A MOLECULAR PHYLOGENY FOR THE DROSOPHILA-MELANOGASTER SUBGROUP AND THE PROBLEM OF POLYMORPHISM DATA

Drosophila melanogaster belongs to a closely related group of eight sp ecies collectively known as the melanogaster subgroup; all are native to sub-Saharan Africa and islands off the east coast of Africa. The ph ylogenetic relationships of most species in this subgroup have been we ll documented; however, the three most closely related species, D. sim ulans, D. sechellia, and D. mauritiana, have remained problematic from a phylogenetic standpoint as no data set has unambiguously resolved t hem. We present new DNA sequence data on the nullo and Serendipity-alp ha genes and combine them with all available nuclear DNA sequence data ; the total data encompass 12 genes and the ITS of rDNA. A methodologi cal problem arose because nine of the genes had information on intrasp ecific polymorphisms in at least one species. We explored the effect o f inclusion/exclusion of polymorphic sites and found that it had very little effect on phylogenetic inferences, due largely to the fact that 82% of polymorphisms are autapomorphies (unique to one species). We h ave also reanalyzed our previous DNA-DNA hybridization data with a boo tstrap procedure. The combined sequence data set and the DNA-DNA hybri dization data strongly support the sister status of the two island spe cies, D. sechellia and D. mauritiana. This at least partially resolves what had been a paradox of parallel evolution in these two species.