Mitochondrial phylogenomics reveals the evolutionary and biogeographical history of fruit flies Diptera: Tephritidae

Tephritidae is one of the largest families of Diptera, with high diversity and a wide global distribution, and includes numerous important agricultural pests. However, the origin, phylogeny, and evolutionary history remain poorly understood. We undertook the first comprehensive mitogenomic study covering phylogenetic reconstruction, divergence time estimation, and historical biogeography analyses by analyzing 147 mitochondrial genomes representing three sub-families, seven tribes, 11 genera, and 82 species. Within the Dacini subfamily, our phylogeny strongly supported the sister group relationship of (Zeugodacus + Dacus) + Bactrocera, which further supported to the elevation of Zeugodacus to the generic level of Dacini. On the other hand, our molecular phylogenetic analyses did not align well with the currently recog-nized subgeneric designations within Ceratitis, Dacus, and Zeugodacus. Some subgenera were recovered as polyphyletic or paraphyletic, implying the incongruence between morphological characters and mitogenomic data. Neither the taxa within the Ceratitis FARQ complex (formerly FAR complex) nor those within the Bactrocera dorsalis complex could be clearly distinguished by mitochondrial phylogenetic trees as distinct species corresponding to the morphospecies. Divergence time estimation and historical biogeography analyses indicated that the earliest common ancestor of Tephritidae, originated in the Palaearctic realm at 138.92-71.44 Ma (million years ago), with the subsequent divergence into Dacinae + Trypetinae and Tephritinae at 115.19-67.45 Ma equally in the Palaearctic realm. Dacini might have originated in Laurasia rather than Gondwana, and diverged into Bactrocera and Dacus + Zeugodacus at 48.43-28.70 Ma after the India plate docked with Laurasia.