Population Genetic Inference With MIGRATE

摘要

Many evolutionary biologists collect genetic data from natural populations and then need to investigate the relationship among these populations to compare different biogeographic hypotheses. MIGRATE, a useful tool for exploring relationships betweenpopulations and comparing hypotheses, has existed since 1998. Throughout the years, it has steadily improved in both the quality of algorithms used and in the efficiency of carrying out those calculations, thus allowing for a larger number of loci to beevaluated. This efficiency has been enhanced, as MIGRATE has been developed to perform many of its calculations concurrently when running on a computer cluster. The program is based on the coalescence theory and uses Bayesian inference to estimate posterior probability densities of all the parameters of a user-specified population model. Complex models, which include migration and colonization parameters, can be specified. These models can be evaluated using marginal likelihoods, thus allowing a user tocompare the merits of different hypotheses. The three presented protocols will help novice users to develop sophisticated analysis techniques useful for their research projects.