Phylogenomics illuminates the complex evolutionary history of Bibionomorpha (Diptera)

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 timetree using data-driven calibration priors. Different data types and models were utilized to produce a robust backbone phylogeny. Bibionomorpha, comprising Bibionoidea, Sciaroidea, Anisopodoidea, and Scatopsoidea, 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. Phylogenetic network analysis suggests a possible reticulation event for Bolitophilidae, while mitochondrial data support a highly sex-specific hybridization event between ancestral Cecidomyiidae and Sciaridae + Diadocidiidae group. Timetree analyses suggest a Lower Triassic or deeper origin of Bibionomorpha, with implications of ancient explosive radiations.