Data from: 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.