Concatenated amino acid (AA) phylogenetic dataset of nuclear gene orthologs for Ephydroidea (Diptera)

The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes
eight families, ranging from the well-known vinegar flies (Drosophilidae)
and shore flies (Ephydridae), to several small, relatively unusual groups,
the phylogenetic placement of which has been particularly challenging for
systematists. Extraordinary diversity in life histories, feeding habits,
and morphology are hallmarks of fly biology, and the Ephydroidea are no
exception. Extreme specialization can lead to “orphaned” taxa with no
clear evidence for their phylogenetic position. To resolve relationships
among a diverse sample of Ephydroidea, including the highly modified flies
in the families Braulidae and Mormotomyiidae, we conducted phylogenomic
sampling. Using exon capture from Anchored Hybrid Enrichment and
transcriptomics to obtain 320 orthologous nuclear genes sampled for 32
species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic
hypothesis for representatives of the superfamily. These data strongly
support monophyly of Ephydroidea with Ephydridae as an early branching
radiation and the placement of Mormotomyiidae as a family-level lineage
sister to all remaining families. We confirm the placement of
Cryptochetidae as a sister taxon to a large clade containing both
Drosophilidae and Braulidae – the latter a family of honeybee
ectoparasites. Our results reaffirm that sampling of both taxa and
characters is critical in hyperdiverse clades and that these factors have
a major influence on phylogenomic reconstruction of the history of the
schizophoran fly radiation.