A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data

Drosophila melanogaster belongs to a closely related group of eight speciescollectively known as the melanogaster subgroup; all are native tosub-Saharan Africa and islands off the east coast of Africa. Thephylogenetic relationships of most species in this subgroup have been welldocumented; however, the three most closely related species, D. simulans,D. sechellia, and D. mauritiana, have remained problematic from aphylogenetic standpoint as no data set has unambiguously resolved them. Wepresent new DNA sequence data on the nullo and Serendipity-alpha genes andcombine them with all available nuclear DNA sequence data; the total dataencompass 12 genes and the ITS of rDNA. A methodological problem arosebecause nine of the genes had information on intraspecific polymorphisms inat least one species. We explored the effect of inclusion/exclusion ofpolymorphic sites and found that it had very little effect on phylogeneticinferences, due largely to the fact that 82% of polymorphisms areautapomorphies (unique to one species). We have also reanalyzed ourprevious DNA-DNA hybridization data with a bootstrap procedure. Thecombined sequence data set and the DNA-DNA hybridization data stronglysupport the sister status of the two island species, D. sechellia and D.mauritiana. This at least partially resolves what had been a paradox ofparallel evolution in these two species.