Homology of male genitalic structures in the lower Brachycera is examined and implications for the phylogenetic relationships of the included families are discussed in light of other characters. The following character states belong to the ground plan of the Brachycera: the aedeagus is enclosed in a parameral sheath; the sperm pump possesses paired articulated lateral sclerites, and a large ejaculatory apodeme with a terminal endoaedeagal process; the epandrium and hypandrium are separate; the hypandrium is separate from the gonocoxites; and the gonostyli articulate and move in the horizontal plane. The placement of Heterostomus in Xylophagomorpha is supported, based on modifications of the sperm pump. The presence ofaedeagal tines suggests that Bolbomyia, which is currently placed in the Rhagionidae, may be more closely related to Athericidae + Tabanidae. The expanded first segment of the female cercus supports the monophyly of the Tabanomorpha, including Vermileonidae. The transfer of the Pantophthalmidae to the Stratiomyomorpha is confirmed on the basis of modifications of the sperm pump. The Stratiomyomorpha is hypothesized to be the sister group of the Muscomorpha (sensu Woodley 1989) based on the apomorphic development of a composite structure termed the phallus. The monophyly of the Muscomorpha is supported by gonostyli that articulate and move obliquely or dorsoventrally. The presence of acanthophorites in females is considered apomorphic for the Heterodactyla (Bombyliidae + Asiloidea + Eremoneura). Bombyliidae (exclusive of Mythicomyiinae and Heterotropus) is defined on the basis of reduced gonocoxal apodemes. Gonostyli retracted to a subapical position and a hinged larval metacephalic rod are considered apomorphic for the Asiloidea (exclusive of Bombyliidae) + Eremoneura. Hilarimorpha and Apystomyia are removed from the Bombyliidae based on the subapical placement of the gonostyli, and together with Apsilocephala are placed as incertae sedis in Therevidae. Apiocera is considered the sister group to the remaining apiocerids + Mydidae on the basis of absence of gonostyli and lateral ejaculatory processes in the latter lineage.

Homologies of male genitalic structures in the Eremoneura (Empidoidea + Cyclorrhapha) are examined and implications for the phylogenetic relationships of the included families are discussed in light of other characters. A revised epandrial hypothesis for the evolution of male genitalia within the Eremoneura is presented, based on comparison of male genitalic features throughout the Brachycera, and a periandrial hypothesis is rejected. Ground plan modifications of the genitalia of Eremoneura include complete sclerotization of the subepandrial membrane along its length to form a subepandrial sclerite, formation of bacilliform sclerites, loss of the lateral ejaculatory processes of the sperm pump, development of a deeply emarginate epandrium, and fusion of the hypandrium with the gonocoxites. Ground plan apomorphies of the Cyclorrhapha, including Opetiidae, consist of a sperm pump separated from the base of the phallus, circumversion of the genitalia, loss of the gonocoxal apodemes, and development of surstyli. The ground plan of the Empidoidea is characterized by the apomorphic loss of gonostyli, and the development of a sperm pump with a lever-like ejaculatory apodeme. Surstyli have developed independently in several lineages of Empidoidea, parallel to their development in Cyclorrhapha, as have losses of the gonocoxal apodemes. The above characters support the monophyly of the Eremoneura and also indicate that the Empidoidea and Cyclorrhapha are sister groups, as opposed to alternative hypotheses that suggest the Empidoidea is paraphyletic with respect to the Cyclorrhapha. The monophyly of Cyclorrhapha, exclusive of Opetiidae, is supported by the presence of a phallapodeme. The Lonchopteridae and Phoroidea are united partially on the basis of a similar reduction of pregenital sclerites in the male. The Phoroidea is characterized by the apomorphic loss of gonostyli and abdominal spiracle 7 in the male. The Syrphoidea and Schizophora are hypothesized to share a synapomorphic lever-like phallapodeme. The Syrphoidea is characterized by a right-side deflexion of the hypopygium, whereas the Schizophora possess gonostyli that are adducted against the hypandrium, and circumversion that is completed entirely within the puparium.

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