Data from: Whole mitochondrial genome phylogeny of the family Drosophilidae

A total of 241 mitochondrial genomes were assembled and annotated from the
SRA database to reconstruct a mtDNA genome phylogeny for the genus
Drosophila, the family Drosophilidae, and close relatives. The resulting
mtDNA genome phylogeny is largely congruent with previous higher-level
analyses of Drosophila species with the exception of the relationships
between the melanogaster, montium, anannassae, saltans and obscura groups.
Although relationships within these species groups are congruent between
nuclear and mtDNA studies, the mtDNA genome phylogeny of the groups is
different when compared to earlier studies. Monophyly of known species
groups within the genus Drosophila are highly supported and, as in
previous work, the genera Lordiphosa, Hirtodrosophila, Zaprionus and
Scaptomya are all imbedded within the genus Drosophila. Incongruence and
partitioned support analyses indicate that DNA sequences are better at
resolving the phylogeny than their translated protein sequences. Such
analyses also indicate that genes on the minus strand of the circular
molecule (Lrrna, Srrna, ND4, ND4L and ND5) provide most of the support for
the overall phylogenetic hypothesis.