Articles citing either the manual or one of the articles introducing Migrate in chronological order

Stevens, V. M., Verkenne, C., Vandewoestijne, S., Wesselingh, R. A., and Baguette, M., 2006 Gene ﬂow and functional connectivity in the natterjack toad. Mol. Ecology 15: 2333–2344, 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.

Steele, C. A. and Storfer, A., 2006 Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Paciﬁc Northwest for the Paciﬁc giant salamander (Dicamptodon tenebrosus). Mol. Ecology 15: 2477– 2487, Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Paciﬁc Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia inﬂuencing genetic variation of endemic organisms. One such endemic is the Paciﬁc giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species’ phylogeny and use a coalescent modeling approach to test ﬁve hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20 000 years ago), mid-Pleistocene (800 000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and ’g’ distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Paciﬁc Northwest.

Domingues, V. S., SantoS, R. S., Brito, A., and Almada, V. C., 2006 Historical population dynamics and demography of the eastern Atlantic pomacentrid Chromis limbata (Valenciennes, 1833). Mol. Phylogenetics Evolution

40: 139–147, 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.

Sampson, K. Y., 2006 Structured coalescent with nonconservative migration. J. Appl. Probability 43: 351–362, 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)).

Ward, R. D., 2006 The importance of identifying spatial population structure in restocking and stock enhancement programmes. Fisheries Research 80: 9–18, 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.

Vuilleumier, S. and Possingham, H. P., 2006 Does colonization asymmetry matter in metapopulations? Proc. Royal Soc. B-biological Sciences 273: 1637–1642, 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 50connectivity 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.

Packert, M., Dietzen, C., Martens, J., Wink, M., and Kvist, L., 2006 Radiation of Atlantic goldcrests Regulus regulus spp.: evidence of a new taxon from the Canary islands. J. Avian Biol. 37: 364–380, Phylogenetic relationships between goldcrest populations from the Atlantic Islands (Azores and Canary Islands) were investigated by two molecular markers (mitochondrial control region and cytochrome b sequences), and partly by morphology and territorial song. The Azorean goldcrest populations are closely related to European nominate R. r. regulus. Most probably, the Azores were colonized by goldcrests in a single late-pleistocene invasion, while colonization of the Canary Islands presumably occurred in two steps: An early invasion to Tenerife and La Gomera 1.9-2.3 million years (my) ago and a more recent one to El Hierro and La Palma 1.3-1.8 my ago. Distribution of haplotypes on the Azores suggests a division of R. r. azoricus on Sao Miguel into an eastern population with close aﬃnities to

R. r. sanctaemariae and a western population belonging to the lineage of R. r. inermis on the central and western island group. The Canarian populations are genetically substructured into a northeastern group embracing Tenerife and La Gomera and a second, southwestern group including El Hierro and La Palma. Genetic distances between members of the two Canarian clades range at 3.1-3.4Diﬀerentiation between the two groups is also supported by morphology and by territorial song. Substitution rate estimates for the both genes range at approximately the same values of 0.0031 and 0.0044 substitutions per site and lineage per my which roughly corresponds 0.61-0.83Regulus lineages per my. Highest local rates occur in island clades of the Azorean and the Canarian population and in R.

r. japonensis from the Russian Far East and Japan. However, a general acceleration of a molecular clock in island populations is not evident from the Regulus data set due to extremely low local rate estimates in the Canarian clade of Tenerife and La Gomera. As a taxonomic consequence of the marked diﬀerentiation of the two Canarian goldcrest clades the populations from El Hierro and La Palma are described as a taxon new to science and are named Regulus regulus ellenthalerae n. ssp.

Lopes, I. F., de Brito, R. A., Henrique-Silva, F., and Lama, S. N. D., 2006 Demographic history of wood stork (Mycteria americana) Brazilian Pantanal colonies revealed by mitochondrial DNA analysis. Genetics Mol. Biol. 29: 241–250, 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.

Santiago-Alarcon, D., Tanksley, S. M., and Parker, P. G., 2006 Morphological variation and genetic structure of Galapagos Dove (Zenaida galapagoensis) populations: Issues in conservation for the Galapagos bird fauna. Wilson J. Ornithology 118: 194–207, 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.

Azzurro, E., Golani, D., Bucciarelli, G., and Bernardi, G., 2006 Genetics of the early stages of invasion of the Lessepsian rabbitﬁsh Siganus luridus. J. Experimental Marine Biol. Ecology 333: 190–201, 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.

Aylor, D. L., Price, E. W., and Carbone, I., 2006 Snap: Combine and Map modules for multilocus population genetic analysis. Bioinformatics 22: 1399–1401, 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.

Vaxevanidou, Z., Gonzalez-Martinez, S. C., Climent, J., and Gil, L., 2006 Tree populations bordering on extinction: A case study in the endemic Canary Island pine. Biological Conservation 129: 451–460, Marginal populations are usually located at the edge of the species’ range, constituting small isolates that grow in suboptimal environments. In widely distributed conifers, such as pines, marginal populations have often been considered recent or rare colonizing events without ecological relevance. The Canary Island pine provides an excellent case to study the signiﬁcance of critically endangered marginal populations (from 20 to a few hundred trees) in an endemic conifer that is also extensively used in commercial plantations. Our chloroplast microsatellite (cpSSR) survey showed contrasting values of haplotypic genetic diversity in marginal populations of Canary island pine, from very low at Garabato (northern La Gomera) and Anaga (Tenerife), located within broad-leaved tree formations, to very high in Gran Canaria marginal populations (Arguineguin and Galdar). Competition with broad-leaved vegetation, after rare long-distance colonization events, might explain present-day low levels of variation in Garabato and Anaga. Gran Canaria and southern La Gomera relict populations, which contain high haplotypic diversity, are probably remnants of larger populations severely reduced by adverse climatic conditions and human activities, the latter starting shortly after the European colonization of the islands in the XV century. Given the extremely low population numbers and a general lack of natural regeneration, the risk of extinction in the near future is high in marginal populations of Canary Island pine. Conservation activities are urgently required and should focus on the highly diverse Gran Canaria and southern La Gomera pine marginal populations. Here, the establishment of in situ genetic reserves (Arguineguin and Imada), and multifunctional ex situ collections (Arguineguin and Galdar), such as seed orchards, is highly recommended. In addition, common garden experiments to test the performance of potentially drought-tolerant genotypes from Arguineguin (southernmost Gran Canaria’s relict) and potential risks due to inbreeding and/or outbreeding depression should be established. (c) 2005 Elsevier Ltd. All rights reserved.

Pidugu, S. R. and Schlotterer, C., 2006 ms2ms.pl: a PERL script for generating microsatellite data. Mol. Ecology Notes 6: 580–581, 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.

Jolly, M. T., Viard, F., Gentil, F., Thiebaut, E., and Jollivet, D., 2006 Comparative phylogeography of two coastal polychaete tubeworms in the Northeast Atlantic supports shared history and vicariant events. Mol. Ecology 15: 1841–1855, 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.

Waser, P. M., Busch, J. D., McCormick, C. R., and DeWoody, J. A., 2006 Parentage analysis detects cryptic precapture dispersal in a philopatric rodent. Mol. Ecology 15: 1929–1937, 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.

Zhang, J. B., Cai, Z. P., and Huang, L. M., 2006 Population genetic structure of crimson snapper Lutjanus erythropterus in East Asia, revealed by analysis of the mitochondrial control region. Ices J. Marine Science 63: 693– 704, 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.

Sambatti, J. B. M. and Rice, K. J., 2006 Local adaptation, patterns of selection, and gene ﬂow in the Californian serpentine sunﬂower (Helianthus exilis). Evolution 60: 696–710, 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.

Ewing, G. and Rodrigo, A., 2006 Coalescent-based estimation of population parameters when the number of demes changes over time. Mol. Biol. Evolution 23: 988–996, 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.

Carmen, M. A. and Ablan, A., 2006 Genetics and the study of ﬁsheries connectivity in Asian developing countries. Fisheries Research 78: 158–168, 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.

Martinez, P., Gonzalez, E. G., Castilho, R., and Zardoya, R., 2006 Genetic diversity and historical demography of Atlantic bigeye tuna (Thunnus obesus). Mol. Phylogenetics Evolution 39: 404–416, 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.

Cassone, B. J. and Boulding, E. G., 2006 Genetic structure and phylogeography of the lined shore crab, Pachygrapsus crassipes, along the northeastern and western Paciﬁc coasts. Marine Biol. 149: 213–226, 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.

Goodreau, S. M., 2006 Assessing the eﬀects of human mixing patterns on human immunodeﬁciency virus-1 interhost phylogenetics through social network simulation. Genetics 172: 2033–2045, 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.

Muniz-Salazar, R., Talbot, S. L., Sage, G. K., Ward, D. H., and Cabello-Pasini, A., 2006 Genetic structure of eelgrass Zostera marina meadows in an embayment with restricted water ﬂow. Marine Ecology-progress Series

309: 107–116, 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.

Nosil, P., Sandoval, C. P., and Crespi, B. J., 2006 The evolution of host preference in allopatric vs. parapatric populations of Timema cristinae walking-sticks. J. Evolutionary Biol. 19: 929–942, 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.

Natoli, A., Canadas, A., Peddemors, V. M., Aguilar, A., Vaquero, C., Fernandez-Piqueras, P., and Hoelzel, A. R., 2006 Phylogeography and alpha taxonomy of the common dolphin (Delphinus sp.). J. Evolutionary Biol. 19: 943–954, The resolution of taxonomic classiﬁcations for delphinid cetaceans has been problematic, especially for species in the genera Delphinus, Tursiops and Stenella. The frequent lack of correspondence between morphological and genetic diﬀerentiation in these species raises questions about the mechanisms responsible for their evolution. In this study we focus on the genus Delphinus, and use molecular markers to address questions about speciation and the evolution of population structure. Delphinus species have a worldwide distribution and show a high degree of morphological variation. Two distinct morphotypes, long-beaked and short-beaked, have been considered diﬀerent species named D. capensis and D. delphis, respectively. However, genetic diﬀerentiation between these two forms has only been demonstrated in the Paciﬁc. We analysed samples from eight diﬀerent geographical regions, including two morphologically deﬁned long-beaked form populations, and compared these with the eastern North Paciﬁc populations. We found high diﬀerentiation among the populations described as long-beaked instead of the expected monophyly, suggesting that these populations may have evolved from independent events converging on the same morphotype. We observed low genetic diﬀerentiation among the short-beaked populations across a large geographical scale. We interpret these phylogeographical patterns in the context of life history and population structure in related species.

Waples, R. S. and Gaggiotti, O., 2006 What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol. Ecology 15: 1419–1439, 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.

Garrick, R. C. and Sunnucks, P., 2006 Development and application of three-tiered nuclear genetic markers for basal Hexapods using single-stranded conformation polymorphism coupled with targeted DNA sequencing. Bmc Genetics 7, 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.

Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z. S., Munro,

H. M., Abecasis, G. R., and Donnelly, P., 2006 A comparison of phasing algorithms for trios and unrelated individuals. Am. J. Human Genetics 78: 437–450, 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 0.1from 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.

Ciofi, C., Wilson, G. A., Beheregaray, L. B., Marquez, C., Gibbs, J. P., Tapia, W., Snell, H. L., Caccone, A., and Powell, J. R., 2006 Phylogeographic history and gene ﬂow among giant Galapagos tortoises on southern Isabela island. Genetics 172: 1727–1744, 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.

Matson, C. W., Lambert, M. M., McDonald, T. J., Autenrieth, R. L., Donnelly, K. C., Islamzadeh, A., Politov, D. I., and Bickham, J. W., 2006 Evolutionary toxicology: Population-level eﬀects of chronic contaminant exposure on the marsh frogs (Rana ridibunda) of azerbaijan. Environmental Health Perspectives 114: 547–552, 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.

Leberg, P., 2005 Genetic approaches for estimating the eﬀective size of populations. J. Wildlife Management 69: 1385–1399, 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.

Gow, J. L., Peichel, C. L., and Taylor, E. B., 2006 Contrasting hybridization rates between sympatric three-spined sticklebacks highlight the fragility of reproductive barriers between evolutionarily young species. Mol. Ecology 15: 739–752, 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.

Adams, C. E., Hamilton, D. J., Mccarthy, I., Wilson, A. J., Grant, A., Alexander, G., Waldron, S., Snorasson, S. S., Ferguson, M. M., and Skulason, S., 2006 Does breeding site ﬁdelity drive phenotypic and genetic sub-structuring of a population of arctic charr? Evolutionary Ecology 20: 11–26, 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.

Kuhner, M. K., 2006 Lamarc 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22: 768–770, 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.

Felsenstein, J., 2006 Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci? Mol. Biol. Evolution 23: 691–700, 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.

Nuismer, S. L., 2006 Parasite local adaptation in a geographic mosaic. Evolution 60: 24–30, 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.

Beerli, P., 2006 Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22: 341–345, 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.

Hardy, O. J., Maggia, L., Bandou, E., Breyne, P., Caron, H., Chevallier, M. H., Doligez, A., Dutech, C., Kremer, A., Latouche-Halle, C., Troispoux, V., Veron, V., and Degen, B., 2006 Fine-scale genetic structure and gene dispersal inferences in 10 Neotropical tree species. Mol. Ecology 15: 559–571, 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.

Bell, J. D., Rothlisberg, P. C., Munro, J. L., Loneragan, N. R., Nash, W. J., Ward, R. D., and Andrew,

N. L., 2005 Restocking and stock enhancement of marine invertebrate ﬁsheries. Restocking Stock Enhancement Marine Invertebrate Fisheries 49: 1–+.

Riginos, C., 2005 Cryptic vicariance in Gulf of California ﬁshes parallels vicariant patterns found in Baja California mammals and reptiles. Evolution 59: 2678–2690, 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.

Bowie, R. C. K., Fjeldsa, J., Hackett, S. J., Bates, J. M., and Crowe, T. M., 2006 Coalescent models reveal the relative roles of ancestral polymorphism, vicariance, and dispersal in shaping phylogeographical structure of an African montane forest robin. Mol. Phylogenetics Evolution 38: 171–188, 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.

Theodorakis, C. W., Lee, K. L., Adams, S. M., and Law, C. B., 2006 Evidence of altered gene ﬂow, mutation rate, and genetic diversity in redbreast sunﬁsh from a pulp-mill-contaminated river. Environmental Science & Technology 40: 377–386, 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.

Sellas, A. B., Wells, R. S., and Rosel, P. E., 2005 Mitochondrial and nuclear DNA analyses reveal ﬁne scale geographic structure in bottlenose dolphins (Tursiops truncatus) in the Gulf of mexico. Conservation Genetics 6: 715–728, 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.

Kelly, M. W. and Rhymer, J. M., 2005 Population genetic structure of a rare unionid (Lampsilis cariosa) in a recently glaciated landscape. Conservation Genetics 6: 789–802, 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.

Voight, B. F., Adams, A. M., Frisse, L. A., Qian, Y. D., Hudson, R. R., and Rienzo, A. D., 2005 Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc. National Acad. Sciences United States Am. 102: 18508–18513, 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.

Crispo, E., Bentzen, P., Reznick, D. N., Kinnison, M. T., and Hendry, A. P., 2006 The relative inﬂuence of natural selection and geography on gene ﬂow in guppies. Mol. Ecology 15: 49–62, 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.

Hickerson, M. J., Dolman, G., and Moritz, C., 2006 Comparative phylogeographic summary statistics for testing simultaneous vicariance. Mol. Ecology 15: 209–223, 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.

Geml, J., Laursen, G. A., O’Neill, K., Nusbaum, H. C., and Taylor, D. L., 2006 Beringian origins and cryptic speciation events in the ﬂy agaric (Amanita muscaria). Mol. Ecology 15: 225–239, 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.

Leman, S. C., Chen, Y. G., Stajich, J. E., Noor, M. A. F., and Uyenoyama, M. K., 2005 Likelihoods from summary statistics: Recent divergence between species. Genetics 171: 1419–1436, 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.

Pomilla, C. and Rosenbaum, H. C., 2005 Against the current: an inter-oceanic whale migration event. Biol. Lett.

1: 476–479, 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.

Wang, X. H. and Kang, L., 2005 Diﬀerences in egg thermotolerance between tropical and temperate populations of the migratory locust Locusta migratoria (Orthoptera : Acridiidae). J. Insect Physiology 51: 1277–1285, 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.

Rhymer, J. M., McAuley, D. G., and Ziel, H. L., 2005 Phylogeography of the American woodcock (Scolopax minor): Are management units based on band recovery data reﬂected in genetically based management units? Auk 122: 1149–1160, 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.

Manier, M. K. and Arnold, S. J., 2005 Population genetic analysis identiﬁes source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis). Mol. Ecology 14: 3965–3976, 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.

Domingues, V. S., Bucciarelli, G., Almada, V. C., and Bernardi, G., 2005 Historical colonization and demography of the Mediterranean damselﬁsh, Chromis chromis. Mol. Ecology 14: 4051–4063, 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.

Bernardi, G. and Lape, J., 2005 Tempo and mode of speciation in the Baja California disjunct ﬁsh species Anisotremus davidsonii. Mol. Ecology 14: 4085–4096, The Baja California region provides a natural setting for studying the early mechanisms of allopatric speciation in marine systems. Disjunct ﬁsh populations from several species that occur in the northern Gulf of California and northern Paciﬁc coast of Baja California, but are absent from its southern shores, were previously shown to be genetically isolated, making them excellent candidates for studying allopatry. In addition, one of these species, the sargo Anisotremus davidsonii, has two pairs of congeneric Panamic trans-isthmian geminate species that allow for internal molecular clock calibration. Phylogeographic and demographic approaches based on mitochondrial ( cytochrome b) and nuclear (S7 ribosomal protein) sequences showed that A. davidsonii entered the gulf from the south, and later colonized the Paciﬁc coast, approximately 0.6-0.16 million years ago. Paciﬁc coast colonization may have used a route either around the southern cape of Baja California or across the peninsula through a natural seaway. However, while several seaways have been described from diﬀerent geological times, none matches the dates of population disjunction, yet much geological work remains to be done in that area. At the present time, there is no evidence for dispersal around the southern tip of the Baja California Peninsula. Signatures of incipient allopatric speciation were observed, such as the reciprocal monophyly of disjunct populations for the mitochondrial marker. However, other characteristics were lacking, such as a strong diﬀerence in divergence and coalescence times. Taken together, these results suggest that disjunct populations of

A. davidsonii may be consistent with the earliest stages of allopatric speciation.

Bilodeau, A. L., Felder, D. L., and Neigel, J. E., 2005 Population structure at two geographic scales in the burrowing crustacean Callichirus islagrande (Decapoda, Thalassinidea): Historical and contemporary barriers to planktonic dispersal. Evolution 59: 2125–2138, 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.

Lee, T. and Foighil, D. O., 2005 Placing the Floridian marine genetic disjunction into a regional evolutionary context using the scorched mussel, Brachidontes exustus, species complex. Evolution 59: 2139–2158, 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.

Hrbek, T., Farias, I. P., Crossa, M., Sampaio, I., Porto, J. I. R., and Meyer, A., 2005 Population genetic analysis of Arapaima gigas, one of the largest freshwater ﬁshes of the Amazon basin: implications for its conservation. Animal Conservation 8: 297–308, 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.

Bryan, M. B., Zalinski, D., Filcek, K. B., Libants, S., Li, W., and Scribner, K. T., 2005 Patterns of invasion and colonization of the sea lamprey (Petromyzon marinus) in North America as revealed by microsatellite genotypes. Mol. Ecology 14: 3757–3773, 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.

Nielsen, R., 2005 Peopling the americas. European J. Human Genetics 13: 1100–1101.

Waples, R. S., 2005 Genetic estimates of contemporary eﬀective population size: to what time periods do the estimates apply? Mol. Ecology 14: 3335–3352, 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.

Dalebout, M. L., Robertson, K. M., Frantzis, A., Engelhaupt, D., Mignucci-Giannoni, A. A., Rosario-Delestre, R. J., and Baker, C. S., 2005 Worldwide structure of mtDNA diversity among Cuvier’s beaked whales (Ziphius cavirostris): implications for threatened populations. Mol. Ecology 14: 3353–3371, 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.

McKay, J. K., Christian, C. E., Harrison, S., and Rice, K. J., 2005 ”how local is local?” -A review of practical and conceptual issues in the genetics of restoration. Restoration Ecology 13: 432–440, 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.

Pavlova, A., Zink, R. M., and Rohwer, S., 2005 Evolutionary history, population genetics, and gene ﬂow in the common roseﬁnch (Carpodacus erythrinus). Mol. Phylogenetics Evolution 36: 669–681, 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.

Petren, K., Grant, P. R., Grant, B. R., and Keller, L. F., 2005 Comparative landscape genetics and the adaptive radiation of Darwin’s ﬁnches: the role of peripheral isolation. Mol. Ecology 14: 2943–2957, 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.

Harley, E. H., Baumgarten, I., Cunningham, J., and O’Ryan, C., 2005 Genetic variation and population structure in remnant populations of black rhinoceros, Diceros bicornis, in africa. Mol. Ecology 14: 2981–2990, 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.

Brito, P. H., 2005 The inﬂuence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western europe. Mol. Ecology 14: 3077–3094, 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.

Iorio, M. D., Griffiths, R. C., Leblois, R., and Rousset, F., 2005 Stepwise mutation likelihood computation by sequential importance sampling in subdivided population models. Theoretical Population Biol. 68: 41–53, 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.

Natoli, A., Birkun, A., Aguilar, A., Lopez, A., and Hoelzel, A. R., 2005 Habitat structure and the dispersal of male and female bottlenose dolphins (Tursiops truncatus). Proc. Royal Soc. B-biological Sciences 272: 1217– 1226, Bottlenose dolphins (Tursiops truncatus) are widely distributed and a high degree of morphometric and genetic diﬀerentiation has been found among both allopatric and parapatric populations. We analysed 145 samples along a contiguous distributional range from the Black Sea to the eastern North Atlantic for mitochondrial and nuclear genetic diversity, and found population structure with boundaries that coincided with transitions between habitat regions. These regions can be characterized by ocean ﬂoor topography, and oceanographic features such as surface salinity, productivity and temperature. At the extremes of this range there was evidence for the directional emigration of females. Bi-parentally inherited markers did not show this directional bias in migration, suggesting a diﬀerent dispersal strategy for males and females at range margins. However, comparative assessment based on mitochondrial DNA and nuclear markers indicated that neither sex showed a strong bias for greater dispersal on average. These data imply a mechanism for the evolutionary structuring of populations based on local habitat dependence for both males and females.

Herron, M. D., Waterman, J. M., and Parkinson, C. L., 2005 Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of xerus. Mol. Ecology 14: 2773–2788, 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.

Mu, J. B., Joy, D. A., Duan, J. H., Huang, Y. M., Carlton, J., Walker, J., Barnwell, J., Beerli, P., Charleston, M. A., Pybus, O. G., and Su, X. Z., 2005 Host switch leads to emergence of Plasmodium vivax malaria in humans. Mol. Biol. Evolution 22: 1686–1693, The geographical origin of Plasmodium vivax, the most widespread human malaria parasite, is controversial. Although genetic closeness to Asian primate malarias has been conﬁrmed by phylogenetic analyses, genetic similarities between P. vivax and Plasmodium simium, a New World primate malaria, suggest that humans may have acquired P. vivax from New World monkeys or vice versa. Additionally, the near ﬁxation of the Duﬀy-negative blood type (FY X B-null/FY X B-null) in West and Central Africa, consistent with directional selection, and the association of Duﬀy negativity with complete resistance to vivax malaria suggest a prolonged period of host-parasite coevolution in Africa. Here we use Bayesian and likelihood methods in conjunction with cophylogeny mapping to reconstruct the genetic and coevolutionary history of P. vivax from the complete mitochondrial genome of 176 isolates as well as several closely related Plasmodium species. Taken together, a haplotype network, parasite migration patterns, demographic history, and cophylogeny mapping support an Asian origin via a host switch from macaque monkeys.

Anderson, E. C., 2005 An eﬃcient Monte Carlo method for estimating N-e from temporally spaced samples using a coalescent-based likelihood. Genetics 170: 955–967, 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.

Carstens, B. C., Bankhead, A., Joyce, P., and Sullivan, J., 2005 Testing population genetic structure using parametric bootstrapping and migrate-n. Genetica 124: 71–75, We present a method for investigating genetic population structure using sequence data. Our hypothesis states that the parameters most responsible for the formation of genetic structure among diﬀerent populations are the relative rates of mutation (mu) and migration (M). The evolution of genetic structure among diﬀerent populations requires rates of M ¡¡ mu because this allows population-speciﬁc mutation to accumulate. Rates of mu ¡¡ M will result in populations that are eﬀectively panmictic because genetic diﬀerentiation will not develop among demes. Our test is implemented by using a parametric bootstrap to create the null distribution of the likelihood of the data having been produced under an appropriate model of sequence evolution and a migration rate suﬃcient to approximate panmixia. We describe this test, then apply it to mtDNA data from 243 plethodontid salamanders. We are able to reject the null hypothesis of no population structure on all but smallest geographic scales, a result consistent with the apparent lack of migration in Plethodon idahoensis. This approach represents a new method of investigating population structure with haploid DNA, and as such may be particularly useful for preliminary investigation of non-model organisms in which multi-locus nuclear data are not available.

Hey, J., 2005 On the number of New World founders: A population genetic portrait of the peopling of the americas. Plos Biol. 3: 965–975, 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.

Johnson, S. G., 2005 Age, phylogeography and population structure of the microendemic banded spring snail, Mexipyrgus churinceanus. Mol. Ecology 14: 2299–2311, 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.

Bowen, B. W., Bass, A. L., Soares, L., and Toonen, R. J., 2005 Conservation implications of complex population structure: lessons from the loggerhead turtle (Caretta caretta). Mol. Ecology 14: 2389–2402, 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.

Hamilton, G., Currat, M., Ray, N., Heckel, G., Beaumont, M., and Excoffier, L., 2005 Bayesian estimation of recent migration rates after a spatial expansion. Genetics 170: 409–417, 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.

Banke, S. and McDonald, B. A., 2005 Migration patterns among global populations of the pathogenic fungus Mycosphaerella graminicola. Mol. Ecology 14: 1881–1896, 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.

Russell, A. L., Medellin, R. A., and McCracken, G. F., 2005 Genetic variation and migration in the Mexican free-tailed bat (Tadarida brasiliensis mexicana). Mol. Ecology 14: 2207–2222, 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.

Walsh, H. E. and Edwards, S. V., 2005 Conservation genetics and Paciﬁc ﬁsheries bycatch: Mitochondrial diﬀerentiation and population assignment in black-footed albatrosses (Phoebastria nigripes). Conservation Genetics 6: 289–295.

Oyler-McCance, S. J., John, J. S., Knopf, F. L., and Quinn, T. W., 2005 Population genetic analysis of Mountain Plover using mitochondrial DNA sequence data. Condor 107: 353–362, 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.

Brumfield, R. T., 2005 Mitochondrial variation in Bolivian populations of the variable antshrike (Thamnophilus caerulescens). Auk 122: 414–432, 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.

Panaram, K. and Borowsky, R., 2005 Gene ﬂow and genetic variability in cave and surface populations of the Mexican Tetra, Astyanax mexicanus (Telcostei : Characidae). Copeia pp. 409–416, 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.

Drummond, A. J., Rambaut, A., Shapiro, B., and Pybus, O. G., 2005 Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evolution 22: 1185–1192, 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.

Qu, Y. H., Ericson, P. G. P., Lei, F. M., and Li, S. H., 2005 Postglacial colonization of the Tibetan plateau inferred from the matrilineal genetic structure of the endemic red-necked snow ﬁnch, Pyrgilauda ruﬁcollis. Mol. Ecology 14: 1767–1781, 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.

Jehle, R., Wilson, G. A., Arntzen, J. W., and Burke, T., 2005 Contemporary gene ﬂow and the spatiotemporal genetic structure of subdivided newt populations (Triturus cristatus, t-marmoratus). J. Evolutionary Biol. 18: 619–628, 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.

Kochzius, M. and Blohm, D., 2005 Genetic population structure of the lionﬁsh Pterois miles (Scorpaenidae, Pteroinae) in the Gulf of Aqaba and northern Red sea. Gene 347: 295–301, 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.

Fu, R. W., Dey, D. K., and Holsinger, K. E., 2005 Bayesian models for the analysis of genetic structure when populations are correlated. Bioinformatics 21: 1516–1529, 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.

Pruett, C. L. and Winker, K., 2005 Northwestern song sparrow populations show genetic eﬀects of sequential colonization. Mol. Ecology 14: 1421–1434, 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.

Addison, J. A. and Hart, M. W., 2005 Colonization, dispersal, and hybridization inﬂuence phylogeography of North Atlantic sea urchins (Strongylocentrotus droebachiensis). Evolution 59: 532–543, 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.

Moyer, G. R., Winemiller, K. O., McPhee, M. V., and Turner, T. F., 2005 Historical demography, selection, and coalescence of mitochondrial and nuclear genes in Prochilodus species of northern South america. Evolution

59: 599–610, 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.

Schwartz, M. K., Ralls, K., Williams, D. F., Cypher, B. L., Pilgrim, K. L., and Fleischer, R. C., 2005 Gene ﬂow among San Joaquin kit fox populations in a severely changed ecosystem. Conservation Genetics 6: 25– 37, 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.

Lexer, C., Fay, M. F., Joseph, J. A., Nica, M. S., and Heinze, B., 2005 Barrier to gene ﬂow between two ecologically divergent Populus species, P alba (white poplar) and P tremula (European aspen): the role of ecology and life history in gene introgression. Mol. Ecology 14: 1045–1057, 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.

Barrowclough, G. F., Groth, J. G., Mertz, L. A., and Gutierrez, R. J., 2005 Genetic structure, introgression, and a narrow hybrid zone between northern and California spotted owls (Strix occidentalis). Mol. Ecology 14: 1109–1120, 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%.

Pinceel, J., Jordaens, K., Pfenninger, M., and Backeljau, T., 2005 Rangewide phylogeography of a terrestrial slug in Europe: evidence for Alpine refugia and rapid colonization after the Pleistocene glaciations. Mol. Ecology

14: 1133–1150, 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.

Wright, T. F., Rodriguez, A. M., and Fleischer, R. C., 2005 Vocal dialects, sex-biased dispersal, and microsatellite population structure in the parrot Amazona auropalliata. Mol. Ecology 14: 1197–1205, 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.

Slade, P. F. and Wakeley, J., 2005 The structured ancestral selection graph and the many-demes limit. Genetics

169: 1117–1131, 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.

Delaney, K. S. and Wayne, R. K., 2005 Adaptive units for conservation: Population distinction and historic extinctions in the Island scrub-jay. Conservation Biol. 19: 523–533, 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.

Hickerson, M. J. and Cunningham, C. W., 2005 Contrasting quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal ﬁsh (Xiphister) revealed by multilocus DNA analysis. Evolution 59: 344– 360, 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.

Muniz-Salazar, R., Talbot, S. L., Sage, G. K., Ward, D. H., and Cabello-Pasini, A., 2005 Population genetic structure of annual and perennial populations of Zostera marina L. along the Paciﬁc coast of Baja California and the Gulf of california. Mol. Ecology 14: 711–722, 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.

Wares, J. P. and Cunningham, C. W., 2005 Diversiﬁcation before the most recent glaciation in Balanus glandula.

Biological Bulletin 208: 60–68, 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.

Kvist, L., Broggi, J., Illera, J. C., and Koivula, K., 2005 Colonisation and diversiﬁcation of the blue tits (Parus caeruleus teneriﬀae-group) in the Canary islands. Mol. Phylogenetics Evolution 34: 501–511, The blue tit (Parus caeruleus teneriﬀae group) is proposed to have colonised the Canary Islands from North Africa according to an east-to-west stepping stone model, and today, the species group is divided into four subspecies, diﬀering in morphological, acoustic, and ecological characters. This colonisation hypothesis was tested and the population structure between and within the islands studied using mitochondrial DNA sequences of the non-coding and relatively fast evolving control region. Our results suggest that one of the central islands, Tenerife, was colonised ﬁrst and the other islands from there. Three of the presently recognised four subspecies are monophyletic, exception being the subspecies teneriﬀae, which consists of two monophyletic groups, the one including birds of Tenerife and La Gomera and the other birds of Gran Canaria. The Gran Canarian birds are well diﬀerentiated from birds of the other islands and should be given a subspecies status. In addition, the teneriﬀae subspecies group is clearly distinct from the European caeruleus group, and therefore the blue tit assemblage should be divided into two species. (C) 2004 Elsevier Inc. All rights reserved.

Smith, T. B., Calsbeek, R., Wayne, R. K., Holder, K. H., Pires, D., and Bardeleben, C., 2005 Testing alternative mechanisms of evolutionary divergence in an African rain forest passerine bird. J. Evolutionary Biol. 18: 257–268, 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-geneﬂow 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.

Tripet, F., Dolo, G., and Lanzaro, G. C., 2005 Multilevel analyses of genetic diﬀerentiation in Anopheles gambiae ss reveal patterns of gene ﬂow important for malaria-ﬁghting mosquito projects. Genetics 169: 313–324, 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.

Okuyama, T. and Bolker, B. M., 2005 Combining genetic and ecological data to estimate sea turtle origins. Ecological Applications 15: 315–325, 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.

Rex, M. A., McClain, C. R., Johnson, N. A., Etter, R. J., Allen, J. A., Bouchet, P., and Waren, A., 2005 A source-sink hypothesis for abyssal biodiversity. Am. Naturalist 165: 163–178, 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.

Price, E. W. and Carbone, I., 2005 Snap: workbench management tool for evolutionary population genetic analysis. Bioinformatics 21: 402–404, 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.

Vandewoestijne, S., Martin, T., Liegeois, S., and Baguette, M., 2004 Dispersal, landscape occupancy and population structure in the butterﬂy Melanargia galathea. Basic Appl. Ecology 5: 581–591, 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.

Slatkin, M., 2005 Seeing ghosts: the eﬀect of unsampled populations on migration rates estimated for sampled populations. Mol. Ecology 14: 67–73, 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.

Ruokonen, M., Aarvak, T., and Madsen, J., 2005 Colonization history of the high-arctic pink-footed goose Anser brachyrhynchus. Mol. Ecology 14: 171–178, 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.

Ewing, G., Nicholls, G., and Rodrigo, A., 2004 Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations. Genetics 168: 2407–2420, 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.

Gemmell, N. J., Schwartz, M. K., and Robertson, B. C., 2004 Moa were many. Proc. Royal Soc. London Series B-biological Sciences 271: S430–S432, 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.

Monsen, K. J. and Blouin, M. S., 2004 Extreme isolation by distance in a montane frog Rana cascadae. Conservation Genetics 5: 827–835, 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.

Pearse, D. E. and Crandall, K. A., 2004 Beyond F-ST: Analysis of population genetic data for conservation. Conservation Genetics 5: 585–602, 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.

Haig, S. M., Mullins, T. D., and Forsman, E. D., 2004 Subspeciﬁc relationships and genetic structure in the spotted owl. Conservation Genetics 5: 683–705, 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.

Austin, J. D., Lougheed, S. C., and Boag, P. T., 2004 Controlling for the eﬀects of history and nonequilibrium conditions in gene ﬂow estimates in northern bullfrog (Rana catesbeiana) populations. Genetics 168: 1491–1506, 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.

Adams, A. M. and Hudson, R. R., 2004 Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms. Genetics 168: 1699–1712, 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.

Robertson, B. C. and Gemmell, N. J., 2004 Deﬁning eradication units to control invasive pests. J. Appl. Ecology

41: 1042–1048, 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.

Sonsthagen, S. A., Talbot, S. L., and White, C. M., 2004 Gene ﬂow and genetic characterization of Northern Goshawks breeding in utah. Condor 106: 826–836, 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.

Carstens, B. C., Stevenson, A. L., Degenhardt, J. D., and Sullivan, J., 2004 Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Systematic Biol. 53: 781–792, Mesic forests in the North American Paciﬁc Northwest occur in two disjunct areas: along the coastal and Cascade ranges of Oregon, Washington, and British Columbia as well as the Northern Rocky Mountains of Idaho, Montana, and British Columbia. Over 150 species or species complexes have disjunct populations in each area, and a priori hypotheses based on phytogeography and geology potentially explain the disjunction via either dispersal or vicariance. Here, we test these hypotheses in the disjunct salamander complex Plethodon vandykei and P. idahoensis by collecting genetic data ( 669 bp of Cyt b) from 262 individuals. Maximum likelihood analysis indicated reciprocal monophyly of these species, supporting the ancient vicariance hypothesis, whereas parametric bootstrap and Bayesian hypothesis testing allow rejection of the dispersal hypothesis. The coalescent estimate of the time since population divergence ( estimated using MDIV) is 3.75 x 10(6) years, and the 95% credibility interval of this value overlaps with the geological estimate of vicariance, but not the hypothesized dispersal. These results are congruent with the pattern seen in other mesic forest amphibian lineages and suggest disjunction in amphibians may be a concerted response to a geological/climatological event. Within P. idahoensis, we tested the corollary hypothesis of an inland Pleistocene refugium in the Clearwater drainage with nested clade analysis and coalescent estimates of population growth rate ( g). Both analyses support post-Pleistocene expansion from the Clearwater refugium. We corroborated this result by calculating Tajima’s D and mismatch distribution within each drainage, showing strong evidence for recent population expansion within most drainages. This work demonstrates the utility of statistical phylogeography and contributes two novel analytical tools: tests of stationarity with respect to topology in the Bayesian estimation, and the use of coalescent simulations to test the signiﬁcance of the population growth-rate parameter.

Hendry, A. P. and Taylor, E. B., 2004 How much of the variation in adaptive divergence can be explained by gene ﬂow? -An evaluation using lake-stream stickleback pairs. Evolution 58: 2319–2331, 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).

Liu, Y., Nickle, D. C., Shriner, D., Jensen, M. A., Learn, G. H., Mittler, J. E., and Mullins, J. I., 2004 Molecular clock-like evolution of human immunodeﬁciency virus type 1. Virology 329: 101–108, 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.

Carlsson, J., McDowell, J. R., Diaz-Jaimes, P., Carlsson, J. E. L., Boles, S. B., Gold, J. R., and Graves,

J. E., 2004 Microsatellite and mitochondrial DNA analyses of Atlantic blueﬁn tuna (Thunnus thynnus thynnus) population structure in the Mediterranean sea. Mol. Ecology 13: 3345–3356, 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.

Salgueiro, P., Coelho, M. M., Palmeirim, J. M., and Ruedi, M., 2004 Mitochondrial DNA variation and population structure of the island endemic Azorean bat (Nyctalus azoreum). Mol. Ecology 13: 3357–3366, 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.

Estoup, A., Beaumont, M., Sennedot, F., Moritz, C., and Cornuet, J. M., 2004 Genetic analysis of complex demographic scenarios: Spatially expanding populations of the cane toad, Bufo marinus. Evolution 58: 2021– 2036, 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.

Murat, C., Diez, J., Luis, P., Delaruelle, C., Dupre, C., Chevalier, G., Bonfante, P., and Martin, F., 2004 Polymorphism at the ribosomal DNA ITS and its relation to postglacial re-colonization routes of the Perigord truﬄe Tuber melanosporum. New Phytologist 164: 401–411, 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.

Costa, F. O., Neuparth, T., Theodorakis, C. W., Costa, M. H., and Shugart, L. R., 2004 Rapd analysis of southern populations of Gammarus locusta: comparison with allozyme data and ecological inferences. Marine Ecology-progress Series 277: 197–207, 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, FST (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.

Luzier, C. W. and Wilson, R. R., 2004 Analysis of mtDNA haplotypes of kelp bass tests for sibling-dominated recruitment near marine protected areas of the California Channel islands. Marine Ecology-progress Series 277: 221–230, 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.

Tarjuelo, I., Posada, D., Crandall, K. A., Pascual, M., and Turon, X., 2004 Phylogeography and speciation of colour morphs in the colonial ascidian Pseudodistoma crucigaster. Mol. Ecology 13: 3125–3136, 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.

Moya, O., Contreras-Diaz, H. G., Oromi, P., and Juan, C., 2004 Genetic structure, phylogeography and demography of two ground-beetle species endemic to the Tenerife laurel forest (Canary islands). Mol. Ecology

13: 3153–3167, 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.

Ruokonen, M., Kvist, L., Aarvak, T., Markkola, J., Morozov, V. V., Oien, I. J., Syroechkovsky, E. E., Tolvanen, P., and Lumme, J., 2004 Population genetic structure and conservation of the lesser white-fronted goose Anser erythropus. Conservation Genetics 5: 501–512, 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.

Morar, B., Gresham, D., Angelicheva, D., Tournev, I., Gooding, R., Guergueltcheva, V., Schmidt, C., Abicht, A., Lochmuller, H., Tordai, A., Kalmar, L., Nagy, M., Karcagi, V., Jeanpierre, M., Herczegfalvi, A., Beeson, D., Venkataraman, V., Carter, K. W., Reeve, J., de Pablo, R., Kucinskas, V., and Kalaydjieva, L., 2004 Mutation history of the roma/gypsies. Am. J. Human Genetics 75: 596–609, 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.

Wisely, S. M., Buskirk, S. W., Russell, G. A., Aubry, K. B., and Zielinski, W. J., 2004 Genetic diversity and structure of the ﬁsher (Martes pennanti) in a peninsular and peripheral metapopulation. J. Mammalogy 85: 640– 648, 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.

Dean, M. D. and Ballard, J. W. O., 2004 Linking phylogenetics with population genetics to reconstruct the geographic origin of a species. Mol. Phylogenetics Evolution 32: 998–1009, 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.

Lemey, P., Pybus, O. G., Rambaut, A., Drummond, A. J., Robertson, D. L., Roques, P., Worobey, M., and Vandamme, A. M., 2004 The molecular population genetics of HIV-1 group o. Genetics 167: 1059–1068, 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.

Alvarez, I., Royo, L. J., Fernandez, I., Gutierrez, J. P., Gomez, E., and Goyache, F., 2004 Genetic relationships and admixture among sheep breeds from Northern Spain assessed using microsatellites. J. Animal Science 82: 2246–2252, Although many research papers have studied diversity and diﬀerentiation within livestock species, genetic relationships among neighboring populations remain poorly understood. Here we apply recent methodologies to analyze the polymorphism of 14 microsatellites in 238 unrelated individuals belonging to six sheep breeds from Northern Spain to ascertain their historical relationships and the relative genetic contributions existing between populations. Individual genotypes were analyzed to assess the existence of an underlying genetic structure. Long-term and recent migration rates were estimated to identify patterns of relative genetic contribution among breeds. The complete data set showed a strong population structure derived from both diﬀerent ancestral origins and some geographical patterns of recent gene ﬂow. Two of the analyzed breeds (Black-faced Latxa and Churra) had a marked genetic background, supporting the hypothesis that, regardless of their phenotypical. similarities, they have diﬀerent ancestral origins. Some of the more presumably related breeds had negative long-term admixture coeﬃcients, showing that they diverged only recently. In addition, we show how methodologies for estimation of long-term gene ﬂow and recent patterns of migration are complementary, providing information about migration rates on diﬀerent timescales.

Wooding, S., Ostler, C., Prasad, B. V. R., Watkins, W. S., Sung, S., Bamshad, M., and Jorde, L. B., 2004 Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Y-chromosomal data. Human Genetics 115: 221–229, 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.

Kulikova, I. V., Zhuravlev, Y. N., and McCracken, K. G., 2004 Asymmetric hybridization and sex-biased gene ﬂow between Eastern Spot-billed Ducks (Anas zonorhyncha) and Mallards (A-platyrhynchos) in the Russian Far east. Auk 121: 930–949, 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.

Baker, C. S. and Clapham, P. J., 2004 Modelling the past and future of whales and whaling. Trends In Ecology & Evolution 19: 365–371, 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.

Hey, J. and Nielsen, R., 2004 Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and d-persimilis. Genetics 167: 747–760, 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.

Alvarez-Castaneda, S. T. and Patton, J. L., 2004 Geographic genetic architecture of pocket gopher (Thomomys bottae) populations in Baja California, mexico. Mol. Ecology 13: 2287–2301, 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.

Hoekstra, H. E., Drumm, K. E., and Nachman, M. W., 2004 Ecological genetics of adaptive color polymorphism in pocket mice: geographic variation in selected and neutral genes. Evolution 58: 1329–1341, 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.

Tishkoff, S. A. and Verrelli, B. C., 2003 Patterns of human genetic diversity: Implications for human evolutionary history and disease. Ann. Rev. Genomics Human Genetics 4: 293–340, 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.

Holder, K., Montgomerie, R., and Friesen, V. L., 2004 Genetic diversity and management of Nearctic rock ptarmigan (Lagopus mutus). Canadian J. Zoology-revue Canadienne De Zoologie 82: 564–575, 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.

Knaepkens, G., Verheyen, E., Galbusera, P., and Eens, M., 2004 The use of genetic tools for the evaluation of a potential migration barrier for the bullhead. J. Fish Biol. 64: 1737–1744, 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.

Kryger, U., Robinson, T. J., and Bloomer, P., 2004 Population structure and history of southern African scrub hares, Lepus saxatilis. J. Zoology 263: 121–133, 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.

Rice, K. J. and Emery, N. C., 2003 Managing microevolution: restoration in the face of global change. Frontiers In Ecology Environment 1: 469–478, 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.

Dyer, R. J. and Nason, J. D., 2004 Population Graphs: the graph theoretic shape of genetic structure. Mol. Ecology 13: 1713–1727, 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.

Zardoya, R., Castilho, R., Grande, C., Favre-Krey, L., Caetano, S., Marcato, S., Krey, G., and Patarnello, T., 2004 Diﬀerential population structuring of two closely related ﬁsh species, the mackerel (Scomber scombrus) and the chub mackerel (Scomber japonicus), in the Mediterranean sea. Mol. Ecology 13: 1785–1798, 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.

Shanker, K., Ramadevi, J., Choudhury, B. C., Singh, L., and Aggarwal, R. K., 2004 Phylogeography of olive ridley turtles (Lepidochelys olivacea) on the east coast of India: implications for conservation theory. Mol. Ecology 13: 1899–1909, 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.

Barrowclough, G. F., Groth, J. G., Mertz, L. A., and Gutierrez, R. J., 2004 Phylogeographic structure, gene ﬂow and species status in blue grouse (Dendragapus obscurus). Mol. Ecology 13: 1911–1922, 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.

Iorio, M. D. and Griffiths, R. C., 2004 Importance sampling on coalescent histories. i. Adv. In Appl. Probability

36: 417–433, 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.

Carbone, I., Liu, Y. C., Hillman, B. I., and Milgroom, M. G., 2004 Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent. Genetics 166: 1611–1629, 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.

Galbusera, P., Githiru, M., Lens, L., and Matthysen, E., 2004 Genetic equilibrium despite habitat fragmentation in an Afrotropical bird. Mol. Ecology 13: 1409–1421, 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.

Gay, L., Rau, P. D. D., Mondain-Monval, J. Y., and Crochet, P. A., 2004 Phylogeography of a game species: the red-crested pochard (Netta ruﬁna) and consequences for its management. Mol. Ecology 13: 1035–1045, 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.

Beaumont, M. A., 2004 Recent developments in genetic data analysis: what can they tell us about human demographic history? Heredity 92: 365–379, 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.

Blum, M. G. B., Damerval, C., Manel, S., and Francois, O., 2004 Brownian models and coalescent structures. Theoretical Population Biol. 65: 249–261, 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.

Shriner, D., Shankarappa, R., Jensen, M. A., Nickle, D. C., Mittler, J. E., Margolick, J. B., and Mullins, J. I., 2004 Inﬂuence of random genetic drift on human immunodeﬁciency virus type I env evolution during chronic infection. Genetics 166: 1155–1164, 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.

Chaix, R., Austerlitz, F., Morar, B., Kalaydjieva, L., and Heyer, E., 2004 Vlax Roma history: What do coalescent-based methods tell us? European J. Human Genetics 12: 285–292, 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.

Gold, J. R., Saillant, E., Burridge, C. P., Blanchard, A., and Patton, J. C., 2004 Population structure and eﬀective size in critically endangered cape fear shiners Notropis mekistocholas. Southeastern Naturalist 3: 89– 102, 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.

Hoglund, J. and Shorey, L., 2004 Genetic divergence in the superspecies manacus. Biological J. Linnean Soc. 81: 439–447, The bearded manakins in the genus Manacus are lekking, neotropical passerines. Male plumage colour varies with geographical location and classiﬁcation is based solely on these plumage patterns. It has recently been suggested that in this group of birds, plumage patterns may be a misleading taxonomic character. In this study we used microsatellite variation in a collection of museum samples to establish the amount of genetic divergence between the previously described bearded manakin species/subspecies. We found substantial genetic substructuring between species/subspecies and that plumage patterns indeed may be a misleading taxonomic character because the presence of yellow in male nuptial plumage is found in most divergent forms. We did not detect a signiﬁcant isolation by distance relationship although the P-value was close to signiﬁcance. Physical barriers such as rivers and mountains may aﬀect gene ﬂow and play a role in shaping genetic structure of the genus Manacus. Accordingly, boundaries between species/subspecies often coincide with large rivers, mountains and seas. (C) 2004 The Linnean Society of London, Biological.

Rivera, M. A. J., Kelley, C. D., and Roderick, G. K., 2004 Subtle population genetic structure in the Hawaiian grouper, Epinephelus quernus (Serranidae) as revealed by mitochondrial DNA analyses. Biological J. Linnean Soc. 81: 449–468, 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,.

Nichols, R. A. and Freeman, K. L. M., 2004 Using molecular markers with high mutation rates to obtain estimates of relative population size and to distinguish the eﬀects of gene ﬂow and mutation: a demonstration using data from endemic Mauritian skinks. Mol. Ecology 13: 775–787, 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.

Beerli, P., 2004 Eﬀect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Mol. Ecology 13: 827–836, 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.

Abdo, Z., Crandall, K. A., and Joyce, P., 2004 Evaluating the performance of likelihood methods for detecting population structure and migration. Mol. Ecology 13: 837–851, 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 MIGRATE-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.[PB rant: I only agree with their last sentence, because if your data (as their simulation data) contains mostly NO INFORMATION about the past processes the program migrate will fail, like any other. From 9 simulation cells, three contained randomized data, two contained no or almost no variable sites, and the other four cells delivered similar results to earlier own reports (Beerli, 1999). Following the manual would have improved their results, too.].

Holsinger, K. E. and Wallace, L. E., 2004 Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (orchidaceae). Mol. Ecology 13: 887–894, 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.

Nosil, P. and Crespi, B. J., 2004 Does gene ﬂow constrain adaptive divergence or vice versa? A test using ecomorphology and sexual isolation in Timema cristinae walking-sticks. Evolution 58: 102–112, 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.

Criscione, C. D. and Blouin, M. S., 2004 Life cycles shape parasite evolution: Comparative population genetics of salmon trematodes. Evolution 58: 198–202, 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.

Segelbacher, G., Storch, I., and Tomiuk, J., 2003 Genetic evidence of capercaillie Tetrao urogallus dispersal sources and sinks in the alps. Wildlife Biol. 9: 267–273, The aim of our study was to identify ﬁne-scale genetic population structure of capercaillie Tetra urogallus populations in the Bavarian Alps, Germany. We studied ﬁve local populations and estimated genetic variation using 10 polymorphic microsatellite markers. We found no diﬀerences in the number of alleles per locus or the degree of heterozygosity between pairs of populations, but signiﬁcant genetic variation among all populations. We detected signiﬁcant genetic diﬀerentiation for pairs of populations separated by distances as short as 10 km. Genetically detected eﬀective population sizes agreed with ﬁeld data for relative population densities. Populations of peripheral study areas bordering the dairy-farming lowlands tended to show sink characteristics with immigration exceeding emigration. Our study conﬁrmed that microsatellites have the potential to detect dispersal sources and sinks at a local scale and the results of studies like ours may help to develop improved, eﬀective conservation plans for capercaillie.

Turner, T. F., McPhee, M. V., Campbell, P., and Winemiller, K. O., 2004 Phylogeography and intraspeciﬁc genetic variation of prochilodontid ﬁshes endemic to rivers of northern South america. J. Fish Biol. 64: 186–201, 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.

Wilson, A. J., Hutchings, J. A., and Ferguson, M. M., 2004 Dispersal in a stream dwelling salmonid: Inferences from tagging and microsatellite studies. Conservation Genetics 5: 25–37, 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.

Banke, S., Peschon, A., and McDonald, B. A., 2004 Phylogenetic analysis of globally distributed Mycosphaerella graminicola populations based on three DNA sequence loci. Fungal Genetics Biol. 41: 226–238, DNA sequence data from three nuclear loci were collected from 384 isolates representing fourteen globally distributed populations of the plant pathogenic fungus Mycosphaerella graminicola. Gene genealogies were constructed for the actin and beta-tubulin loci as well as for the previously characterized RFLP locus STS2. The STS2 and beta-tubulin loci showed greater potential for phylogenetic studies than the actin locus. Greater sequence diversity was found in the ”Old World” populations (Middle East and Europe) than in the ”New World” populations (North and South America and Australia). The gene trees were rooted using homologous DNA sequences of Septoria passerinii, the closest known relative to M. graminicola, as well as coalescent rooting. Based on the rooted trees, a tentative phylogenetic history of these populations was inferred. The Middle East appears to be the most likely center of origin, while European populations are more ancient than New World populations. A test for neutrality indicated that the intron in the actin locus could be under selection, while the other two sequence loci were neutral. (C) 2003 Elsevier Inc. All rights reserved.

Pfenninger, M., Posada, D., and Magnin, F., 2003 Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soos 1926) (Helicellinae, stylommatophora). Bmc Evolutionary Biol. 3, 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.

Gysels, E. S., Hellemans, B., Pampoulie, C., and Volckaert, F. A. M., 2004 Phylogeography of the common goby, Pomatoschistus microps, with particular emphasis on the colonization of the Mediterranean and the North sea. Mol. Ecology 13: 403–417, 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.

Knowles, L. L., 2004 The burgeoning ﬁeld of statistical phylogeography. J. Evolutionary Biol. 17: 1–10, 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.

Schlotterer, C., 2004 The evolution of molecular markers -just a matter of fashion? Nature Rev. Genetics 5: 63–69.

Vogl, C., Das, A., Beaumont, M., Mohanty, S., and Stephan, W., 2003 Population subdivision and molecular sequence variation: Theory and analysis of Drosophila ananassae data. Genetics 165: 1385–1395, 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.

Nathan, R., Perry, G., Cronin, J. T., Strand, A. E., and Cain, M. L., 2003 Methods for estimating long-distance dispersal. Oikos 103: 261–273, 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.

Idaghdour, Y., Broderick, D., Korrida, A., and Chbel, F., 2004 Mitochondrial control region diversity of the houbara bustard Chlamydotis undulata complex and genetic structure along the Atlantic seaboard of North africa. Mol. Ecology 13: 43–54, 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.

Fraser, D. J., Lippe, C., and Bernatchez, L., 2004 Consequences of unequal population size, asymmetric gene ﬂow and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis). Mol. Ecology 13: 67–80, 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.

Gum, B., Gross, R., Rottmann, O., Schroder, W., and Kuhn, R., 2003 Microsatellite variation in Bavarian

populations of European grayling (Thymallus thymallus): Implications for conservation. Conservation Genetics

4: 659–672, 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.

Calsbeek, R. and Smith, T. B., 2003 Ocean currents mediate evolution in island lizards. Nature 426: 552– 555, 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.

Soliva, M. and Widmer, A., 2003 Gene ﬂow across species boundaries in sympatric, sexually deceptive Ophrys (Orchidaceae) species. Evolution 57: 2252–2261, 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.

Roderick, G. K. and Navajas, M., 2003 Genes in new environments: Genetics and evolution in biological control. Nature Rev. Genetics 4: 889–899, 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.

Shrimpton, J. M. and Heath, D. D., 2003 Census vs. eﬀective population size in chinook salmon: large-and small-scale environmental perturbation eﬀects. Mol. Ecology 12: 2571–2583, 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 (81691) 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.

Rawson, P. D., Macnamee, R., Frick, M. G., and Williams, K. L., 2003 Phylogeography of the coronulid barnacle, Chelonibia testudinaria, from loggerhead sea turtles, Caretta caretta. Mol. Ecology 12: 2697–2706.

Zeh, J. A., Zeh, D. W., and Bonilla, M. M., 2003 Phylogeography of the harlequin beetle-riding pseudoscorpion and the rise of the Isthmus of panama. Mol. Ecology 12: 2759–2769, 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.

Kennington, W. J., Gockel, J., and Partridge, L., 2003 Testing for asymmetrical gene ﬂow in a Drosophila melanogaster body-size cline. Genetics 165: 667–673, 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.

Vieira, V., Pintureau, B., Tavares, J., and McNeil, J. N., 2003 Diﬀerentiation and gene ﬂow among island and mainland populations of the true armyworm, Pseudaletia unipuncta (Haworth) (Lepidoptera : Noctuidae). Canadian J. Zoology-revue Canadienne De Zoologie 81: 1367–1377, 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-6phosphate 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.

Mohle, M. and Sagitov, S., 2003 Coalescent patterns in diploid exchangeable population models. J. Math. Biol.

47: 337–352, 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.

Nosil, P., Crespi, B. J., and Sandoval, C. P., 2003 Reproductive isolation driven by the combined eﬀects of ecological adaptation and reinforcement. Proc. Royal Soc. London Series B-biological Sciences 270: 1911–1918, 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.

Morrell, P. L., Lundy, K. E., and Clegg, M. T., 2003 Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp spontaneum) despite migration. Proc. National Acad. Sciences United States Am. 100: 10812–10817, 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.

Rannala, B. and Yang, Z. H., 2003 Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645–1656, 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.

Drummond, A. J., Pybus, O. G., Rambaut, A., Forsberg, R., and Rodrigo, A. G., 2003 Measurably evolving populations. Trends In Ecology & Evolution 18: 481–488, 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.

McDonald, D. B., 2003 Microsatellite DNA evidence for gene ﬂow in neotropical lek-mating long-tailed manakins. Condor 105: 580–586, 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.

Beaumont, M. A., 2003 Estimation of population growth or decline in genetically monitored populations. Genetics

164: 1139–1160, 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.

Luttikhuizen, P. C., Drent, J., and Baker, A. J., 2003 Disjunct distribution of highly diverged mitochondrial lineage clade and population subdivision in a marine bivalve with pelagic larval dispersal. Mol. Ecology 12: 2215– 2229, 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.

Bittner, T. D. and King, R. B., 2003 Gene ﬂow and melanism in garter snakes revisited: a comparison of molecular markers and island vs. coalescent models. Biological J. Linnean Soc. 79: 389–399, 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.

Roman, J. and Palumbi, S. R., 2003 Whales before whaling in the North atlantic. Science 301: 508–510, 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.

Hey, J. and Machado, C. A., 2003 The study of structured populations -New hope for a diﬃcult and divided science. Nature Rev. Genetics 4: 535–543, 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.

Miller, D. G. and Crespi, B., 2003 The evolution of inquilinism, host-plant use and mitochondrial substitution rates in Tamalia gall aphids. J. Evolutionary Biol. 16: 731–743, 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.

Douglas, M. R., Brunner, P. C., and Douglas, M. E., 2003 Drought in an evolutionary context: molecular variability in Flannelmouth Sucker (Catostomus latipinnis) from the Colorado River Basin of western North america. Freshwater Biol. 48: 1254–1273, 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.

Fillatre, E. K., Etherton, P., and Heath, D. D., 2003 Bimodal run distribution in a northern population of sockeye salmon (Oncorhynchus nerka): life history and genetic analysis on a temporal scale. Mol. Ecology 12: 1793– 1805, 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.

Wilson, I. J., Weale, M. E., and Balding, D. J., 2003 Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. J. Royal Statistical Soc. Series A-statistics In Soc. 166: 155–188, 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.

Yang, Z. H., Stephens, D., Dawson, K. J., Drummond, A., Nicholls, G., Griffiths, R. C., Wilkinson-Herbots, H. M., Beaumont, M. A., Baird, S. J. E., Lascoux, M., Leblois, R., Estoup, A., Nielsen, R., Hey, J., Stumpf, M. P. H., and Wilkinson-Herbots, H. M., 2003 Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities -discussion. J. Royal Statistical Soc. Series A-statistics In Soc. 166: 188–201.

Imbert, E. and Lefevre, F., 2003 Dispersal and gene ﬂow of Populus nigra (Salicaceae) along a dynamic river system. J. Ecology 91: 447–456, 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.

Wlasiuk, G., Garza, J. C., and Lessa, E. P., 2003 Genetic and geographic diﬀerentiation in the Rio Negro tucotuco (Ctenomys rionegrensis): Inferring the roles of migration and drift from multiple genetic markers. Evolution

57: 913–926, 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.

Fu, R. W., Gelfand, A. E., and Holsinger, K. E., 2003 Exact moment calculations for genetic models with migration, mutation, and drift. Theoretical Population Biol. 63: 231–243, 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.

Nickle, D. C., Jensen, M. A., Shriner, D., Brodie, S. J., Frenkel, L. M., Mittler, J. E., and Mullins, J. I., 2003 Evolutionary indicators of human immunodeﬁciency virus type 1 reservoirs and compartments. J. Virology

77: 5540–5546, 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.

Castric, V. and Bernatchez, L., 2003 The rise and fall of isolation by distance in the anadromous brook charr (Salvelinus fontinalis mitchill). Genetics 163: 983–996, 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.

Porter, A. H., 2003 A test for deviation from island-model population structure. Mol. Ecology 12: 903–915, 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.

Dieringer, D. and Schlotterer, C., 2003 Microsatellite ANALYSER (MSA): a platform independent analysis tool for large microsatellite data sets. Mol. Ecology Notes 3: 167–169, 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.

McDaniel, S. F. and Shaw, A. J., 2003 Phylogeographic structure and cryptic speciation in the trans-antarctic moss Pyrrhobryum minoides. Evolution 57: 205–215, 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.

Zheng, X. G., Arbogast, B. S., and Kenagy, G. J., 2003 Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest. Mol. Ecology 12: 711–724, 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.

Wang, J. L. and Whitlock, M. C., 2003 Estimating eﬀective population size and migration rates from genetic samples over space and time. Genetics 163: 429–446, 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.

Akey, J. M., Zhang, K., Xiong, M. M., and Jin, L., 2003 The eﬀect of single nucleotide polymorphism identiﬁcation strategies on estimates of linkage disequilibrium. Mol. Biol. Evolution 20: 232–242, 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.

Martins, E. P. and Housworth, E. A., 2002 Phylogeny shape and the phylogenetic comparative method. Systematic Biol. 51: 873–880, 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.

Ray, N., Currat, M., and Excoffier, L., 2003 Intra-deme molecular diversity in spatially expanding populations. Mol. Biol. Evolution 20: 76–86, 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.

Turner, T. F., Wares, J. P., and Gold, J. R., 2002 Genetic eﬀective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine ﬁsh (Sciaenops ocellatus). Genetics 162: 1329–1339, 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.

Slatkin, M., 2002 A vectorized method of importance sampling with applications to models of mutation and migration. Theoretical Population Biol. 62: 339–348, 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.

Knowles, L. L. and Maddison, W. P., 2002 Statistical phylogeography. Mol. Ecology 11: 2623–2635, 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.

Pearce, R. L., Wood, J. J., Artukhin, Y., Birt, T. P., Damus, M., and Friesen, V. L., 2002 Mitochondrial DNA suggests high gene ﬂow in Ancient murrelets. Condor 104: 84–91, 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.

Liukkonen-Anttila, T., Uimaniemi, L., Orell, M., and Lumme, J., 2002 Mitochondrial DNA variation and the phylogeography of the grey partridge (Perdix perdix) in Europe: from Pleistocene history to present day populations. J. Evolutionary Biol. 15: 971–982, 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.

Pfenninger, M. and Posada, D., 2002 Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): Fragmentation, corridor migration, and secondary contact. Evolution 56: 1776–1788, 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.

Britten, H. B. and Glasford, J. W., 2002 Genetic population structure of the Dakota skipper (Lepidoptera : Hesperia dacotae): A North American native prairie obligate. Conservation Genetics 3: 363–374, 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-bydistance 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.

Goldstein, D. B. and Chikhi, L., 2002 Human migrations and population structure: What we know and why it matters. Ann. Rev. Genomics Human Genetics 3: 129–152, 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.

Huelsenbeck, J. P., Larget, B., Miller, R. E., and Ronquist, F., 2002 Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biol. 51: 673–688, 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.

Friesen, V. L., Anderson, D. J., Steeves, T. E., Jones, H., and Schreiber, E. A., 2002 Molecular support for species status of the Nazca Booby (Sula granti). Auk 119: 820–826, 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.

Osier, M. V., Cheung, K. H., Kidd, J. R., Pakstis, A. J., Miller, P. L., and Kidd, K. K., 2002 Alfred: An allele frequency database for anthropology. Am. J. Phys. Anthropology 119: 77–83, 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.

Williamson, S. and Orive, M. E., 2002 The genealogy of a sequence subject to purifying selection at multiple sites. Mol. Biol. Evolution 19: 1376–1384, 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.

Neigel, J. E., 2002 Is F-ST obsolete? Conservation Genetics 3: 167–173, 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.

Patirana, A., Hatch, S. A., and Friesen, V. L., 2002 Population diﬀerentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial dna. Conservation Genetics 3: 335–340, 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.

Wares, J. P., 2002 Community genetics in the Northwestern Atlantic intertidal. Mol. Ecology 11: 1131–1144, 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.

Drummond, A. J., Nicholls, G. K., Rodrigo, A. G., and Solomon, W., 2002 Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307– 1320, 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.

Wilke, T. and Pfenninger, M., 2002 Separating historic events from recurrent processes in cryptic species: phylogeography of mud snails (Hydrobia spp.). Mol. Ecology 11: 1439–1451, 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.

Hendry, A. P., Taylor, E. B., and McPhail, J. D., 2002 Adaptive divergence and the balance between selection and gene ﬂow: Lake and stream stickleback in the misty system. Evolution 56: 1199–1216, 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.

Weale, M. E., Weiss, D. A., Jager, R. F., Bradman, N., and Thomas, M. G., 2002 Y chromosome evidence for Anglo-Saxon mass migration. Mol. Biol. Evolution 19: 1008–1021, 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.

Jehle, R. and Arntzen, J. W., 2002 Microsatellite markers in amphibian conservation genetics. Herpetological J.

12: 1–9, 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.

Tang, H., Siegmund, D. O., Shen, P. D., Oefner, P. J., and Feldman, M. W., 2002 Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition. Genetics 161: 447–459, 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.

Rosenberg, N. A. and Nordborg, M., 2002 Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Rev. Genetics 3: 380–390, 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.

Marshall, H. D. and Ritland, K., 2002 Genetic diversity and diﬀerentiation of Kermode bear populations. Mol. Ecology 11: 685–697, 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.

Machado, C. A., Kliman, R. M., Markert, J. A., and Hey, J., 2002 Inferring the history of speciation from multilocus DNA sequence data: The case of Drosophila pseudoobscura and close relatives. Mol. Biol. Evolution 19: 472–488, 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.

Moran, P., 2002 Current conservation genetics: building an ecological approach to the synthesis of molecular and quantitative genetic methods. Ecology Freshwater Fish 11: 30–55, 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.

Heath, D. D., Busch, C., Kelly, J., and Atagi, D. Y., 2002 Temporal change in genetic structure and eﬀective population size in steelhead trout (Oncorhynchus mykiss). Mol. Ecology 11: 197–214, 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.

King, R. B. and Lawson, R., 2001 Patterns of population subdivision and gene ﬂow in three sympatric natricine snakes. Copeia pp. 602–614, 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.

de Brito, R. A., Manfrin, M. H., and Sene, F. M., 2002 Nested cladistic analysis of Brazilian populations of Drosophila serido. Mol. Phylogenetics Evolution 22: 131–143, 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.

Vitalis, R., 2002 Sex-speciﬁc genetic diﬀerentiation and coalescence times: estimating sex-biased dispersal rates. Mol. Ecology 11: 125–138, 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).

Estoup, A., Wilson, I. J., Sullivan, C., Cornuet, J. M., and Moritz, C., 2001 Inferring population history from microsatellite and enzyme data in serially introduced cane toads, Bufo marinus. Genetics 159: 1671–1687, 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.

Petit, E., Balloux, F., and Excoffier, L., 2002 Mammalian population genetics: why not y? Trends In Ecology & Evolution 17: 28–33, 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.

Kvist, L., Martens, J., Ahola, A., and Orell, M., 2001 Phylogeography of a Palaearctic sedentary passerine, the willow tit (Parus montanus). J. Evolutionary Biol. 14: 930–941, We analysed variation of the mitochondrial control region from willow tits through its Palaearctic distribution range. Although we found high amount of genetic variation (pi = 1.114%), there was almost no diﬀerentiation between Subspecies or geographical localities. This may be because of a combination of several ecological and genetic factors, including a relatively homogenic habitat through the distribution range, lack of geographical barriers, high gene ﬂow and a large long-term eﬀective population size. On the contrary, in the songar tit, which is sometimes considered to be conspeciﬁc with the willow tit, the mitochondrial lineages seem to correlate with the geographical locality and are clearly distinct from the willow tit. We concluded that the common ancestors of willow and songar tits existed sonic 1.5-2 Myr ago in the south-eastern Asia. After the last Ice Ages, the willow tit expanded all through the Palaearctic, whereas the songar tit remained in eastern Asia.

Huelsenbeck, J. P., Ronquist, F., Nielsen, R., and Bollback, J. P., 2001 Evolution -Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310–2314, 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.

Fearnhead, P. and Donnelly, P., 2001 Estimating recombination rates from population genetic data. Genetics

159: 1299–1318, 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.

Mitchell-Olds, T., 2001 Arabidopsis thaliana and its wild relatives: a model system for ecology and evolution. Trends In Ecology & Evolution 16: 693–700, 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.

Hare, M. P., 2001 Prospects for nuclear gene phylogeography. Trends In Ecology & Evolution 16: 700–706, 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.

Emerson, B. C., Paradis, E., and Thebaud, C., 2001 Revealing the demographic histories of species using DNA sequences. Trends In Ecology & Evolution 16: 707–716, 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.

Arbogast, B. S. and Kenagy, G. J., 2001 Comparative phylogeography as an integrative approach to historical biogeography. J. Biogeography 28: 819–825, 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.

Michalak, P., Minkov, I., Helin, A., Lerman, D. N., Bettencourt, B. R., Feder, M. E., Korol, A. B., and Nevo, E., 2001 Genetic evidence for adaptation-driven incipient speciation of Drosophila melanogaster along a microclimatic contrast in ”Evolution Canyon,” israel. Proc. National Acad. Sciences United States Am. 98: 13195– 13200, 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.

Gorroochurn, P., 2001 Post-data inference of coalescence times and segregating-site distribution in a two-island model with symmetric migration. Adv. In Appl. Probability 33: 600–616, 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.

Wakeley, J. and Aliacar, N., 2001 Gene genealogies in a metapopulation. Genetics 159: 893–905, 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.

Nielsen, R., 2001 Mutations as missing data: Inferences on the ages and distributions of nonsynonymous and synonymous mutations. Genetics 159: 401–411, 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.

Sinclair, E. A., Swenson, E. L., Wolfe, M. L., Choate, D. C., Bates, B., and Crandall, K. A., 2001 Gene ﬂow estimates in Utah’s cougars imply management beyond utah. Animal Conservation 4: 257–264, 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.

Chikhi, L., Bruford, M. W., and Beaumont, M. A., 2001 Estimation of admixture proportions: A likelihood-based approach using Markov chain Monte carlo. Genetics 158: 1347–1362, 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.

Castric, V., Bonney, F., and Bernatchez, L., 2001 Landscape structure and hierarchical genetic diversity in the brook charr, Salvelinus fontinalis. Evolution 55: 1016–1028, 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.

Miura, G. I. and Edwards, S. V., 2001 Cryptic diﬀerentiation and geographic variation in genetic diversity of Hall’s Babbler Pomatostomus halli. J. Avian Biol. 32: 102–110, 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.

Carbone, I. and Kohn, L. M., 2001 A microbial population-species interface: nested cladistic and coalescent inference with multilocus data. Mol. Ecology 10: 947–964, 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.

Beerli, P. and Felsenstein, J., 2001 Maximum likelihood estimation of a migration matrix and eﬀective population sizes in n subpopulations by using a coalescent approach. Proc. National Acad. Sciences United States Am. 98: 4563–4568, 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.

Black, W. C., Baer, C. F., Antolin, M. F., and DuTeau, N. M., 2001 Population genomics: Genome-wide sampling of insect populations. Ann. Rev. Entomology 46: 441–469, 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.

Wright, T. F. and Wilkinson, G. S., 2001 Population genetic structure and vocal dialects in an amazon parrot. Proc. Royal Soc. London Series B-biological Sciences 268: 609–616, 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.

Austerlitz, F. and Smouse, P. E., 2001 Two-generation analysis of pollen ﬂow across a landscape. II. Relation between Phi(ft), pollen dispersal and interfemale distance. Genetics 157: 851–857, 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.

Vitalis, R. and Couvet, D., 2001 Estimation of eﬀective population size and migration rate from one-and two-locus identity measures. Genetics 157: 911–925, 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.

Pannell, J. R. and Charlesworth, B., 2000 Eﬀects of metapopulation processes on measures of genetic diversity. Philosophical Transactions Royal Soc. London Series B-biological Sciences 355: 1851–1864, 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.

Kreitman, M., 2000 Methods to detect selection in populations with applications to the human. Ann. Rev. Genomics Human Genetics 1: 539–559, 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.

Kuhner, M. K., Yamato, J., and Felsenstein, J., 2000 Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393–1401, 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.

Stephens, M. and Donnelly, P., 2000 Inference in molecular population genetics. J. Royal Statistical Soc. Series B-statistical Methodology 62: 605–635, 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.

Wilson, L., Stephens, D. A., Harding, R. M., Griffiths, B., Joyce, P., Edwards, A. W. F., Fearnhead, P., Ewens, W. J., Beaumont, M. A., Kuhner, M. K., Beerli, P., Brooks, S., Gelman, A., Chen, Y. G., Liu, J. S., Emond, M., Raftery, A. E., Steele, R., Felsenstein, J., Larget, B., Markovtsova, L., Marjoram, P., Tavare, S., Mau, B., Meng, X. L., Thompson, E. A., and Ventura, V., 2000 Inference in molecular population genetics -discussion. J. Royal Statistical Soc. Series B-statistical Methodology 62: 636–655.

Schierup, M. H. and Hein, J., 2000 Consequences of recombination on traditional phylogenetic analysis. Genetics

156: 879–891, 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.

Holder, K., Montgomerie, R., and Friesen, V. L., 2000 Glacial vicariance and historical biogeography of rock ptarmigan (Lagopus mutus) in the Bering region. Mol. Ecology 9: 1265–1278, 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.

Cain, M. L., Milligan, B. G., and Strand, A. E., 2000 Long-distance seed dispersal in plant populations. Am. J. Botany 87: 1217–1227, 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.

Kovacevic, M. and Schaeffer, S. W., 2000 Molecular population genetics of X-linked genes in Drosophila pseudoobscura. Genetics 156: 155–172, 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.

Palsson, S., 2000 Microsatellite variation in Daphnia pulex from both sides of the Baltic sea. Mol. Ecology 9: 1075–1088, 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.

Congdon, B. C., Piatt, J. F., Martin, K., and Friesen, V. L., 2000 Mechanisms of population diﬀerentiation in marbled murrelets: Historical versus contemporary processes. Evolution 54: 974–986, 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.

Milot, E., Gibbs, H. L., and Hobson, K. A., 2000 Phylogeography and genetic structure of northern populations of the yellow warbler (Dendroica petechia). Mol. Ecology 9: 667–681, 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.

Mohle, M., 2000 Ancestral processes in population genetics -the coalescent. J. Theoretical Biol. 204: 629–638, 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.

Bahlo, M. and Griffiths, R. C., 2000 Inference from gene trees in a subdivided population. Theoretical Population Biol. 57: 79–95, 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.

Nielsen, R. and Slatkin, M., 2000 Likelihood analysis of ongoing gene ﬂow and historical association. Evolution

54: 44–50, 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.

Vila, C., Amorim, I. R., Leonard, J. A., Posada, D., Castroviejo, J., Petrucci-Fonseca, F., Crandall,

K. A., Ellegren, H., and Wayne, R. K., 1999 Mitochondrial DNA phylogeography and population history of the grey wolf Canis lupus. Mol. Ecology 8: 2089–2103, 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.

Clark, A. G., 1999 The size distribution of homozygous segments in the human genome. Am. J. Human Genetics

65: 1489–1492.

Gaggiotti, O. E., Lange, O., Rassmann, K., and Gliddon, C., 1999 A comparison of two indirect methods for estimating average levels of gene ﬂow using microsatellite data. Mol. Ecology 8: 1513–1520, 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.

Cooper, G., Burroughs, N. J., Rand, D. A., Rubinsztein, D. C., and Amos, W., 1999 Markov Chain Monte Carlo analysis of human Y-chromosome microsatellites provides evidence of biased mutation. Proc. National Acad. Sciences United States Am. 96: 11916–11921, 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.

Ouborg, N. J., Piquot, Y., and Groenendael, J. M. V., 1999 Population genetics, molecular markers and the study of dispersal in plants. J. Ecology 87: 551–568, 1 Long-distance dispersal events are biologically very important for plants because they aﬀect colonization probabilities, the probabilities of population persistence in a fragmented habitat, and metapopulation structure. They are, however, very diﬃcult to investigate because of their low frequency. We reviewed the use of molecular markers in the population genetics approach to studying dispersal. With these methods the consequences of long-distance dispersal are studied, rather than the frequency of the dispersal events themselves. 2 Molecular markers vary, displaying diﬀerent amounts of variation and diﬀerent modes of inheritance: they may be either dominant or codominant, and may or may not be subjected to genetic recombination. Use of markers has inspired the development of maximum likelihood techniques that take the evolutionary history of alleles into account while estimating gene ﬂow. 3 Inferring seed dispersal rates from indirect measurements of gene ﬂow involves three steps: (i) quantifying genetic diﬀerentiation among populations and using this to estimate the rate of gene ﬂow; (ii) producing a genetic dispersal curve by regressing geographical distance among populations against the amount of gene ﬂow; and (iii) separating seed-mediated from pollen-mediated gene ﬂow, by comparing diﬀerentiation in nuclear vs. cytoplasmic molecular markers. In this way, potentially very low levels of gene ﬂow can be detected. 4 The indirect approach is based on a number of assumptions. The validity of each assumption should be assessed by independent methods or the estimates of gene ﬂow and dispersal should be mainly used in a comparative context. In metapopulations, with frequent extinction and colonization, the relationship between genetic diﬀerentiation and gene ﬂow is not straightforward, and other methods should be used. 5 Highly variable molecular markers, especially microsatellites, have facilitated a direct genetic approach to measuring gene ﬂow, based on parental analyses. 6 The population genetic approach provides diﬀerent information about dispersal than ecological methods. Thus population genetic and ecological methods may supplement each other, and together lead to a better insight into the dispersal process than either of the methods on its own.

Beerli, P. and Felsenstein, J., 1999 Maximum-likelihood estimation of migration rates and eﬀective population numbers in two populations using a coalescent approach. Genetics 152: 763–773, A new method for the estimation of migration rates and eﬀective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the eﬀective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized Far-based measure. The program is available on the World Wide Web at http://evolution.genetics.washington.edu/lamarc.html/.

Rodrigo, A. G., Shpaer, E. G., Delwart, E. L., Iversen, A. K. N., Gallo, M. V., Brojatsch, J., Hirsch,

M. S., Walker, B. D., and Mullins, J. I., 1999 Coalescent estimates of HIV-1 generation time in vivo. Proc. National Acad. Sciences United States Am. 96: 2187–2191, The generation time of HIV Type 1 (HIV-1) in vivo has previously been estimated using a mathematical model of viral dynamics and was found to be on the order of one to two days per generation. Here, we describe a new method based on coalescence theory that allows the estimate of generation times to be derived by using nucleotide sequence data and a reconstructed genealogy of sequences obtained over time. The method is applied to sequences obtained from a long-term nonprogressing individual at ﬁve sampling occasions. The estimate of viral generation time using the coalescent method is 1.2 days per generation and is close to that obtained by mathematical modeling (1.8 days per generation), thus strengthening conﬁdence in estimates of a short viral generation time. Apart from the estimation of relevant parameters relating to viral dynamics, coalescent modeling also allows us to simulate the evolutionary behavior of samples of sequences obtained over time.