Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences

Nucleotide sequences from two nuclear loci, alcohol dehydrogenase andinternal transcribed spacer-1 of the nuclear ribosomal DNA repeats, and twomitochondrial genes, cytochrome oxidase I and cytochrome oxidase II, weredetermined from nine species in the Drosophila saltans species group. Thepartition homogeneity test and partitioned Bremer support were used tomeasure incongruence between phylogenetic hypotheses generated fromindividual partitions. Individual loci were generally congruent with eachother and consistent with the previously proposed morphological hypothesis,although they differed in level of resolution. Since extreme conflictbetween partitions did not exist, the data were combined and analyzedsimultaneously. The total evidence method gave a more resolved and highlysupported phylogeny, as indicated by bootstrap proportions and decayindices, than did any of the individual analyses. The cordata and ellipticasubgroups, considered to have diverged early in the history of the D.saltans group, were sister taxa to the remainder of the saltans group. Thesturtevanti subgroup, represented by D. milleri and D. sturtevanti,occupies an intermediate position in this phylogeny. The saltans andparasaltans subgroups are sister clades and occupy the most recentlyderived portion of the phylogeny. As with previous morphological studies,phylogenetic relationships within the saltans subgroup were notsatisfactorily resolved by the molecular data.