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 indiv iduals from each of four species: Drosophila melanogaster, D. simulans , D. mauritiana, and D. sechellia. The species and strains were the sa me as those of a previous study of a 1.9-kbp region of the period locu s. No evidence was found for recent balancing or directional selection or for the accumulation of selected differences between species. Yolk protein 2 has a high level of amino acid replacement variation and a low level of synonymous variation, while zeste has the opposite patter n. This contrast is consistent with information on gene function and p atterns of codon bias. Polymorphism levels are consistent with a ranki ng of effective population sizes, from low to high, in the following o rder: D. sechellia, D. melanogaster, D. mauritiana, and D. simulans. T he apparent species relationships are very similar to those suggested by the period locus study. In particular, D. simulans appears to be a large population that is still segregating variation that arose before the separation of D. mauritiana and D. sechellia. It is estimated tha t the separation of ancestral D. melanogaster from the other species o ccurred 2.5-3.4 Mya. The separations of D. sechellia and D. mauritiana from ancestral D. simulans appear to have occurred 0.58-0.86 Mya, wit h D. mauritiana having diverged from ancestral D. simulans 0.1 Myr mor e recently than D. sechellia.