Population Structure and Migration

Abstract

We begin with a discussion of how population structure is commonly modeled, including island, stepping-stone, and isolation-by-distance models. The structured coalescent is used as an intuitive model for thinking about the fate of alleles in a population whose demes are connected by appreciable gene flow. The migration rate m is defined and its importance to genetic population structure is emphasized. Modifications to the code of forward-simulation program FORTUNA add the ability to simulate gene flow using a single, symmetric value of m or a fully specified migration matrix among demes. An R script that allows visualization of a summary statistic across time and across sequence windows is introduced. Another important addition to FORTUNA is the ability to print out samples of haplotypes on specified generations. These files can be used to compare independent runs of evolution from the same starting point or to examine the molecular evolutionary process at greater resolution. The fixation index, F _ST, is introduced and used to assess genetic connectivity between pairs of demes; the index is calculated using simulated data and an R script. The final addition to FORTUNA in this chapter allows the user to output the basic history of every allele generated during a simulation; this history includes the position of the derived allele, the generation it originated, and the deme in which it originated. These data are then used to explore the fate of alleles as they flow among demes via migration. A curious result is explored in detail to emphasize the importance of confirming that unexpected results have naturally emerged from the simulated model and are not due to an overlooked coding error.