesting that factors presently driving N-e/N to low values among red drum in the northern Gulf may have operated similarly in the past. Models that predict N-e/N exclusively from demographic and life-history features will seriously overestimate N-e if variance in reproductive success and variance in productivity among spatially discrete demes is underestimated. Our results indicate that these variances, especially variance in productivity among demes, must be large for red drum. Moreover, our study indicates that vertebrate populations with enormous adult census numbers may still be at risk relative to decline and extinction from genetic factors.

The paper shows basic mathematical methodology of modeling genetic neutral evolution, including Fisher Wright process statistics, appropriate models of mutation and coalescence method, and overviews recent results in the area. The basic approach is the use of maximum likelihood techniques. However due to computational problems, other more intuitive or approximate methods are also of great importance.

An importance-sampling method is presented for computing the likelihood of the configuration of population genetic data under general assumptions about population history and transitions among states. The configuration of the data is the number of chromosomes sampled that are in each of a finite set of states. Transitions among states are governed by a Markov chain with transition probabilities dependent on one or more parameters. The method assumes that the joint distribution of coalescence times of the underlying gene genealogy is independent of the genetic state of each lineage. Given a set of coalescence times, the probability that a pair of lineages is chosen to coalesce in each replicate is proportional to the contribution that the coalescence event makes to the probability of the data. This method can be applied to gene genealogies generated by the neutral coalescent process and to genealogies generated by other processes, such as a linear birth-death process which provides a good approximation to the dynamics of low-frequency alleles. Two applications are described. In the first, the fit of allele frequencies at two microsatellite loci sampled in a Sardinian population to the one-step mutation model is tested. The one-step model is rejected for one locus but not for the other. The second application is to low-frequency alleles in a geographically subdivided population. The geographic location is the allelic state, and the alleles are assumed to be sufficiently rare that their dynamics can be approximated by a linear birth-death process in which the birth and death rates are independent of geographic location. The analysis of eight low-frequency allozyme alleles found in the glaucous-winged gull, Larus glaucescens, illustrates how geographically restricted dispersal can be detected. (C) 2002 Elsevier Science (USA). All rights reserved.

While studies of phylogeography and speciation in the past have largely focused on the documentation or detection of significant patterns of population genetic structure, the emerging field of statistical phylogeography aims to infer the history and processes underlying that structure, and to provide objective, rather than ad hoc explanations. Methods for parameter estimation are now commonly used to make inferences about demographic past. Although these approaches are well developed statistically, they typically pay little attention to geographical history. In contrast, methods that seek to reconstruct phylogeographic history are able to consider many alternative geographical scenarios, but are primarily nonstatistical, making inferences about particular biological processes without explicit reference to stochastically derived expectations. We advocate the merging of these two traditions so that statistical phylogeographic methods can provide an accurate representation of the past, consider a diverse array of processes, and yet yield a statistical estimate of that history. We discuss various conceptual issues associated with statistical phylogeographic inferences, considering especially the stochasticity of population genetic processes and assessing the confidence of phylogeographic conclusions. To this end, we present some empirical examples that utilize a statistical phylogeographic approach, and then by contrasting results from a coalescent-based approach to those from Templeton's nested cladistic analysis (NCA), we illustrate the importance of assessing error. Because NCA does not assess error in its inferences about historical processes or contemporary gene flow, we performed a small-scale study using simulated data to examine how our conclusions might be affected by such unconsidered errors. NCA did not identify the processes used to simulate the data, confusing among deterministic processes and the stochastic sorting of gene lineages. There is as yet insufficent justification of NCA's ability to accurately infer or distinguish among alternative processes. We close with a discussion of some unresolved problems of current statistical phylogeographic methods to propose areas in need of future development.

Ancient Murrelets (Synthliboramphus antiquus) are subarctic seabirds that breed on islands from British Columbia through Alaska to China. In this study, we used sequence variation in the mitochondrial control region and cytochrome b gene to estimate the extent of genetic differentiation and gene flow among populations both within British Columbia and across the North Pacific. Results suggest that genetic differentiation is low and female-mediated gene flow is high among colonies within British Columbia, in agreement with banding studies. Surprisingly, genetic differentiation appears to be low and gene flow high between British Columbia and Asia. The effective female population size appears to be stable, but the species may have undergone a range expansion. These results suggest that Ancient Murrelets from throughout the North Pacific may represent a single management unit for conservation.

For a phylogeographical analysis of European grey partridge (Perdix perdix) we sequenced 390 nucleotides of the 5 end of the mitochondrial control region (CR) of 227 birds from several localities. The birds were divided into two major clades (western and eastern) which differed in control region 1 (CR1) by 14 nucleotide substitutions (3.6%). For estimation of the time of divergence, the whole CR of 14 specimens was sequenced. The major clades differed by 2.2%, corresponding to an estimated coalescence time of c. 1.1 million years. On CR1, 45 haplotypes were found. Western clade haplotypes were found in France, England, Germany, Poland, Italy and Austria. Eastern clade haplotypes were found in Finland, Bulgaria, Greece, and Ireland. One Finnish population and all Bulgarian and Irish populations were mixed, but only in Bulgaria was the mixing assumed to be natural. Nucleotide and haplotype diversities varied between populations, and both clades showed geographical structuring. The distribution of pairwise nucleotide differences in the eastern clade fitted the expectations of an expanding population. About 80% of the genetic structure in the grey partridge could be explained by the clades. The western clade presumably originates on the Iberian Peninsula (with related subtypes in Italy), and the eastern clade either on the Balkan or Caucasian refugia. Largescale hand-rearing and releasing of western partridges have introduced very few mtDNA marks into the native eastern populations in Finland.

We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.

A range-wide survey of Dakota skipper (Hesperia dacotae) populations assessed levels of genetic variability and geographic scale of population structure in this species of conservation concern. This species exists on isolated patches of native tall- and mixed-grass prairie within a highly modified landscape dominated by agriculture. It has been extirpated from the southern portion of its range and has suffered range-wide declines. Nine populations were sampled from western Minnesota, eastern South Dakota, and southern Manitoba. Starch gel electrophoresis was used to resolve 21 isozyme loci in 278 Dakota skippers. Dakota skipper populations were approximately as variable as other lepidopterans found in isolated habitats. Genetic distances indicated that Manitoba populations were somewhat distinct from ones in Minnesota and South Dakota. Isolation-by-distance was detected range-wide and among the seven southern-most populations. Genetically effective immigration rates were small at both range-wide and regional scales and effective populations sizes were low suggesting that Dakota skipper populations are genetically isolated from one another, although they were likely more connected in the recent past. Genotype assignment tests revealed two clusters of populations in Minnesota and South Dakota that were not apparent from the isolation-by-distance results. Significant heterozygote deficiencies relative to Hardy-Weinberg expectations and high inbreeding coefficients suggest structure within sample locations. Management recommendations include the maximization of effective population size in each Dakota skipper population to offset the effects of drift and habitat corridors in some cases. Habitat management should consider the within-site population structure and possible temporal population structure detected in this study.

The increasingly obvious medical relevance of human genetic variation is fueling the development of a rich interface between medical genetics and the study of human genetic history. A key feature of this interface is a step increase in the size and diversity of genetic data sets, permitting a range of new questions to be addressed concerning our evolutionary history. Similarly, methodologies first developed to study genetic history are being tailored to address medical challenges, including mapping genes that influence diseases and variable drug reactions. In this paper we do not attempt a comprehensive review of human genetic history. Rather we briefly outline some of the complications and challenges in the study of human genetic history, drawing particular attention to new opportunities created by the explosive growth in genetic information and technologies. First we discuss the complexity of human migration and demographic history, taking both a genetic and archaeological perspective. Then we show how these apparently academic issues are becoming increasingly important in medical genetics, focusing on association studies, the common disease/common variant hypothesis, the evaluation of variable drug response, and inferences about gene function from patterns of genetic variation. Finally we describe some of the inferential approaches available for interpreting human genetic variation, focusing both on current limitations and future developments.

Only recently has Bayesian inference of phylogeny been proposed. The method is now a practical alternative to the other methods; indeed, the method appears to possess advantages over the other methods in terms of ability to use complex models of evolution, ease of interpretation of the results, and computational efficiency. However, the method should be used cautiously. The results of a Bayesian analysis should be examined with respect to the sensitivity of the results to the priors used and the reliability of the Markov chain Monte Carlo approximation of the probabilities of trees.

Pitman and Jehl (1998) recently argued that Masked Boobies (formerly Sula dactylatra granti) breeding on the Nazca Plate in the eastern Pacific Ocean are morphologically and ecologically distinct from other Masked Boobies and may represent a full species. The American Ornithologists' Union subsequently elevated that subspecies to a full species: the Nazca Booby (S. granti). To evaluate that change in classification, we compared sequence variation in the mitochondrial cytochrome-b gene among 75 Nazca Boobies and 37 Masked Boobies representing three subspecies from the central and eastern Pacific and Atlantic oceans. Results indicated strong differentiation of cytochrome-b variation among taxa. Sequences constituted three distinct groups: Nazca Boobies, Masked Boobies from the central and eastern Pacific (S. d. personata and S. d. californica), and Masked Boobies (S. d. dactylatra) from the Caribbean and Atlantic. Those three groups probably diverged within a very short period, 400,000-500,000 years ago. Our results support the proposal that S. granti represents a distinct species.

The deluge of data from the human genome project (HGP) presents new opportunities for molecular anthropologists to study human variation through the promise of vast numbers of new polymorphisms (e.g., single nucleotide polymorphisms or SNPs). Collecting the resulting data into a single, easily accessible resource will be important to facilitate this research. We created a prototype Web-accessible database named ALFRED (ALelle FREquency Database, http://alfred.med.yale.edu/alfred/) to store and make publicly available allele frequency data on diverse polymorphic sites for many populations. In constructing this database, we considered many different concerns relating to the types of information needed for anthropology, population genetics, molecular genetics, and statistics, as well as issues of data integrity and ease of access to data. We also developed links to other Web-based databases as well as procedures for others to make links to the data in ALFRED. Here we present an overview of the issues considered and provisional solutions, as well as an example of data already available. It is our hope that this database will be useful for research and teaching in a wide range of fields, and that colleagues from various fields will contribute to making ALFRED an important resource for many studies as yet unforeseen. (C) 2002 Wiley-Liss, Inc.

We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely unchanged. This result is relevant to the large number of coalescent estimation procedures, which generally assume neutrality for segregating polymorphisms-applying these estimators to evolutionarily constrained sequences could lead to a significant degree of bias. We also estimate the statistical power of several neutrality tests in detecting weak to moderate purifying selection and find that the power is quite good for some parameter combinations. This result contrasts with previous studies, which predicted low statistical power because of the minor effect that weak purifying selection has on the shape of a genealogy. Finally, we investigate the effect of Hill-Robertson interference among linked deleterious mutations on patterns of molecular variation. We find that dependence among selected loci can substantially reduce the efficacy of even fairly strong purifying selection.

Since the introduction of allozyme methods in the mid 1960s it has been a standard practice to report Wright's measure of population subdivision, F-ST, for surveys of genetic variation. Its widespread use has provided us with a sense of what values can be expected in particular situations and how they can be interpreted. With some theoretical justification, F-ST has also been used to estimate rates of gene flow. However there are conditions under which F-ST is inappropriate for gene flow estimation and can lead to incorrect or even absurd conclusions. These pitfalls have prompted critics to suggest that F-ST has failed to deliver what its proponents have promised and should be abandoned. A further challenge has been the development of new methods that offer even greater promise. Thus it is reasonable to ask if perhaps it is time to retire F-ST and turn to new and more powerful methods for the inference of gene flow from genetic markers. Here I will argue that although gene flow should be estimated by more powerful approaches whenever practical, F-ST remains a useful measure of the average effects of gene flow and will continue to be used for comparative purposes.

Population decline in red-legged kittiwakes (Rissa brevirostris) over recent decades has necessitated the collection of information on the distribution of genetic variation within and among colonies for implementation of suitable management policies. Here we present a preliminary study of the extent of genetic structuring and gene flow among the three principal breeding locations of red-legged kittiwakes using the hypervariable Domain I of the mitochondrial control region. Genetic variation was high relative to other species of seabirds, and was similar among locations. Analysis of molecular variance indicated that population genetic structure was statistically significant, and nested clade analysis suggested that kittiwakes breeding on Bering Island maybe genetically isolated from those elsewhere. However, phylogeographic structure was weak. Although this analysis involved only a single locus and a small number of samples, it suggests that red-legged kittiwakes probably constitute a single evolutionary significant unit; the possibility that they constitute two management units requires further investigation.

Our ability to make inferences about the processes acting upon a biological system can be dramatically improved through integration of information from other fields. In particular, this is true of the field of phylogeography, a discipline that attempts to describe geographical variation in species using neutral genetic diversity as a correlate of time. Through comparisons of information from multiple species, as well as background information about the abiotic environment and how it has changed over time, we should be able to reassemble many of the forces that were important in assembling the communities and community interactions found in a given region. Here I review the information available for coastal species in the northwestern Atlantic, and argue that an integration of ecological, genetic, geological and oceanographic information can illustrate emergent patterns of community genetics.

Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences.

The present study combines methods that were designed to infer intraspecific relationships (e.g. nested-clade analysis (NCA), mismatch distributions and maximum likelihood gene flow analysis) to analyse historic events and recurrent processes in the cryptic mud snail species Hydrobia acuta and H. glyca . Specifically, we test the proposed allopatry of cryptic species and whether the peculiar range-subdivision of the putative subspecies H. a. acuta and H. a. neglecta is a result of long-distance dispersal or continuous range expansion. The NCA indicates a past fragmentation of the two H. acuta subspecies as well as past fragmentations within H. glyca . Gene-flow analyses show extensive gene flow in an E-W direction (towards the Atlantic) in the Mediterranean H. a. acuta , generally low gene flow in a W-E direction in the Atlantic H. a. neglecta and complex gene-flow pattern in a N-S but also in a S-N direction (against the Gulf Stream) in H. glyca . Based on these data and supportive ecological and oceanographical data, we hypothesize that the separation of the two H. acuta subspecies was not caused by long-distance dispersal but by a range shift and/or range expansion of the closely related competitor H. glyca as a result of an interglacial warming with a subsequent range shift in H. acuta . Moreover, our data do not show evidence for a long-term, stable sympatry of Hydrobia species, supporting the concept of allopatric relationships within cryptic radiations. NCA and gene-flow analyses indicate that the only sympatric population found in our study is the result of a recent dispersal event from the nearby Mediterranean. It is assumed that allopatric relationships in ephemeral Hydrobia populations constitute an evolutionary advantage relative to competition, recruitment and re-establishment of habitats. Mechanisms that could be of relevance for maintaining allopatry are discussed.

We investigated the interplay between natural selection and gene flow in the adaptive divergence of threespine stickleback (Gasterosteus acideatus) that reside parapatrically in lakes and streams. Within the Misty Lake system (Vancouver Island, British Columbia), stickleback from the inlet stream (flowing into the lake) have fewer gill rakers and deeper bodies than stickleback from the lake-differences thought to facilitate foraging (benthic macroinvertebrates in the stream vs. zooplankton in the open water of the lake). Common-garden experiments demonstrated that these differences have a genetic basis. Reciprocal transplant enclosure experiments showed that lake and inlet stickleback grow best in their home environments (although differences were subtle and often not significant). Release-recapture experiments in the inlet showed that lake fish are less well-suited than inlet fish for life in the stream (higher mortality or emigration in lake fish). Morphological divergence in the wild and under common rearing was greater between the lake and the inlet than between the lake and the outlet. Genetic divergence (mitochondrial DNA and microsatellites) was greatest between the lake and the upper inlet (1.8 km upstream from the lake), intermediate between the lake and the lower inlet (0.9 km upstream), and least between the lake and the outlet stream (1.2 km downstream). Relative levels of gene flow estimated from genetic data showed the inverse pattern. The negative association between morphological divergence and gene flow is consistent with the expectation that gene flow can constrain adaptation. Estimated absolute levels of gene flow also implied a constraint on adaptation in the outlet but not the inlet. Our results suggest that natural selection promotes the adaptive divergence of lake and stream stickleback, but that the magnitude of divergence can be constrained by gene flow.

British history contains several periods of major Cultural change. It remains controversial as to how much these periods coincided with substantial immigration from continental Europe. even for those that Occurred most recently. In this study, we examine genetic data for evidence of male immigration at particular times into Central England and North Wales. To do this, we used 12 biallelic polymorphisms and six microsatellite markers to define high-resolution Y chromosome haplotypes in a sample of 3 13 males from seven towns located along an east-west transect from East Anglia to North Wales. The Central English towns were genetically very similar, whereas the two North Welsh towns differed significantly both from each other and from the Central English towns. When we compared our data with an additional 177 samples collected in Friesland and Norway. We found that the Central English and Frisian samples were statistically indistinguishable. Using novel population genetic models that incorporate both mass migration and continuous gene flow, we conclude that these striking patterns are best explained by a substantial migration of Anglo-Saxon Y chromosomes into Central England (contributing 50%-100% to the gene pool Lit that time) but not into North Wales.

Recent technical advances allow straightforward access to genetic information directly drawn from DNA. The present article highlights the suitability of high variation molecular genetic markers, such as microsatellites, for studies relevant to amphibian conservation. Molecular markers appear particularly useful for i) measuring local gene flow and migration, ii) assigning individuals to their most likely population of origin, iii) measuring effective population size through the between-generation comparison of allele frequencies, and iv) detecting past demographic bottlenecks through allele frequency distortions. We demonstrate the use of some newly developed analytical tools on newt (Triturus sp.) microsatellite data, discuss practical aspects of using microsatellites for amphibians, and outline potential future research directions.

This article proposes a method of estimating the time to the most recent common ancestor (TMRCA) of a sample of DNA sequences. The method is based on the molecular clock hypothesis, but avoids assumptions about population structure. Simulations show that in a wide range of situations, the point estimate has small bias and the confidence interval has at least the nominal coverage probability. We discuss conditions that can lead to biased estimates. Performance of this estimator is compared with existing methods based on the coalescence theory. The method is applied to sequences of Y chromosomes and mtDNAs to estimate the coalescent times of human male and female populations.

Improvements in genotyping technologies have led to the increased use of genetic polymorphism for inference about population phenomena, such as migration and selection. Such inference presents a challenge, because polymorphism data reflect a unique, complex, non-repeatable evolutionary history. Traditional analysis methods do not take this into account. A stochastic process known as the `coalescent' presents a coherent statistical framework for analysis of genetic polymorphisms.

The Kermode bear is a white phase of the North American black bear that occurs in low to moderate frequency on British Columbia's mid-coast. To investigate the genetic uniqueness of populations containing the white phase, and to ascertain levels of gene flow among populations, we surveyed 10 highly polymorphic microsatellite loci, assayed from trapped bear hairs. A total of 216 unique bear genotypes, 18 of which were white, was sampled among 12 localities. Island populations, where Kermodes are most frequent, show approximate to 4% less diversity than mainland populations, and the island richest in white bears (Gribbell) exhibited substantial genetic isolation, with a mean pairwise F-ST of 0.14 with other localities. Among all localities, F-ST for the molecular variant underlying the coat-colour difference (A893G) was 0.223, which falls into the 95th percentile of the distribution of F-ST values among microsatellite alleles, suggestive of greater differentiation for coat colour than expected under neutrality. Control-region sequences confirm that Kermode bears are part of a coastal or western lineage of black bears whose existence predates the Wisconsin glaciation, but microsatellite variation gave no evidence of past population expansion. We conclude that Kermodism was established and is maintained in populations by a combination of genetic isolation and somewhat reduced population sizes in insular habitat, with the possible contribution of selective pressure and/or nonrandom mating.

The divergence of Drosophila pseudoobscura from its close relatives, D. persimilis and D. pseudoobscura bogotana, was examined using the pattern of DNA sequence variation in a common set of 50 inbred lines at I I loci from diverse locations in the genome. Drosophila pseudoobscura and D. persimilis show a marked excess of low-frequency variation across loci, consistent with a model of recent population expansion in both species. The different loci vary considerably. both in polymorphism levels and in the levels of polymorphisms that are shared by different species pairs. A major question we address is whether these patterns of shared variation are best explained by gene flow or by persistence since common ancestry. A new test of gene flow. based on patterns of linkage disequilibrium, is developed. The results from these. and other tests, support a model in which D. pseudoobscura and D. persimilis have exchanged genes at some loci. However, the pattern of variation suggests that most gene flow, although occurring after speciation be-an, was not recent. There is less evidence of gene flow between D. pseudoobscura and D. p. bogotana. The results are compared with recent work on the genomic locations of genes that contribute to reproductive isolation between D. pseudoobscura and D. persimilis. We show that there is a good correspondence between the genomic regions associated with reproductive isolation and the regions that show little or no evidence of gene flow.

Although neutral molecular markers have long been important tools for describing genetic variation in threatened fish species, many of the most critical questions in conservation relate more to quantitative genetic variation than to neutral markers. Quantitative genetic studies are typically expensive and time-consuming to conduct, especially in some of the long-lived vertebrates of conservation concern. The present review of recent literature in fish conservation genetics examines the traditional role of molecular studies in describing conservation units and providing indirect inference about local adaptation and adaptive potential. Of special interest are approaches that use a combination of molecular and quantitative genetic methods. Such studies are likely to provide important new insights into many conservation-related problems. The review also explores how increasing interest in non-neutral molecular markers is contributing to our understanding of the geographic scale and evolutionary importance of local adaptation in threatened populations. It is increasingly clear that advanced genetic technologies for the exploration of neutral and non-neutral molecular variation are leading to a fundamental shift in the way complex phenotypic traits are studied. This new synthesis of methods will have dramatic implications for fish conservation genetics and biology in general.

There is a wealth of published molecular population genetic studies, however, most do not include historic samples and thus implicitly assume temporal genetic stability. We tested for changes in genetic diversity and structure in three populations of steelhead trout (Oncorhynchus mykiss) from a northern British Columbia watershed using seven microsatellite loci over 40 years. We found little change in genetic diversity (mean allele numbers and observed and expected heterozygosity), despite large variation in the estimated numbers of steelhead returning to the watershed over the same time period. However, the temporal stability in genetic diversity is not reflected in population structure, which appears to be high among populations, yet significantly variable over time. The neighbour-joining tree showed that, overall, two of the populations (Zymoetz and Kispiox) clustered separately from the third (Babine); a finding which was not consistent with their geographical separation. The clustering pattern was also not temporally consistent. We used the temporal method to estimate the effective number of breeders (N-b) for the three populations; our values (N-b = 17-102) were low for the large and presumed vigorous populations of steelhead trout sampled. The low N-b values were also not consistent with the generally high genetic diversity estimates, suggesting the possibility of intermittent gene flow among the three populations. The use of temporal analyses in population genetic samples should be a priority; first, to verify observed patterns in contemporary data, and second, to build a data-set of temporal analyses to allow generalizations to be made concerning temporal genetic stability and effective population size in natural populations.

Patterns of population subdivision and gene flow were quantified using allozymes in three sympatric species of natricine snakes from the island region of western Lake Erie. Species share similar population history (post-Pleistocene range expansion followed by subdivision into island and mainland demes) and life-history characteristics. However, species differ in anticipated rates of gene flow because of differences in body size and degree to which they use aquatic habitats. Significant population subdivision was present in all three species, and isolation by distance was evident in water snakes (Nerodia sipedon) and, to a lesser degree, in brown snakes (Storeria dekayi) but not in garter snakes (Thamnophis sirtalis). As predicted, water snakes, the largest and most aquatic of the three species, showed significantly less population structure (lower values of F-ST) than did the smaller and more terrestrial garter snakes and brown snakes. Furthermore, variance in locus-specific estimates of F-ST was highest for brown snakes, intermediate for garter snakes, and lowest for water snakes. Estimates of F-ST obtained in this study are similar in magnitude to those reported for other snake species that have undergone post-Pleistocene range expansion but are lower than those reported for some southern U.S. species that may have experienced longer periods of isolation.

The effects of Quaternary climatic cycles were investigated in Drosophila serido, a Brazilian cactophilic fly widely distributed outside the Amazonian region. Previous studies have indicated this species displays remarkable karyotypic, male genitalia, and mtDNA variation, so much so that it has been described as a species complex, or superspecies. In the present study we expand the analysis of the mtDNA COI gene on D. serido populations, particularly in central Brazil, by obtaining DNA sequences from 248 individuals distributed across 47 localities. This allowed us to perform a nested clade analysis to discriminate historical from recurrent forces shaping the evolution of D. serido populations. The nested analysis indicates one event of past fragmentation separating populations from south and central Brazil (referred to as type B) from populations in central and northeast Brazil (type D) and 15 other significant events. The most common outcome of our analysis was contiguous range expansion and we discuss why this was expected in D. serido. Our data indicate that D. serido has been distributed across Brazil at least since the Mid-Pleistocene, which contradicts the hypothesis of current distribution being determined by last glaciation cycle. Nonetheless, we present evidence that climatic cycles during the Quaternary and before have had a significant impact on the differentiation of D. serido in Brazil. Our study confirms the usefulness of the nested clade analysis for disentangling the effects of historical and present-day forces shaping the evolution and distribution of a taxon. (C) 2002 Elsevier Science.

I derive the equilibrium values of sex-specific F-ST parameters, in an island model for a dioecious species with sex-biased dispersal and binomial distribution of family size before dispersal (as assumed in a Wright-Fisher population). I show that F-ST may take different values among males and among females whenever dispersal is a trait conditioned on gender. This has not always been recognized, because some models assumed that genes are sampled before dispersal. In particular, the ratios of sex-specific F-ST parameters evaluated after dispersal over F-ST evaluated before dispersal are simple functions of sex-specific dispersal rates. Therefore, a simple moment-based estimator of sex-specific dispersal rate is proposed. This method is based on the comparison of F-ST estimated before and after dispersal and assumes equilibrium between migration and drift. I evaluate this method through stochastic simulations for a range of sex-specific dispersal rates and sampling effort (sample size, number of loci scored).

Much progress has been made on inferring population history from molecular data. However, complex demographic scenarios have been considered rarely or have proved intractable. The serial introduction of the South-Central American cane Load Bufo marinas in various Caribbean and Pacific islands involves four major phases: a possible genetic admixture during the first introduction, a bottleneck associated with founding, a transitory, population boom, and finally, a demographic stabilization. A large amount of historical and demographic information is available for those introductions and can be combined profitably with molecular data. We used a Bayesian approach to combine this information With microsatellite (10 loci) and enzyme (22 loci) data and used a rejection algorithm to simultaneously estimate the demographic parameters describing the four major phases of the introduction history,. The general historical trends supported by microsatellites and enzymes were similar. However, there was a stronger support for a larger bottleneck at introductions for microsatellites than enzymes and for a more balanced genetic admixture for enzymes than for microsatellites. Verb, little information was obtained from either marker about the transitory population boom observed after each introduction. Possible explanations for differences in resolution of demographic events and discrepancies between results obtained with microsatellites and enzymes were explored. Limits Of Our model and method for the analysis of nonequilibrium populations were discussed.

Studying the population genetics of the Y chromosome is the most simple and direct way to gain independent information on male-specific historic and contemporary evolutionary processes. Y chromosomal polymorphisms can now be accessed thanks to recent developments in cytogenetic technologies, thus allowing the direct study of male population genetics. More interestingly, because males are the heterogametic sex in mammals, the use of both Y specific and mitochondrial polymorphisms with autosomal loci offers a unique opportunity to infer sex-specific population parameters and to explore crucial aspects of both breeding systems and dispersal strategies.

As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phyto logeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.

We introduce a new method for estimating recombination rates from population genetic data. The method uses a computationally intensive statistical procedure (importance sampling) to calculate the likelihood under a coalescent-based model. Detailed comparisons of the new algorithm with two existing methods (the importance sampling method of Griffiths and Marjoram and the MCMC method of Kuhner and colleagues) show it to be substantially more efficient. (The improvement over the existing importance sampling scheme is typically by four orders of magnitude.) The existing approaches riot infrequently led to misleading results on the problems we investigated. We also performed a simulation study to look at the properties of the maximum-likelihood estimator of the recombination rate and its robustness to misspecification of the demographic model.

The postgenomics era will bring many changes to ecology and evolution. information about genomic sequence and function provides a new foundation for organismal biology. The crucifer Arabidopsis thaliana and its wild relatives will play an important role in this synthesis of genomics and ecology. We discuss the need for model systems in ecology, the biology and relationships of crucifers, and the molecular resources available for these experiments. The scientific potential of this model system is illustrated by several recent studies in plant-insect interactions, developmental plasticity, comparative genomics and molecular evolution.

In phylogeography, an empirical focus on gene lineages enables the history of population processes to be inferred from the simultaneous analysis of temporal and spatial patterns. Rapidly evolving cytoplasmic DNA has been the empirical workhorse propelling the success of this nascent field. Now, as more sophisticated historical models are being tested, there is a growing need for phylogeography to expand from a largely marker-specific discipline to a more general analytical approach that can be applied across independent loci. Recent results using nuclear haplotypes to study phylogeography indicate that the anticipated technical and biological hurdles can be overcome in many taxa to achieve phylogeographical comparisons across unlinked loci. Although many challenges remain, a more complete understanding of the historical, demographic and selective processes shaping phylogeographical patterns is emerging.

Various methodological approaches using molecular sequence data have been developed and applied across several fields, including phylogeography, conservation biology, virology and human evolution. The aim of these approaches is to obtain predictive estimates of population history from DNA sequence data that can then be used for hypothesis testing with empirical data. This recent work provides opportunities to evaluate hypotheses of constant population size through time, of population growth or decline, of the rate of growth or decline, and of migration and growth in subdivided populations. At the core of many of these approaches is the extraction of information from the structure of phylogenetic trees to infer the demographic history of a population, and underlying nearly all methods is coalescent theory. With the increasing availability of DNA sequence data, it is important to review the different ways in which information can be extracted from DNA sequence data to estimate demographic parameters.

Phylogeography has become a powerful approach for elucidating contemporary geographical patterns of evolutionary subdivision within species and species complexes. A recent extension of this approach is the comparison of phylogeographic patterns of multiple co-distributed taxonomic groups, or `comparative phylogeography.' Recent comparative phylogeographic studies have revealed pervasive and previously unrecognized biogeographic patterns which suggest that vicariance has played a more important role in the historical development of modern biotic assemblages than current taxonomy would indicate. Despite the utility of comparative phylogeography for uncovering such `cryptic vicariance', this approach has yet to be embraced by some researchers as a valuable complement to other approaches to historical biogeography. We address here some of the common misconceptions surrounding comparative phylogeography, provide an example of this approach based on the boreal mammal fauna of North America, and argue that together with other approaches, comparative phylogeography can contribute importantly to our understanding of the relationship between earth history and biotic diversification.

Substantial genetic differentiation, as great as among species, exists between populations of Drosophila melanogaster inhabiting opposite slopes of a small canyon. Previous work has shown that prezygotic sexual isolation and numerous differences in stress-related phenotypes have evolved between D. melanogaster populations in “Evolution Canyon,” Israel, in which slopes 100-400 m apart differ dramatically in aridity, solar radiation, and associated vegetation. Because the canyon's width is well within flies' dispersal capabilities, we examined genetic changes associated with local adaptation and incipient speciation in the absence of geographical isolation. Here we report remarkable genetic differentiation of microsatellites and divergence in the regulatory region of hsp70Ba which encodes the major inducible heat shock protein of Drosophila, in the two populations. Additionally, an analysis of microsatellites suggests a limited exchange of migrants and lack of recent population bottlenecks. We hypothesize that adaptation to the contrasting microclimates overwhelms gene flow and is responsible for the genetic and phenotypic divergence between the populations.

In this paper, we present the distribution of the coalescence time of two DNA sequences (or genes) subject to symmetric migration between two islands, and conditional on the observed number of segregating sites in the sequences. The distribution for the segregating-site pattern is also obtained. Some surprising results emerge when both genes are initially on the same island. First, the post-data mean coalescence time is shown to be dependent on the migration parameter, as opposed to the pre-data mean. Second, both the post-data density and expectation for the coalescence time are shown to converge, in the weak-migration limit, to the corresponding parmictic results, as opposed to the pre-data situation where there is convergence in the density but not in the expectation. Finally, it is shown that there is convergence in the weak-migration limit in the distribution of the number of segregating sites but not in the expectation and variance. Numerical and graphical results for samples of size greater than two are also presented.

A simple genealogical process is found for samples from a metapopulation, which is a population that is subdivided into a large number of demes, each of which is subject to extinction and recolonization and receives migrants from other demes. As in the migration-only models studied previously, the genealogy of any sample includes two phases: a brief sample-size adjustment followed by a coalescent process that dominates the history. This result will hold for metapopulations that are composed of a large number of domes. It is robust to the details of population structure, as long as the number of possible source domes of migrants and colonists for each deme is large. Analytic predictions about levels of genetic variation are possible, and results for average numbers of pairwise differences within and between domes are given. Further analysis of the expected number of segregating sites in a sample from a single dome illustrates some previously known differences between migration and extinction/recolonization. The ancestral process is also amenable to computer simulation. Simulation results show that migration and extinction/recolonization have very different effects on the site-frequency distribution in a sample from a single deme. Migration can cause a U-shaped site-frequency distribution, which is qualitatively similar to the pattern reported recently for positive selection. Extinction and recolonization, in contrast, can produce a mode in the site-frequency distribution at intermediate frequencies, even in a sample from a single dome.

This article describes a new Markov chain Monte Carlo (MCMC) method applicable to DNA sequence data, which treats mutations in the genealogy as missing data. The method facilitates inferences regarding the age and identity of specific mutations while taking the full complexities of the mutational process in DNA sequences into account. We demonstrate the utility of the method in three applications. First, we demonstrate how the method can be used to make inferences regarding population genetical parameters such as theta (the effective population size times the mutation rate). Second, we show how the method can be used to estimate the ages of mutations in finite sites models and for making inferences regarding the distribution and ages of nonsynonymous and synonymous mutations. The method is applied to two previously published data sets and we demonstrate that in one of the data sets the average age of nonsynonymous mutations is significantly, lower than the average age of synonymous mutations, suggesting the presence of slightly deleterious mutations. Third, we demonstrate how the method in general can be used to evaluate the posterior distribution of a function of a mapping of mutations on a gene genealogy. This application is useful for evaluating the uncertainty associated with methods that rely on mapping mutations on a phylogeny or a gene genealogy.

We present results from a study of genetic variation in Utah's cougar population. Estimates were based on data for 50 animals at nine microsatellite loci with five individuals sampled for each of ten management units throughout Utah. Levels of variation were moderate (average genetic diversity across populations was estimated to be 0.4687 for all 50 individuals), and comparable with other large mammals. But this level of variation for the microsatellite loci translated into an inbreeding effective population size of only 571 animals, much lower than the current estimates of census sizes of around 2000-3000. A lack of differentiation among the sampled populations across Utah (average N(e)m = 6.2) indicates that gene flow occurs over a large area. Since cougars are capable of movement beyond the Utah state borders (and certainly across management units), a better understanding of migration rates and patterns of dispersal will be achieved by sampling a much larger geographic region incorporating much of the western USA. Successful management and conservation of this species will then require a far more integrated approach, involving agencies across a number of states, as opposed to current management practices involving individual units within states.

When populations are separated for long periods and then brought into contact for a brief episode in part of their range, this can result in genetic admixture. To analyze this type of event we considered a simple model under which two parental populations (P-1 and P-2) mix and create a hybrid population (H). After that event, the three populations evolve under pure drift without exchange during T generations. We developed a new method, which allows the simultaneous estimation of the time since the admixture event (scaled by the population size t(i) = T/N-ii, where N-i is the effective population size of population i) and the contribution of one of two parental populations (which we call p(1)). This method takes into account drift since the admixture event, variation caused by sampling, and uncertainty in the estimation of the ancestral allele frequencies. The method is tested on simulated data sets and then applied to a human data set. We find that (i) for single-locus data, point estimates are poor indicators of the real admixture proportions even when there are many alleles; (ii) biallelic loci provide little information about the admixture proportion and the time since admixture, even for very small amounts of drift, but can be powerful when many loci are used; (iii) the precision of the parameters' estimates increases with sample size (n = 50 vs. n = 200) but this effect is larger for the t(i)'s than for p(1); and (iv) the increase in precision provided by multiple loci is quite large, even when there is substantial drift (we found, for instance, that it is preferable to use five loci than one locus, even when drift is 100 times larger for the five loci). Our analysis of a previously studied human data set illustrates that the joint estimation of drift and p(1)can provide additional insights into the data.

Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis.

Explaining the extent, causes, and consequences of biotic distributions in space is fundamental to our understanding of how species evolve and cope with particular environments. Yet, identifying extrinsic barriers to migration imposed by landscape structure and predicting their impacts on intraspecific genetic diversity remains a major challenge in population biology. In this study, 30 populations (771 individuals) of brook charr (Salvelinus fontinalis, Salmonidae) representing six major river drainages from Maine, USA, were characterized at six microsatellite loci to quantify the role of landscape features, such as habitat site, altitude, contemporary and historical connectivity, in shaping genetic diversity at three spatial scales: within lakes, within river drainages, and among river drainages. Within-population expected heterozygosity was negatively correlated with altitude, whereas no significant correlation was observed with lake size. Conversely, the extent of heterozygote deficiency within lakes was negatively associated with habitat size. The hierarchical analysis of genetic variance revealed that the extent of among-drainage differentiation was unexpectedly low relative to the pronounced population structuring within drainage. Geographically proximate St. John and Penobscot River drainages were characterized by opposite effects of altitude and geographic distance in shaping the pattern of population differentiation within drainages. The geographic pattern of differentiation among drainages could not be accounted for either by an isolation by distance or by a stepwise range expansion model. Overall, this study provided evidence for the role of contemporary landscape features in shaping the observed pattern of genetic diversity at smaller geographic scales (within and among populations within river drainage). On a broader geographic scale, contemporary landscape structure appeared to be only a minor factor determining the observed pattern of genetic structuring among drainages. These results add to the increasing evidence for nonequilibrium conditions between drift and migration in a wide array of animal taxa. The development of more realistic theoretical descriptions of nonequilibrium population structure thus appears to be important to better understand the relative influence of historical and ecological factors in shaping genetic variation in young habitats, such as recently deglaciated areas.

A Markov chain Monte Carlo method for estimating the relative effects of migration and isolation on genetic diversity in a pair of populations from DNA sequence data is developed and tested using simulations. The two populations are assumed to be descended from a panmictic ancestral population at some time in the past and may (or may not) after that be connected by migration. The use of a Markov chain Monte Carlo method allows the joint estimation of multiple demographic parameters in either a Bayesian or a likelihood framework. The parameters estimated include the migration rate for each population, the time since the two populations diverged from a common ancestral population, and the relative size of each of the two current populations and of the common ancestral population. The results show that even a single nonrecombining genetic locus can provide substantial power to test the hypothesis of no ongoing migration and/or to test models of symmetric migration between the mio populations. The use of the method is illustrated in an application to mitochondrial DNA sequence data from a fish species: the threespine stickleback (Gasterosteus aculeatus).

Sequence variation was examined in domain I of the mitochondrial control region in three Queensland populations of Hall's Babbler Pomatostomus halli. a geographically restricted, monotypic songbird in eastern Australia. Surprisingly, we found that domain I sequences were strongly differentiated into two major clades differing by 3.29%. These two clades exhibited nearly complete geographic concordance with northern and southern populations, except for two haplotypes which were sampled in the north of the range but were phylogenetically allied to the southern clade. We also round a seven-fold higher level of genetic diversity in the northern than in the southern populations. Neutrality and molecular clock tests suggested that selection or differences in substitution rates were not responsible for this difference in diversity. However. a maximum likelihood analysis of ene flow between the north and south suggested that the difference in diversity could be due to both greater population size in the north and asymmetric gene flow dominated by south to north dispersal events. A likelihood ratio test rejected a model in which population sizes were equal and rates of gene flow symmetric, and came close to rejecting a model in which only population sizes were constrained to be equal. These results suggest that different population sizes and asymmetric gene flow could be a major source of differences in genetic variation between populations of Hall's Babbler, although ecological and biogeographic causes for these differences are obscure.

A simple genealogical structure is found for a general finite island model of population subdivision. The model allows for variation in the sizes of demes, in contributions to the migrant pool, and in the fraction of each deme that is replaced by migrants every generation. The ancestry of a sample of non-recombining DNA sequences has a simple structure when the sample size is much smaller than the total number of demes in the population. This allows an expression for the probability distribution of the number of segregating sites in the sample to be derived under the infinite-sites mutation model. It also yields easily computed estimators of the migration parameter for each deme in a multi-deme sample. The genealogical process is such that the lineages ancestral to the sample tend to accumulate in demes with low migration rates and/or which contribute disproportionately to the migrant pool. In addition, common ancestor or coalescent events tend to occur in demes of small size. This provides a framework for understanding the determinants of the effective size of the population, and leads to an expression for the probability that the root of a genealogy occurs in a particular geographic region, or among a particular set of demes. (C) 2001 Academic Press.

Using sequence data from seven nuclear loci in 385 isolates of the haploid, plant parasitic, ascomycete fungus, Sclerotinia divergence times of populations and of species were distinguished. The evolutionary history of haplotypes on both population and species scales was reconstructed using a combination of parsimony, maximum likelihood and coalescent methods, implemented in a specific order. Analysis of site compatibility revealed recombination blocks from which alternative (marginal) networks were inferred, reducing uncertainty in the network due to recombination. Our own modifications of Templeton and co-workers' cladistic inference method and a coalescent approach detected the same phylogeographic processes. Assuming neutrality and a molecular clock, the boundary between divergent populations and species is an interval of time between coalescence (to a common ancestor) of populations and coalescence of species.

A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed. The method uses a Markov chain Monte Carlo approach to investigate possible genealogies with branch lengths and with migration events. Properties of the new method are shown by using simulated data from a four-population n-island model and a source-sink population model. Our estimation method as coded in MIGRATE is tested against GENETREE; both programs deliver a very similar likelihood surface. The algorithm converges to the estimates fairly quickly, even when the Markov chain is started from unfavorable parameters. The method was used to estimate gene flow in the Nile valley by using mtDNA data from three human populations.

Modern population genetics underwent a major paradigm shift during the last decade of the 20th century with the discovery that thousands of genes of known function and position in a genome can be analyzed simultaneously in a single individual. The impact of this technology on insect population genetics is potentially profound, Sampling distributions of genetic statistics can now be derived from many individual loci or among many segregating sites within a gene. Inferences regarding random mating, gene flow, effective population sizes, disequilibrium, and relatedness among populations can now be based on patterns of variation at many loci. More importantly, genome-wide sampling enables population geneticists to distinguish effects that act on the whole genome from those that act on individual loci or nucleotides. We introduce the term “population genomics” to describe the process of simultaneous sampling of numerous variable loci within a genome and the inference of locus-specific effects from the sample distributions. The four critical assumptions implicit in the population genomics approach are explained in detail. Studies adopting this paradigm are reviewed, and the steps necessary to complete a population genomics study are outlined.

The relationship between cultural and genetic evolution was examined in the yellow-naped amazon Amazona auropalliata. This species has previously been shown to have regional dialects defined by large shifts in the acoustic structure of its learned contact call. Mitochondrial DNA sequence variation from a 680 base pair segment of the first domain of the control region was assayed in 41 samples collected from two neighbouring dialects in Costa Rica. The relationship of genetic variation to vocal variation was examined using haplotype analysis, genetic distance analysis, a maximum-likelihood estimator of migration rates and phylogenetic reconstructions. All analyses indicated a high degree of gene flow and, thus, individual dispersal across dialect boundaries. Calls sampled from sound libraries suggested that temporally stable contact call dialects occur throughout the range of the yellow-naped amazon, while the presence of similar dialects in the sister species Amazona ochrocephala suggests that the propensity to form dialects is ancestral in this clade. These results indicate that genes and culture are not closely associated in the yellow-naped amazon. Rather, they suggest that regional diversity in vocalizations is maintained by selective pressures that promote social learning and allow individual repertoires to conform to local call types.

We study the behavior of Phi (ft), a recently introduced estimator of instantaneous pollen flow, which is basically the intraclass correlation of inferred pollen cloud genetic frequencies among a sample of females drawn from a single population. Using standard theories of identity by descent and spatial processes, we show that Phi (ft), depends on the average distance of pollen dispersal (delta) and on the average distance between sampled mothers ((x(1)) over bar). Provided that mothers are sampled far enough apart ((x(1)) over bar > 5 delta), Phi (ft), becomes independent of (x(1)) over bar, and is then inversely proportional to the square of delta. Provided that this condition is fulfilled, delta is directly estimable from Phi (ft). Even when (x(1)) over bar < 5<delta>, estimation can easily be achieved via numerical evaluation. We show that the relation between Phi (ft) and delta is only modestly affected by the shape of the distribution function, a result of importance, since this shape is generally unknown. We also study the impact of adult density within the population on Phi (ft) showing that to achieve the correct inference of delta from Phi (ft), it must be taken into account, but that it has no effect on the distance at which mothers must be sampled.

Standard methods for inferring demographic parameters from genetic data are based mainly on one-locus theor). However, the association of genes at different loci (e.g., two-locus identity disequilibrium) may also contain some information about demographic parameters of populations. In this article, we define one- and two-locus parameters of population structure as functions of one- and two-locus probabilities for the identity in state of genes. Since these parameters are known functions of demographic parameters in an infinite island model, we develop moment-based estimators of effective population size and immigration rate from one- and two-locus parameters. We evaluate this method through simulation, Although variance and bias may be quite large, increasing the number of loci on which the estimates are derived improves the method. We simulate an infinite allele model and a K allele model of mutation. Bias and variance are smaller with increasing numbers of alleles per locus. This is, to our knowledge, the first attempt of a joint estimation of local effective population size and immigration rate.

Many species persist as a metapopulation under a balance between the local extinction of subpopulations or demes and their recolonization through dispersal from occupied patches. Here we review the growing body of literature dealing with the genetic consequences of such population turnover. We focus our attention principally on theoretical studies of a classical metapopulation with a `finite-island' model of population structure, rather than on `continent-island' models or `source-sink' models. In particular, we concern ourselves with the subset of geographically subdivided population models in which it is assumed that all demes are liable to extinction from time to time and that all demes receive immigrants. Early studies of the genetic effects of population turnover focused on population differentiation, such as measured by F-ST A key advantage of F-ST over absolute measures of diversity is its relative independence of the mutation process, so that different genes in the same species may be compared. Another advantage is that F-ST Will usually equilibrate more quickly following perturbations than will absolute levels of diversity. However, because F-ST is a ratio of between-population differentiation to total diversity, the genetic effects of metapopulation processes may be difficult to interpret in terms of F-ST-on its own, so that the analysis of absolute measures of diversity in addition is likely to be informative. While population turnover may either increase or decrease F-ST, depending on the mode of colonization, recurrent extinction and recolonization is expected always to reduce levels of both within-population and species-wide diversity (pi (S) and pi (T), respectively). One corollary of this is that pi (S) cannot be used as an unbiased estimate of the scaled mutation rate, theta, as it can, with some assumptions about the migration process, in species whose demes do not fluctuate in size. The reduction of pi (T) in response to population turnover reflects shortened mean coalescent times, although the distribution of coalescence times under extinction-colonization equilibrium is not yet known. Finally we review current understanding of the effect of metapopulation dynamics on the effective population size.

The development of statistical tests of natural selection at the DNA level in population samples has been ongoing for the past 13 years. The current state of the field is reviewed, and the available tests of selection are described. All tests use predictions from the theory of neutrally evolving sites as a null hypothesis. Departures from equilibrium-neutral expectations can indicate the presence of natural selection acting either at one or more of the sites under investigation or at a sufficiently tightly linked site. Complications can arise in the interpretation of departures from neutrality if populations are not at equilibrium for mutation and genetic drift or if populations are subdivided, both of which are likely scenarios for humans. Attempts to understand the nonequilibrium configuration of silent polymorphism in human mitochondrial DNA illustrate the difficulty of distinguishing between selection and alternative demographic hypotheses. The range of plausible alternatives to selection will become better defined, however, as additional population genetic data sets become available, allowing better mil models to be constructed.

We describe a method for co-estimating r = C/mu (where Cis the per-site recombination rate and mu is the per-site neutral mutation rate) and Theta = 4N(e)mu (where N-e is the effective population size) from a population sample of molecular data. The technique is Metropolis-Hastings sampling: we explore a large number of possible reconstructions of the recombinant genealogy, weighting according to their posterior probability with regard to the data and working values of the parameters. Different relative rates of recombination at different locations can be accommodated if they are known from external evidence, but the algorithm cannot itself estimate rate differences. The estimates of Theta are accurate and apparently unbiased for a wide range of parameter values. However, when both Theta and r are relatively low, very long sequences are needed to estimate r accurately, and the estimates tend to be biased upward. We apply this method to data from the human lipoprotein lipase locus.

full likelihood-based inference for modern population genetics data presents methodological and computational challenges. The problem is of considerable practical importance and has attracted recent attention, with the development of algorithms based on importance sampling (IS) and Markov chain Monte Carlo (MCMC) sampling. Here we introduce a new IS algorithm. The optimal proposal distribution for these problems can be characterized, and we exploit a detailed analysis of genealogical processes to develop a practicable approximation to it. We compare the new method with existing algorithms on a variety of genetic examples. Our approach substantially outperforms existing IS algorithms, with efficiency typically improved by several orders of magnitude. The new method also compares favourably with existing MCMC methods in some problems, and less favourably in others, suggesting that both IS and MCMC methods have a continuing role to play in this area. We offer insights into the relative advantages of each approach, and we discuss diagnostics in the IS framework.

We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.

Analysis of the coalescent structure of a population may provide information useful in mapping disease loci. Current coalescent-based genealogy samplers require haplotyped data, but haplotypes are not always available, and it is not practical to sum over all haplotype assignments for large data sets. We describe a method of adding haplotype re-evaluation to the sampler, so that it samples not only among genealogies explaining a given haplotype configuration, but also among different haplotype configurations. Several different haplotype-rearrangement strategies are considered, but the simplest-inverting the phase of a single site in a single individual-appears to be the most successful. The straightforward haplotype sampler does not mix well; heating approaches can greatly improve its performance. Genet. Epidemiol. 19(Suppl 1):S15-S21, 2000. (C) 2000 Wiley-Liss, Inc.

In this paper, we address alternative hypotheses for the evolution of subspecies of rock ptarmigan (Lagopus mutus) endemic to the Aleutian Archipelago. To do this we examined patterns of genetic differentiation among populations of rock ptarmigan in the Aleutian Islands and parts of both Alaska and Siberia. Variation in mitochondrial control region sequences of 105 rock ptarmigan from 10 subspecies within the Bering region revealed three major phylogenetic lineages, two of which are endemic to the Aleutian Islands. Accordingly, haplotype and nucleotide diversities of rock ptarmigan within the archipelago are much higher than within mainland Alaska or Siberia. For Aleutian rock ptarmigan, analyses of molecular variance indicated significant genetic structuring and low estimates of gene flow among populations, despite small interisland distances within the archipelago. However; isolation by distance did not describe the pattern of gene flow or differentiation at this scale. Our estimates of divergence times of lineages suggest that Aleutian rock ptarmigan became isolated prior to the most recent Pleistocene glaciation event (late Wisconsin Stade) and that current patterns of genetic variation reflect the postglacial redistribution of divergent lineages and subsequent limited gene flow In addition, genetic divergence among lineages was concordant with the distribution of plumage types among subspecies. The patterns of genetic variation described here for rock ptarmigan provide evidence for the role of glacial vicariance in contributing to genetic diversity within this and other Bering region species.

Long-distance seed dispersal influences many key aspects of the biology of plants, including spread of invasive species, metapopulation dynamics, and diversity and dynamics in plant communities. However, because long-distance seed dispersal is inherently hard to measure, there are few data sets that characterize the tails of seed dispersal curves. This paper is structured around two lines of argument. First, we argue that long-distance seed dispersal is of critical importance and, hence, that we must collect better data from the tails of seed dispersal curves. To make the case for the importance of long-distance seed dispersal, we review existing data and models of long-distance seed dispersal, focusing on situations in which seeds that travel long distances have a critical impact (colonization of islands, Holocene migrations, response to global change, metapopulation biology). Second, we argue that genetic methods provide a broadly applicable way to monitor long-distance seed dispersal; to place this argument in context, we review genetic estimates of plant migration rates. At present, several promising genetic approaches for estimating long-distance seed dispersal are under active development, including assignment methods, likelihood methods, genealogical methods, and genealogical/demographic methods. We close the paper by discussing important but as yet largely unexplored areas for future research.

This article presents a nucleotide sequence analysis of 500 bp determined in each of five X-linked genes, runt, sisterlessA, period, esterase 5, and Heat-shock protein 83, in 40 Drosophila pseudoobscura strains collected from two populations. Estimates of the neutral migration parameter for the five loci show that gene flow among D. pseudoobscura populations is sufficient to homogenize inversion frequencies across the range of the species. Nucleotide diversity at each locus fails to reject a neutral model of molecular evolution. The sample of 40 chromosomes included six Sex-ratio inversions, a series of three nonoverlapping inversions that are associated with a strong meiotic drive phenotype. The selection driven by the Sex-ratio meiotic drive element has not fixed variation across the X chromosome of D. pseudoobscura because, while significant linkage disequilibrium was observed within the sisterlessA, period, and esterase 5 genes, we did not find evidence for nonrandom association among loci. The Sex-ratio chromosome was estimated to be 25,000 years old based on the decomposition of linkage disequilibrium between esterase 5 and Heat-shock protein 83 or 1 million years old based on the net divergence of esterase 5 between Standard and Sex-ratio chromosomes. Genetic diversity was depressed within esterase 5 within Sex-ratio chromosomes, while the four other genes failed to show a reduction in heterozygosity in the Sex-ratio background. The reduced heterogeneity in esterase 5 is due either to its location near one of the Sex-ratio inversion breakpoints or that it is closely linked to a gene or genes responsible for the Sex-ratio meiotic drive system.

Single nucleotide polymorphism (SNP) data can be used for parameter estimation via maximum likelihood methods as long as the way in which the SNPs were determined is known, so that an appropriate likelihood formula can be constructed. We present such likelihoods for several sampling methods. As a test of these approaches, we consider use of SNPs to estimate the parameter Theta = 4N(e)mu (the scaled product of effective population size and per-site mutation rate), which is related to the branch lengths of the reconstructed genealogy. With infinite amounts of data, ML models using SNP data are expected to produce consistent estimates of Theta. With finite amounts of data the estimates are accurate when Theta is high, but tend to be biased upward when Theta is low. If recombination is present and not allowed for in the analysis, the results are additionally biased upward, but this effect can be removed by incorporating recombination into the analysis. SNPs defined as sites that are polymorphic in the actual sample under consideration (sample SNPs) are somewhat more accurate for estimation of Theta than SNPs defined by their polymorphism in a panel chosen from the same population (panel SNPs). Misrepresenting panel SNPs as sample SNPs leads to large errors in the maximum likelihood estimate of Theta. Researchers collecting SNPs should collect and preserve information about the mettled of ascertainment so that the data can be accurately analyzed.

Despite large genetic differentiation among neighbouring populations of many freshwater zooplankton species, a macrogeographical homogeneity of allozyme variation is generally observed. A study on breeding systems in Scandinavian populations of Daphnia pulex suggested a latitudinally related dine in breeding system with both diploid cyclic parthenogens and diploid obligate parthenogens at the latitude of 60-61 degrees N. Variation at neutral markers may be more affected by selection at linked loci in such species than in strictly sexual species. In this paper I present a study of variation at five microsatellite loci in a total of 34 populations from small ponds and rockpools on both sides of the Baltic Sea at 60-61 degrees N. Two major groups, which may represent different species of the D. pulex complex, are defined with the microsatellites. Neighbouring populations show both similar and well differentiated genetic composition. Populations separated by larger geographical distances show only a large differentiation and a macrogeographic pattern. The large differentiation observed at small distances can be explained with small effective population size: variation at the microsatellite loci has been shaped by population bottlenecks followed with expansion in size, and possibly by selection. No conclusive evidence is found for obligative parthenogenesis.

The collapse of various stock complexes of cod (Gadus morhua) in the northwest Atlantic has prompted a clarification of relationships among stock components. Here we examine the genetic composition of >2300 cod collected during 1994-1997 in the Gulf of St. Lawrence and its approaches to determine whether: (1) stock components can be genetically identified; (2) population structure is temporally stable; (3) components are always separated and, if not, where and when are they mixed; and (4) component contributions to mixtures can be estimated. We use polymorphism at six microsatellite DNA loci from cod collected on or near their spring and summer spawning grounds to examine structure and then employ maximum likelihood analyses to estimate contributions of each component to mixtures overwintering near the entrance to the Gulf. Estimates of genetic structure (F-ST and R-ST) reveal significant differences among cod populations during stock-separated periods, and the structure appears to be temporally stable. Multidimensional scaling analysis of estimates of genetic distance (D-A) suggest that the structure results from differences among cod collected within the Gulf of St. Lawrence and those collected near the entrance to the Gulf on either side of the Laurentian Channel in the Cabot Strait, as well as among cod collected south of Newfoundland along the north side of the Channel. Weak genetic heterogeneity among seven regional mixed-stock collections during the overwintering period suggests that cod aggregations characteristically found in the overwintering region represent population mixtures that differ in the proportion of cod contributed to them by the various stock components, Maximum likelihood estimates indicate no significant temporal changes in component contributions to the mixed-stock samples between 1996 and 1997 when all of the winter mixed-stock samples were pooled. The combined contribution of cod from the southern and northern Gulf of St. Lawrence to the mixed-stock samples ranged between 46% and 71% (expected 64%), More precise estimates of contributions from these two regions are precluded by the weak genetic differentiation detected in our samples. The contribution by cod from the Cape Breton Island region was small and estimated at 3%. Contributions by cod from the eastern Scotian Shelf, southwest Newfoundland and south-central Newfoundland were in the range of 13-14%, 4%, and 8%, respectively. Contributions by inshore cod from Placentia and Fortune Bays in south Newfoundland were small to negligible (similar to 3% each). The results indicate that future management could be designed around the spatial and temporal scale of the stock structure identified during the stock-separated period and around the spatially varying contributions to the overwintering mixed-stock fishery.

Mechanisms of population differentiation in highly vagile species such as seabirds are poorly understood. Previous studies of marbled murrelets (Brachyramphus marmoratus; Charadriiformes: Alcidae) found significant population genetic structure, but could not determine whether this structure is due to historical vicariance (e.g., due to Pleistocene glaciers), isolation by distance, drift or selection in peripheral populations, or nesting habitat selection. To discriminate among these possibilities, we analyzed sequence variation in nine nuclear introns from 120 marbled murrelets sampled from British Columbia to the western Aleutian Islands. Mismatch distributions indicated that murrelets underwent at least one population expansion during the Pleistocene and probably are not in genetic equilibrium. Maximum-likelihood analysis of allele frequencies suggested that murrelets from “mainland” sites (from the Alaskan Peninsula east) are genetically different from those in the Aleutians and that these two lineages diverged prior to the last glaciation. Analyses of molecular variance, as well as estimates of gene flow derived using coalescent theory, indicate that population genetic structure is best explained by peripheral isolation of murrelets in the Aleutian Islands, rather than by selection associated with different nesting habitats. No isolation-by-distance effects could be detected. Our results are consistent with a rapid expansion of murrelets from a single refugium during the early-mid Pleistocene, subsequent isolation and divergence in two or more refugia during the final Pleistocene glacial advance, and secondary contact following retreat of the ice sheets. Population genetic structure now appears to be maintained by distance effects combined with small populations and a highly fragmented habitat in the Aleutian Islands.

Phylogeographic patterns of intraspecific variation can provide insights into the population-level processes responsible for speciation and yield information useful for conservation purposes. To examine phylogeography and population structure in a migratory passerine bird at both continental and regional geographical scales, we analysed 344 bp of mitochondrial DNA (mtDNA) control region sequence from 155 yellow warblers (Dendroica petechia) collected from seven locations across Canada and from Alaska. There is a major subdivision between eastern (Manitoba to Newfoundland) and western (Alaska and British Columbia) populations which appears to have developed during the recent Pleistocene. Some localities within these two regions also differ significantly in their genetic composition, suggesting further subdivision on a regional geographical scale. Eastern and western birds form distinct phylogeographic entities and the clustering of all western haplotypes with two eastern haplotypes suggests that the western haplotypes may be derived from an eastern lineage. Analyses based on coalescent models support this explanation for the origin of western haplotypes. These results are consistent with important features of Mengel's model of warbler diversification. From a conservation perspective they also suggest that individual populations of migrant birds may form demographically isolated management units on a smaller scale than previously appreciated.

A special stochastic process, called the coalescent, is of fundamental interest in population genetics. For a large class of population models this process is the appropriate tool to analyse the ancestral structure of a sample of n individuals or genes, if the total number of individuals in the population is sufficiently large. A corresponding convergence theorem was first proved by Kingman in 1982 for the Wright-Fisher model and the Moran model. Generalizations to a large class of exchangeable population models and to models with overlying mutation processes followed shortly later. One speaks of the “robustness” of the coalescent, as this process appears in many models as the total population size tends to infinity. This publication can be considered as an introduction to the theory of the coalescent as well as a review of the most important “ convergence-to-the-coalescent-theorems”. Convergence theorems are not only presented for the classical exchangeable haploid case but also for larger classes of population models, for example for diploid, two-sex or non-exchangeable models. A review-like summary of further examples and applications of convergence to the coalescent is given including the most important biological forces like mutation, recombination and selection. The general coalescent process allows for simultaneous multiple mergers of ancestral lines. (C) 2000 Academic Press.

This paper studies gene trees in subdivided populations which are constructed as perfect phylogenies from the pattern of mutations in a sample of DNA sequences and presents a new recursion for the probability distribution of such gene trees. The underlying evolutionary model is the coalescent process in a subdivided population. The infinitely-many-sites model of mutation is assumed. Ancestral inference questions that are discussed are maximum likelihood estimation of migration and mutation rates; detection of population growth by likelihood techniques; determining the distribution of the time to the most recent common ancestor of a sample of sequences; determining the distribution of the age of the mutations on the gene tree; determining in which subpopulation the most recent common ancestor of all the sequences was; determining subpopulation ancestors, where they were, and times to them; and determining in which subpopulations mutations occurred. A computational technique of Griffiths and Tavare used is a computer intensive Markov chain simulation, which simulates gene trees conditional on their topology implied by the mutation pattern in the sample of DNA sequences. The software GENETREE, which implements these ancestral inference techniques, is available. (C) 2000 Academic Press.

We develop a Monte Carlo-based likelihood method for estimating migration rates and population divergence times from data at unlinked loci at which mutation rates are sufficiently low that, in the recent past, the effects of mutation can be ignored. The method is applicable to restriction fragment length polymorphisms (RFLPs) and single nucleotide polymorphisms (SNPs) sampled from a subdivided population. The method produces joint maximum-likelihood estimates of the migration rate and the time of population divergence, both scaled by population size, and provides a framework in which to test either for no ongoing gene flow or for population divergence in the distant past. We show the method performs well and provides reasonably accurate estimates of parameters even when the assumptions under which those estimates are obtained are not completely satisfied. Furthermore, we show that, provided that the number of polymorphic loci is sufficiently large, there is some power to distinguish between ongoing gene how and historical association as causes of genetic similarity between pairs of populations.

The grey wolf (Canis lupus) and coyote (C. latrans) are highly mobile carnivores that disperse over great distances in search of territories and mates. Previous genetic studies have shown little geographical structure in either species. However, population genetic structure is also influenced by past isolation events and population fluctuations during glacial periods. In this study, control region sequence data from a worldwide sample of grey wolves and a more limited sample of coyotes were analysed. The results suggest that fluctuating population sizes during the late Pleistocene have left a genetic signature on levels of variation in both species. Genealogical measures of nucleotide diversity suggest that historical population sizes were much larger in both species and grey wolves were more numerous than coyotes. Currently, about 300 000 wolves and 7 million coyotes exist. In grey wolves, genetic diversity is greater than that predicted from census population size, reflecting recent historical population declines. By contrast, nucleotide diversity in coyotes is smaller than that predicted by census population size, reflecting a recent population expansion following the extirpation of wolves from much of North America. Both species show little partitioning of haplotypes on continental or regional scales. However, a statistical parsimony analysis indicates local genetic structure that suggests recent restricted gene now.

Some general likelihood and Bayesian methods for analyzing single nucleotide polymorphisms (SNPs) are presented. First, an efficient method for estimating demographic parameters from SNPs in linkage equilibrium is derived. The method is applied in the estimation of growth rates of a human population based on 37 SNP loci. It is demonstrated how ascertainment biases, due to biased sampling of loci, can be avoided, at least in some cases, by appropriate conditioning: when calculating the likelihood function. Second, a Markov chain Monte Carl (MCMC) method for analyzing linked SNPs is del eloped. This method call be used for Bayesian and likelihood inference on linked SNPs. The utility of the method is illustrated by estimating recombination rates in a human data set containing 17 SNPs and 60 individuals. Both methods are based on assumptions of low mutation rates.

We compare the performance of Nm estimates based on F-ST and R-ST obtained from microsatellite data using simulations of the stepwise mutation model with range constraints in allele size classes. The results of the simulations suggest that the use of microsatellite loci can lead to serious overestimations of Nm, particularly when population sizes are large (N > 5000) and range constraints are high (K < 20). The simulations also indicate that, when population sizes are small (N less than or equal to 500) and migration rates are moderate (Nm approximate to 2), violations to the assumption used to derive the Nm estimators lead to biased results. Under ideal conditions, i.e. large sample sizes (n(s) greater than or equal to 50) and many loci (n(l) greater than or equal to 20), R-ST performs better than Fs, for most of the parameter space. However, F-ST-based estimates are always better than R-ST when sample sizes are moderate or small (n(s) less than or equal to 10) and the number of loci scored is low (n(l) < 20). These are the conditions under which many real investigations are carried out and therefore we conclude that in many cases the most conservative approach is to use F-ST.

We describe a Markov Chain Monte Carlo analysis of five human Y-chromosome microsatellite polymorphisms based on samples from five diverse populations. Our analysis provides strong evidence for mutational bias favoring increase in length at all loci. Estimates of population coalescent times and population size from our two largest samples, one African and one European, suggest that the African population is older but smaller and that the English East Anglian population has undergone significant expansion, being larger but younger, We conclude that Markov Chain Monte Carlo analysis of microsatellite haplotypes can uncover information not apparent when the microsatellites are considered independently. Incorporation of population size as a variable should allow us to estimate the timing and magnitude of major historical population trends.