Phylogenetic relationships of files in the family Drosophilidae inferred by combined analysis of molecular and morphological data sets

The phylogenetic relationships of flies within the family Drosophilidae are studied in four clades placed at three different taxonomic levels. The goal of examining phylogenetic relationships of nested clades within Drosophilidae is to study patterns divergence at several points, giving a more informative view of evolution in this family of flies. Two studies presented here examine the phylogenetic relationships within the Drosophila saltans and Drosophila obscura species groups. Another examines the relationships among several species groups within the subgenus Sophophora. The final study examines the phylogenetic relationships among genera within the family Drosophilidae. The molecular data gathered for members of the Drosophila saltans species group are congruent with the conclusions of previous taxonomic studies. All five species subgroups are monophyletic with respect to one another. Relationships among the subgroups indicate that the neocordata and elliptica subgroups are basal in the saltans species group. The saltans and parasaltans subgroups are derived sister taxa and the sturtevanti subgroup occupies an intermediate position within the saltans species group. The results of the Drosophila obscura analyses indicate that all five of the subgroups are monophyletic with respect to one another. Furthermore, the New and Old World obscura species groups are monophyletic, a result which has been suggested by some data in the past. This study also suggests, albeit weakly, that the Afrotropical microlabis subgroup may be the sister taxon of the subobscura subgroup. The results of this study indicate that Sophophora is monophyletic with respect to the subgenus Drosophila. Within Sophophora, the obscura and saltans species groups are highly supported as monophyletic. The willistoni and melanogaster species groups, however, may not be monophyletic. This is possibly due to rapid speciation at the base of these two species groups. The relationships inferred through combined analysis of all available molecular and morphological data indicate that the genus Drosophila is not monophyletic. Several genera, including Engiscaptomyza, Hirtodrosophila, Mycodrosophila, Paramycodrosophila, Samoaia, Scaptomyza, Zaprionus and Zygothrica diverge within the boundaries of what is currently considered the "genus" Drosophila. Furthermore, the subgenus Drosophila is not monophyletic and can be tentatively divided into at least two, and probably more, monophyletic groups. These clades correspond, although not perfectly, with the virilis-repleta and immigrans-tripunctata radiations described in earlier taxonomic studies. Finally, the subgenus Sophophora, previously considered the sister clade of the subgenus Drosophila, is shown to be a lineage distinct from the genus Drosophila.