Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences

Abstract Brachyceran flies constitute a large radiation of the order Diptera, but the phylogenetic relationships among them have remained controversial. In this study, we used next-generation sequencing to determine mitochondrial genomes (mitogenomes) for six brachyceran flies. Two of these species represent Milichiidae (Aldrichiomyza flaviventris and Phyllomyza obliqua); two representing Chloropidae (Pachylophus sp.) and Sphaeroceridae (Leptocera erythrocera) are the first sequenced members of these groups; and two species from Lauxaniidae (Homoneura sp.) and Syrphidae (Paragus quadrifasciatus) were newly sequenced. Together with the published mitogenomes, we included a total of 187 species representing 40 dipteran families to investigate the phylogeny of Brachycera. The results strongly supported Brachycera as a monophyletic group. The infra-orders Stratiomyomorpha, Tabanomorpha and Xylophagomorpha were retrieved as the earliest brachyceran lineages, but the clade (Stratiomyomorpha + (Xylophagomorpha + Tabanomorpha)) was not supported. In most analyses, Platypezoidea were recovered as the sister-group to Cyclorrhapha. Syrphoidea were non-monophyletic with respect to Pipunculus. Milichiidae were non-monophyletic because of Pachylophus. Sphaeroceroidea were, in most cases, placed as the sister-group to Ephydroidea. Within Calyptratae, Hippoboscoidea were sister to an assemblage of lineages composed of a muscoid grade and Oestroidea, the latter being monophyletic in the Bayesian analyses using the PhyloBayes site-heterogeneous mixture model.