Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes

Relationships among families of the lower Diptera (formerly suborder ‘Nematocera’) have been exceptionally difficult to resolve. Multiple hypotheses based on morphology have been proposed to identify the earliest lineages of flies and place the phylogenetic origin of the higher flies (Brachycera), but convincing support is limited. Here we resolve relationships among the major groups of lower Diptera using sequence data from four nuclear markers, including both ribosomal (28S rDNA) and protein-coding (CAD, TPI and PGD) genes. Our results support both novel and traditional arrangements.Most unexpectedly, the small, highly-specialized family Deuterophlebiidae appears to be sister to all remaining Diptera. Other results include the resolution of the traditional infra-orders Culicomorpha (including a novel superfamily Simulioidea ¼ Thaumaleidae þ Simuliidae), Tipulomorpha (Tipulidae sensu lato þ Trichoceridae) and Bibionomorpha sensu lato. We find support for a limited Psychodomorpha (Blephariceridae, Tanyderidae and Psychodidae)
and Ptychopteromorpha (Ptychopteridae), whereas the placement of several enigmatic families (Nymphomyiidae, Axymyiidae and Perissommatidae) remains ambiguous. According to genetic data, the infra-order Bibionomorpha is sister to the Brachycera. Much of the phylogenetic signal for major lineages was found in the 28S rDNA gene, whereas protein-coding genes performed variably at different levels. In
addition to elucidating relationships, we also estimate the age of major lower dipteran clades, based on molecular divergence time estimates using relaxed-clock Bayesian methods and fossil calibration points.