Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)

Early diverging brachyceran fly lineages underwent a rapid radiation approximately 180 million years ago, coincident in part with the origin of flowering plants. This region of the fly tree includes 25,000 described extant species with diverse ecological roles such as blood feeding (haematophagy), parasitoidism, predation, pollination, and wood feeding (xylophagy). Early diverging brachyceran lineages were once considered a monophyletic group of families called Orthorrhapha, based on the shared character of a longitudinal break in the pupal skin made during the emergence of the adult. Yet other morphological and molecular evidence generally supports a paraphyletic arrangement of ‘Orthorrhapha,’ with strong support for one orthorrhaphan lineage — dance flies and relatives — as the closest relative to all higher flies (Cyclorrhapha), together called Eremoneura. In order to establish a comprehensive estimate of the relationships among orthorrhaphan lineages using a thorough sample of publi...