Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex

Two regions of the genome, a 1-kbp portion of the zeste locus and a 1.1-kbp portion of the yolk protein 2 locus, were sequenced in six individualsfrom each of four species: Drosophila melanogaster, D. simulans, D.mauritiana, and D. sechellia. The species and strains were the same asthose of a previous study of a 1.9-kbp region of the period locus. Noevidence was found for recent balancing or directional selection or for theaccumulation of selected differences between species. Yolk protein 2 has ahigh level of amino acid replacement variation and a low level ofsynonymous variation, while zeste has the opposite pattern. This contrastis consistent with information on gene function and patterns of codon bias.Polymorphism levels are consistent with a ranking of effective populationsizes, from low to high, in the following order: D. sechellia, D.melanogaster, D.mauritiana, and D. simulans. The apparent speciesrelationships are very similar to those suggested by the period locusstudy. In particular, D. simulans appears to be a large population that isstill segregating variation that arose before the separation of D.mauritiana and D. sechellia. It is estimated that the separation ofancestral D. melanogaster from the other species occurred 2.5-3.4 Mya. Theseparations of D. sechellia and D. mauritiana from ancestral D. simulansappear to have occurred 0.58- 0.86 Mya, with D. mauritiana having divergedfrom ancestral D. simulans 0.1 Myr more recently than D. sechellia.