Stochastic patterns of polymorphism after a selective sweep over a subdivided population

The geographic structure of a population, which is modelled as a network of several small random-mating populations or demes exchanging migrants between them, limits the rapid spread of a beneficial allele under strong directional selection to the entire population. This weakens or modifies the hitchhiking effect of the beneficial allele on the pattern of genetic variation at linked neutral loci. Previous studies suggested that the characteristic patterns of polymorphism arise with selective sweeps in such a subdivided population. However, they did not fully address the stochastic pattern, as expected in an actual sample of DNA sequence, of such patterns. This study uses a novel method of individual-based forward-in-time simulation to generate multi-locus neutral polymorphism after a selective sweep in a moderately subdivided population. Population subdivision is shown to cause frequency spectrum to shift slightly such that Tajima's D becomes less negative than expected under a panmictic population. Similarly, the pattern of linkage disequilibrium showed very small change due to population subdivision. On the other hand, the value of Wright's F ST at closely linked neutral loci relative to that at unlinked loci greatly increased by population subdivision as predicted by previous studies. Finally, the distribution of the gradient of heterozygosity along the migration path of beneficial mutation, previously suggested to allow the inference of the direction of spread, was investigated. The variance of difference in heterozygosity was much larger than the mean, suggesting that such an inference may not be practical.