Current Version is 3.2.17  [Fall 2011]

NEW in 3.2: microsatellite data can now be used with fragment lengths instead of repeat lengths (but need an additional line in the infile). Migrate can now print trees for all datatypes such as microsatellite and DNA (BEST likelihood tree, or all trees visited in the LASTCHAIN), the default treefile format changed to NEXUS. On macs and linux you can now use compression for the bayesallfile that holds all visited states, by simply adding a .gz extension to the filename. Warning messages are issued when runs are to short or prior distributions for Bayesian inference are too narrow, these are new features and need more feedback from users, in particular for the warning system because with weak data the warnings will be always triggered but blindly increasing  the prior boundaries will not help -- I need to write a more detailed help in this subject.


Important additional information to help recent version of migrate:

  1. •Most recent paper on migrate technology: Beerli and Palczewski 2010: Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations. Genetics (2010) vol. 185 pp. 313--326 (LINK)

  2. •Tutorial on how to compare population genetic models (LINK)

  3. •Opinion about issues with divergence and accuracy of migration rates (LINK)


Known problems with current version:

  1. •For some combination of parameters it seems that on parallel cluster runs the migration parameters do not report correct histograms (they are empty!!!), these cases should be rerun by using the bayes-allfile option. for example in the parmfile use bayes-allfile=YES:1:bayesallfile.gz [the gz suffix forces migrate to write compressed files]

MIGRATE-N

estimation of population sizes

and gene flow using the coalescent

Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters. The analysis can be constrained to subsets of migration patterns, such as setting some migration rates between populations to zero or constrain to symmetric rates or average over all migration rates, or use likelihood ratio tests and AIC values to compare different hypotheses. Migrate can use several different single or multilocus data types: sequence data using Felsenstein's 84 model with or without site rate variation, single nucleotide polymorphism data, microsatellite data using a stepwise mutation model or a brownian motion mutation model, and electrophoretic data using an 'k+1' allele model. The output comes in two flavors: PDF and TEXT file. The file can contain: Maximum likelihood: Estimates of all migration rates and all population sizes, assuming constant mutation rates among loci or a gamma distributed mutation rate among loci. Profile likelihood tables, Percentiles, Likelihood-ratio tests, and simple plots of the log-likelihood surfaces for all populations and all loci. (not all plots are implemented in the PDF, yet). Genealogy with best likelihood (Printable through ET (eventtree -- http://popgen.sc.fsu.edu/Eventtree.html) or after some editing in Figtree (Andrew Rambaut). Bayesian inference: Estimates of maximum posterior values of parameters and credibility intervals in table form, figures of posterior distribution of parameters. Indications of convergence and effective sample size, presentation of frequency of migration events over time, genealogy with best likelihood printable through ET, calculation of marginal likelihood that can be used to compare different models.Eventtree.htmlhttp://popgen.scs.fsu.edu/migabout.htmlshapeimage_2_link_0

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