Mitochondrial phylogenomics and genome rearrangement in Hymenoptera using an expanded taxon sample

The Hymenoptera is one of the most species-rich insect orders, with more than 150,000 described extant species. Many hymenopteran insects have very different mitochondrial genome organizations compared with the putative ancestral organization of insects. In this study, we newly sequenced 18 mitogenomes of Hymenoptera to improve the taxonomic sampling. A total of 475 species were used in phylogenetic analyses, including 18 new mitogenomes and 457 existing mitogenomes. Bayesian inference from amino acid data using the site-heterogeneous model provided the better resolved relationships of Hymenoptera when compared with Maximum likelihood analysis and the coalescent-based species analysis. The Symphyta was supported as a paraphyletic assemblage. The Xyeloidea was the earliest branching clade in Hymenoptera. The Orussoidea was closely related to Apocrita. Within Apocrita, the Parasitoida was non-monophyletic. The monophyly of most Parasitoida superfamilies was well supported. The Proctotrupomorpha was recovered in Bayesian analysis. The Apoidea was monophyletic if Ampulex compressa was excluded from consideration. The superfamilies Vespoidea and Chrysidoidea were non-monophyletic. Comparisons of mitochondrial gene order showed that the lineages with the parasitoid mode of life such as those in the Proctotrupomorpha have the highest frequency of gene rearrangement, followed by Ichneumonoidea and Pompiloidea.