The Drosophila obscura group consists of several dozen Nearctic and Palearctic species, with a phylogeny that remains largely unresolved in spite of numerous morphological, cytogenetic, and molecular investigations. We have partially sequenced two genes, Gpdh (about 1000 bp) and Sod (about 700 bp) in 12-13 species and 1 subspecies in order to settle the issues. Difficulties in resolving the phylogeny emanate from the rapid sequence of successive radiations. Nevertheless, the following conclusions are warranted: (1) The Palearctic species include two monophyletic subgroups, subobscura (which may be the most ancient clade of the whole group) and obscura, plus two other species with unresolved phylogenetic positions, D. bifasciata and D. subsilvestris; (2) the Nearctic species form a monophyletic group consisting of two monophyletic sister clades, the affinis subgroup and the pseudoobscura subgroup. The Palearctic radiation may have resulted from adaptation to expanding temperate forests in the Old World. A second radiation occurred during the colonization of the deciduous forests of the New World by the descendants of a single lineage that soon split into the affinis and pseudoobscura subgroups.

We have sequenced most of the coding region of the gene Dopa decarboxylase (Ddc) in 24 fruitfly species. The Ddc gene is quite informative about Drosophila phylogeny. Several outstanding issues in Drosophila phylogeny are resolved by analysis of the Ddc sequences alone or in combination with three other genes, Sod, Adh, and Gpdh. The three species groups, melanogaster, obscura, and willistoni, are each monophyletic and all three combined form a monophyletic group, which corresponds to the subgenus Sophophora. The Sophophora subgenus is the sister group to all other Drosophila subgenera (including some named genera, previously considered outside the Drosophila genus, namely, Scaptomyza and Zaprionus, which are therefore downgraded to the category of subgenus). The Hawaiian Drosophila and Scaptomyza are a monophyletic group, which is the sister clade to the virilis and repleta groups of the subgenus Drosophila. The subgenus Drosophila appears to be paraphyletic, although this is not definitely resolved. The two genera Scaptodrosophila and Chymomyza are older than the genus Drosophila. The data favor the hypothesis that Chymomyza is older than Scaptodrosophila, although this issue is not definitely resolved. Molecular evolution is erratic. The rates of nucleotide substitution in 3rd codon position relative to positions 1 + 2 vary from one species lineage to another and from gene to gene.