Linking DNA Polymorphisms and Populations' Evolutionary History

This dissertation seeks to provide an understanding of how different evolutionary forces can affect the DNA polymorphism patterns. I use a combination of individual-based simulations and analytical to examine polymorphism patterns during divergence with gene flow, hybridization and territory expansion. In the first chapter, I show how during divergence with gene flow the appearance and maintenance of “Genomic Islands of Divergence” can be explained using standard population genetics terminology, thus removing some of the confusion recently introduced in that literature. In the second chapter I derive the expressions for the distribution of coalescent times and pairwise differences in a hybridization model with migration and show how those equations can be used to estimate model parameters. Finally, in third chapter, I consider the “Serial Founder” (SF) model. Previous work has shown that the SF model without migration can produce a pairwise F_st [fixation index] and heterozygosity patterns consistent to ones reported for human populations. Previous simulation results also suggest that including migration does not cause substantial departures from a model with no migration, but the lack of analytical result limits the ability to precisely describe the effects of migration on F_st and heterozygosity. I fill this void by showing analytically that a SF model with a historical migration can produce qualitatively different F_st and heterozygosity patterns from a model without migration, but not for parameters describing humans.