Congruence and controversy: toward a higher-level phylogeny of Diptera.

The order Diptera (true flies) is one of the most species-rich and ecologically diverse clades of insects. The order probably arose in the Permian, and the main lineages of flies were present in the Triassic. A novel recent proposal suggests that Strepsiptera are the sister-order to Diptera. Within Diptera, evidence is convincing for the monophyly of Culicomorpha, Blephariceromorpha, and Tipulomorpha but weak for the monophyly of the other basal infraorders and for the relationships among them. The lower Diptera (Nematocera) is paraphyletic with respect to Brachycera, and morphological evidence suggests the sister-group of Brachycera lies in the Psychodomorpha. Recent analyses suggest Tipulomorpha are closer to the base of Brachycera than to the base of Diptera. Brachycera are undoubtedly monophyletic, but relationships between the basal lineages of this group are poorly understood. The monophyly of Stratiomyomorpha, Xylophagomorpha, Tabanomorpha, and Muscomorpha is well supported. Eremoneura, and its constituent clades Empidoidea and Cyclorrhapha, are monophyletic. The sister-group of Eremoneura is likely to be part or all of Asiloidea. Several viewpoints on the homology of the male genitalia of eremoneuran flies are discussed. Phylogenetic analyses suggest that lower Cyclorrhapha (Aschiza) are paraphyletic; however, schizophoran monophyly is well supported. The monophyly of Acalyptratae is not well-founded and the relationships between acalyptrate superfamilies remain obscure. Recent advances document the monophyly of the families of Calyptratae and the relationships among them. Areas critical to future advances in understanding dipteran phylogeny include the relationships among the basal infraorders of Diptera and Brachycera and the relationships between the superfamilies of acalyptrates. Progress in dipteran phylogenetics will accelerate with the exploration of novel data sources and the formulation of hypotheses in an explicitly quantitative framework.