A molecular phylogeny of scuttle flies (Diptera: Phoridae) unveils extensive concordance but intriguing divergences from morphological results

Abstract We present the most comprehensive molecular phylogeny of scuttle flies (Diptera: Phoridae) to date based on seven genetic loci—four protein‐coding genes: arginine kinase (AK), carbamoylphosphate synthase 2 domain of CAD (rudimentary; CAD2), cytochrome oxidase I (CO1), NADH1 dehydrogenase (ND1) and three ribosomal DNAs: 12S, 18S and 28S. Our analyses include 122 species including nine outgroup taxa and 113 phorids (representing 61 genera). Phylogenetic relationships based on the approximately 5.3 kb of sequence data were inferred by maximum likelihood and Bayesian methods. Results are broadly congruent with recent morphological phylogenies of the group, with some significant exceptions. Our data support the monophyletic Sciadocerinae as sister to the remainder of the family. However, we found Ctenopleuriphora Liu to be sister to Phorinae with low support, and subfamilies Chonocephalinae and Termitoxeniinae are placed deep within Phorinae, and their monophyly is not consistently recovered. Our dating analyses indicate a lower Cretaceous origin of Phoridae at 120.8 Ma (125.4–111.2 Ma).