Phylogenetic resolution of the fly superfamily Ephydroidea - molecular systematics of the enigmatic and diverse relatives of Drosophilidae

The schizophoran superfamily Ephydroidea (Diptera: Cyclorrahapha) includes eight families of flies. The families range from the vinegar flies (Drosophilidae) and the shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematics. 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 representatives o the superfamily.