Characterization of the Complete Mitogenomes of Four Dacinae Species (Diptera: Tephritidae) with Phylogenetic Analysis

TL;DR

This study sequenced and analyzed the complete mitochondrial genomes of four fruit fly species to better understand their evolutionary relationships and phylogenetic structure.

Contribution

The study provides the first complete mitogenomes for four Gastrozonini species and offers insights into Dacinae phylogeny.

Findings

The four mitogenomes each contain 37 mitochondrial genes and an A+T-control region with high AT content.

Phylogenetic analyses support the monophyly of Dacinae and the grouping ((Ceratitidini + Gastrozonini) + Dacini).

Newly sequenced mitogenomes robustly form a clade representing Gastrozonini with strong support.

Abstract

Dacinae comprises over 1400 species and 51 genera divided into three tribes, including Ceratitidini, Dacini, and Gastrozonini. Dacine fruit flies are frugivorous insects that represent a diverse and economically significant group, widely recognized as a notorious major agricultural pest. Mitochondrial genomic data provide powerful tools for elucidating the phylogenetic relationships within Dacinae and offering deeper insights into the evolutionary history of its major lineages. In this study, we presented the complete mitochondrial genomes of four species including Acroceratitis separata, Acrotaeniostola quadrivittata, Gastrozona parviseta, and Paragastrozona vulgaris from the tribe Gastrozonini. These mitogenomes displayed conserved structural and compositional features consistent with those observed in other fully sequenced dacine genomes. We reconstructed the phylogenetic relationships within Dacinae, indicating robust support for the monophyly of this group. This research substantially expands the available mitogenomic data, thereby enhancing our comprehension of the evolutionary trajectories and phylogenetic structure within the Dacinae.

To enhance our understanding of the phylogenetics and evolutionary processes within Dacinae, we sequenced and analyzed four complete mitogenomes for the first time, specifically Acroceratitis separata, Acrotaeniostola quadrivittata, Gastrozona parviseta, and Paragastrozona vulgaris, which represent Gastrozonini species. Our results indicated that these four mitogenomes, including A. separata, A. quadrivittata, G. parviseta, and P. vulgaris, comprised 37 mitochondrial genes and an A+T-control region, with a total length of 16,603 bp, 16,112 bp, 16,691 bp, and 16,594 bp, revealing a notably high AT content reaching 77.4%, 78.4%, 75.1%, and 75.1%, respectively. Our phylogenetic analyses using Bayesian inference and Maximum Likelihood methods under site-homogeneous models consistently demonstrated their superiority over the site-heterogeneous mixture model CAT + GTR, given the currently accepted phylogenetic framework. Apart from a few species demonstrating unstable placements, the inferred phylogenetic relationships among the three tribes were strongly supported as monophyletic groups, with the topology represented as ((Ceratitidini + Gastrozonini) + Dacini), and most branches displaying moderate-to-high support values, of which four newly sequenced mitogenomes and A. dissimilis robustly formed a single clade representing Gastrozonini. This study substantially augments the existing mitogenome data, thereby providing more profound insight into the evolutionary history and higher-level phylogenetic structure within the Dacinae.

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