First mitochondrial genomes of the crane fly tribe Elephantomyiini (Diptera, Tipuloidea, Limoniidae): comparative analysis and phylogenetic implications

Abstract

Limoniidae, the most speciose family in the superfamily Tipuloidea, consists of four subfamilies and more than 11,000 species. However, mitochondrial (mt) genome sequences, which have been widely used for phylogenetic study, are available for only 11 species across three subfamilies. Thus, a larger variety of mt genome sequences in Limoniidae are required to improve our understanding of tipuloid phylogeny and genomic evolution. Here we present mt genomes of Elephantomyia (Elephantomyia) inulta Alexander, 1938 and Helius (Helius) pluto Alexander, 1932, representing the first mt genomes of the tribe Elephantomyiini (Limoniidae). The two mt genomes are typical circular DNA molecules and show similar gene order, nucleotide composition and codon usage. Standard ATN start and TAR stop codons are present in most protein-coding genes. All transfer RNA (tRNA) genes exhibited the cloverleaf secondary structure typical for metazoans except in tRNASer(AGN), which lacks the dihydrouridine arm. Phylogenetic analyses were performed based on four nucleotide matrixes for the currently sequenced species of Tipuloidea using Bayesian inference and maximum likelihood methods. Four-cluster likelihood mapping was used to study incongruent signals between different topologies. Pediciidae is supported as the earliest lineage in Tipuloidea, and the sister-group relationship between Cylindrotomidae and Tipulidae is also supported, but the monophyly of Limoniidae is not supported. Our study also supports the monophyly of Elephantomyiini (Elephantomyia + Helius), as one of origins of flower-visiting in Limoniidae. Although Elephantomyiini is sister to Limoniinae + Epiphragma (Limnophilinae) in our study, a more precise understanding of its phylogenetic position in Tipuloidea will require additional studies that include a broader species sample.