At the edge of traditional phylogenetics: recovering the phylogeny of Orthorrhapha (Diptera) using an extremely large matrix

The true flies include many of the most medically and agriculturally important insects. Our understanding of their evolutionary relationships has recently grown by leaps and bounds due to rigorous analyses using nucleotide data. A particularly surprising result of Diptera molecular phylogenetics is the resolution of Orthorrhapha (i.e. Platygenya) as a natural group. This group of flies, which includes many parasitic and predatory species such as robber flies, deer flies, horse flies, and bee flies, was long considered a progression of relationship leading to higher flies such as house flies and fruit flies. Here I construct the largest dataset ever focused on fly phylogenetics to investigate whether this group is corroborated with rigorous analyses on a densely sampled data set. Included are data from over one thousand species of flies. Sampling of Orthorrhapha is nearly complete to the subfamily level. Sixteen genes are included, and sampling for 28s, Cytochrome oxidase I are almost complete. A robustly supported phylogeny of lower flies is presented, along with sensitivity analyses addressing different support in various alignment regimes and analytical methods.