Mitochondrial genomes provide new insights into the phylogeny and evolution of Anthomyiidae (Insecta: Diptera)

Anthomyiidae is a cosmopolitan and diverse family of Calyptratae, and is routinely considered to play key roles in both ecology and agriculture. The higher-level phylogenetic classification of Anthomyiidae has been highly controversial, necessitating further molecular data for precise reconstruction of phylogenetic relationships. In this study, we successfully acquired and annotated 18 new mitogenomes of anthomyiids. Moreover, the mitogenomes of the following genera Eustalomyia, Hyporites, Leucophora, Emmesomyia and Eutrichota are reported for the first time. The 18 mitogenomes are compared with confamilial species to assess genetic variation and to better understand evolutionary relationships within the family Anthomyiidae. In comparisons among 13 mitochondrial protein coding genes (PCG), the calculation of evolutionary rate exhibited nad1 as the fastest evolving gene in Anthomyiidae. Among the anthomyiids investigated, cox2 and nad4 had the lowest genetic distance across the 13 PCGs, suggesting a high degree of conservation for these two genes. Herein, we conducted phylogenetic analyses of the newly sequenced mitogenomes along with 11 known anthomyiids to investigate the interrelationships of Anthomyiidae. Our results indicate that Anthomyiidae is a monophyletic lineage and sister group to Scathophagidae, confirming prior findings based on morphological and molecular analyses. We recovered two subfamilies as monophyletic (Myopininae, Pegomyinae) while Anthomyiinae was polyphyletic. The great species diversity of anthomyiid flies limits the availability of mitogenomes for accurately resolving the phylogeny of Anthomyiidae. Nonetheless, our study provides novel insight into the molecular taxonomy, evolution, and phylogeny of the family Anthomyiidae.