Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis

TLDR

The genetic study of diverging, closely related populations is essential for understanding demography, speciation, biodiversity, and conservation, yet it is unclear whether divergence is due solely to separation or also involves gene flow. The study aims to determine whether divergence is due to separation alone or also involves gene flow by applying a full model of population separation with gene flow using a Markov chain Monte Carlo method. The authors generalized the MCMC method to multiple unlinked loci, allowing inheritance scalars to be constants or estimated parameters, thereby capturing locus‑specific effects such as selective sweeps or background selection, and applied this framework to a large multilocus dataset from *Drosophila pseudoobscura* and *D. persimilis*.

Abstract

The genetic study of diverging, closely related populations is required for basic questions on demography and speciation, as well as for biodiversity and conservation research. However, it is often unclear whether divergence is due simply to separation or whether populations have also experienced gene flow. These questions can be addressed with a full model of population separation with gene flow, by applying a Markov chain Monte Carlo method for estimating the posterior probability distribution of model parameters. We have generalized this method and made it applicable to data from multiple unlinked loci. These loci can vary in their modes of inheritance, and inheritance scalars can be implemented either as constants or as parameters to be estimated. By treating inheritance scalars as parameters it is also possible to address variation among loci in the impact via linkage of recurrent selective sweeps or background selection. These methods are applied to a large multilocus data set from Drosophila pseudoobscura and D. persimilis. The species are estimated to have diverged approximately 500,000 years ago. Several loci have nonzero estimates of gene flow since the initial separation of the species, with considerable variation in gene flow estimates among loci, in both directions between the species.