Inferring patterns of migration from gene frequencies with R (or S-Plus), Version 1.2.0

Jarle Tufto

Abstract:

A collection of R (and S-Plus) functions and some additional c-code for estimating the pattern of migration in a subdivided population from genetic differences generated by local genetic drift is described. The method is applicable to migration matrices of any form. Submodels defining the general form of the migration matrix can be written by the user. Functions are also provided for carrying out likelihood ratio tests between alternative models such as the island model and the stepping stone model, or between alternative user defined submodels. In addition, plots of predicted and observed covariances can be made to assess the fit of a selected model. Finally, code for computing the asymptotic eigenvalue variance effective size of a subdivided population is provided.