Mitochondrial Genomes Provide New Phylogenetic and Evolutionary Insights into Psilidae (Diptera: Brachycera)

Simple Summary Members of Psilidae are commonly known as rust flies. They constitute the largest family of Diopsoidea, with about 340 species being known worldwide. Several species of Psilidae show agricultural significance due to their severe damage of root crops. However, the systematic relationships and intrafamilial classification of Psilidae remained controversial. To provide further information on the phylogeny and evolution of Psilidae, mitogenomes of 6 psilid species are sequenced. Comparative analyses of the 6 newly obtained mitogenomes are conducted. Phylogenetic analyses based on the 6 psilid mitogenomes and public data are carried out, resulting in a monophyletic Psilidae and a non-monophyletic Diopsoidea. The sister relationship between Psilinae and Chylizinae is highly supported. This study provides several new insights into the phylogeny and evolution of Psilidae. Psilidae (Diptera: Brachycera) is a moderate-sized family currently placed in the superfamily Diopsoidea and contains some destructive agricultural and forestry pests. The systematic position and intrafamilial classification of rust flies are in need of further study, and the available molecular data of Psilidae are still limited. In this study, we present the mitochondrial genomes of 6 Psilidae species (Chamaepsila testudinaria Wang and Yang, Chyliza bambusae Wang and Yang, Chy. chikuni Wang, Loxocera lunata Wang and Yang, L. planivena Wang and Yang and L. sinica Wang and Yang). Comparative analyses show a conserved genome structure, in terms of gene composition and arrangement, and a highly Adenine plus Thymine biased nucleotide composition of the 6 psilid mitogenomes. Mitochondrial evolutionary rates vary among the 6 species, with species of Chylizinae exhibiting a slower average rate than species of Psilinae. The length, the nucleotide composition, and the copy number of repeat units of the control region are variable among the 6 species, which may offer useful information for phylogenetic and evolutionary studies of Psilidae. Phylogenetic analyses based on 4 mitogenomic datasets (AA, PCG, PCG12RNA, and PCGRNA) support the monophyly of Psilidae, and the sister relationship between Chylizinae and Psilinae, while Diopsoidea is suggested to be non-monophyletic. Our study enlightens the future application of mitogenomic data in the phylogenetic and evolutionary studies of Psilidae, based on denser taxon sampling.