A traditionally controversial taxon, the Tipulomorpha has been frequently discussed with respect to both its familial composition and relationships with other Nematocera. The interpretation of internal relationships within the Tipuloidea, which include the Tipulidae sensu stricto, Cylindrotomidae, Pediciidae and Limoniidae, is also problematic. We sequenced the first complete mitochondrial (mt) genome of Symplecta hybrida (Meigen, 1804), which belongs to the subfamily Chioneinae of family Limoniidae, and another five nearly complete mt genomes from the Tipuloidea. We did a comparative analysis of these mt genomics and used them, along with some other representatives of the Nematocera to construct phylogenetic trees. Trees inferred by Bayesian methods strongly support a sister-group relationship between Trichoceridae and Tipuloidea. Tipulomorpha are not supported as the earliest branch of the Diptera. Furthermore, phylogenetic trees indicate that the family Limoniidae is a paraphyletic group.

Nematocera (lower Diptera) is a taxonomically diverse group with ~52 000 species in 40 families, including many important agricultural and sanitary pests. The number and composition of nematoceran infraorders have long been subject to debate. The use of mitochondrial genomes for resolving these questions shows considerable promise. Herein, we sequenced and annotated the complete or nearly complete mitochondrial genomes of eight nematoceran species from seven families, representing the first mitochondrial genomes of two infraorders and six families. They range in size from 14 447 to 16 255 bp and all contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and an AT-rich region. Like other nematocerans, the arrangement of genes of their mitochondrial genomes is identical to the presumed ancestral arrangement. A phylogenetic analysis was conducted by using mitochondrial genomes of 116 representatives from Diptera, Mecoptera and Siphonaptera. Our phylogenetic results support both new and traditional arrangements. The small, highly specialized family Deuterophlebiidae appears to be sister to all remaining Diptera, while Nymphomyiidae and Blephariceridae are nested within Culicomorpha and Psychodomorpha, respectively; hence, the recognition of ‘Blephariceromorpha’ as a valid monophyletic infraorder is discouraged. Anisopodidae is supported as the sister group of Brachycera.

This study determined the complete mitochondrial (mt) genome of the stonefly, Kamimuria chungnanshana Wu, 1948. The mt genome is 15, 943 bp in size and contains 37 canonical genes which include 22 transfer RNA genes, 13 protein-coding genes, and two ribosomal RNA genes, the control region is 1062 bp in length. The phylogenetic tree shows that Kamimuria chungnanshana is sister group of Kamimuria wangi.