Integration of mitogenomic and morphological data disentangles the systematics of Pollenia and establishes a revised phylogenetic hypothesis for the Polleniidae

The Polleniidae (Diptera) are a family of flies best known for species of the genus Pollenia, which overwinter inside human dwellings. Previously divided across the Calliphoridae, Tachinidae and Rhinophoridae, the polleniid genera have only recently been united. Several studies have utilized molecular data to analyse polleniid phylogenetic relationships, although all have suffered from low taxon sampling or insufficient phylogenetic signal in molecular markers. To alleviate these problems, we utilized two automated organellar genome extraction software, GetOrganelle and MitoFinder, to assemble mitogenomes from genome skimming data from 22 representatives of the polleniid genera: Dexopollenia, Melanodexia, Morinia, Pollenia and Xanthotryxus. From these analyses, we provide 14 new mitogenomes for the Polleniidae and perform phylogenetic analyses of 13 protein‐coding mitochondrial genes using both maximum likelihood and Bayesian inference. Subfamilial phylogenetic relationships within the Polleniidae are interrogated and Pollenia is found to form a monophyletic clade sister to Melanodexia, Morinia and Dexopollenia, providing no evidence for the synonymisation of any of these genera. Our topology conflicts with previous morphology‐based cladistic interpretations, with the amentaria, griseotomentosa, semicinerea and viatica species‐groups resolving as non‐monophyletic. We provide support for our topology through analysis of adult morphology and male and female terminalia, while identifying new diagnostic characters for some of the clades of the Pollenia. To test the validity of the current diagnostic morphology in the Polleniidae, newly assembled cytochrome C oxidase subunit 1 (COI) data are combined with a polleniid COI barcode reference library and analysed using the species delimitation software ASAP. COI barcodes support the current morphologically defined species within the Pollenia. We utilised two automated organellar genome extraction software, GetOrganelle and MitoFinder, to assemble mitogenomes from genome skimming data from 22 representatives of the pollenid genera: Dexopollenia, Melanodexia, Morinia, Pollenia, and Xanthotryxus. From these analyses, we provide 14 new mitogenomes for the Polleniidae and perform phylogenetic analyses of 13 protein‐coding mitochondrial genes using both maximum likelihood and Bayesian inference. Subfamilial phylogenetic relationships within the Polleniidae are interrogated and Pollenia is found to form a monophyletic cla