Population structure among African and derived populations of Drosophila simulans: Evidence for ancient subdivision and recent admixture

Previous studies based on allozyme variation have found little evidence for genetic differentiation in Drosophila simulans. On the basis of DNA sequen ce variation at two nuclear loci in four African populations of D. simulans , we show that there is significant structure to D. simulans populations wi thin Africa. Variation at one of the loci, vermilion, appears to be neutral and supports an eastern African origin for European and American populatio ns. Samples from the West Indies, Europe, and North America had a nucleotid e diversity lower than that of African populations at vermilion, and show n onequilibrium haplotype distributions at both vermilion and G6pd, consisten t with a hypothesis of recent bottleneck and possibly also admixture in the history of these populations. Directional selection, previously documented at G6pd, appears to have occurred within the coalescence time of the speci es, obscuring deep population history.