Phylogenomics illuminates the complex evolutionary history of Bibionomorpha (Diptera)

Abstract Bibionomorpha is a large and diverse dipteran infraorder, of which its composition and family‐level relationships have long been debated. In this study, we constructed a phylogenomic tree of Bibionomorpha using an extensive dataset of transcriptomic, genomic and anchored hybrid enrichment data. To further investigate the evolutionary timeline of the group, we also generated a fossil‐calibrated time tree using data‐driven calibration priors. Bibionomorpha, comprising Anisopodoidea, Bibionoidea, Scatopsoidea and Sciaroidea, is recovered as the sister group to Brachycera. Axymyiidae and Perissommatidae, which have been considered part of Bibionomorpha by some authorities, are instead recovered as sister to the Bibionomorpha + Brachycera. We discuss recalcitrant nodes within the infraorder, particularly regarding the placements of Bolitophilidae and Cecidomyiidae. Although tentative, phylogenetic network analysis suggests a possible reticulation event leading to Bolitophilidae, while mitochondrial data support a sex‐specific hybridization event between ancestral Cecidomyiidae and Sciaridae + Diadocidiidae group. Time tree analyses suggest a Lower Triassic or deeper origin of Bibionomorpha, consistent with fossil evidence.