Timing and Pattern of Early Diversification in Drosophilidae (Diptera)

Despite their relevance as model organisms, the early diversification patterns in Drosophilidae remain poorly resolved, with most studies focusing on Drosophila. Here, we employed a phylogenomic framework for 33 taxa: 27 drosophilid species representing most tribes of both subfamilies (Drosophilinae and Steganinae) plus 6 taxa from other families of Ephydroidea (Braulidae, Cryptochetidae, Curtonotidae, and Ephydridae). Besides inferring phylogenetic relationships, we estimated divergence times and substitution rates using a fossil-calibrated Bayesian approach. Our results recover Drosophilinae as monophyletic (among the taxa sampled) but place Braula coeca (Braulidae) within Steganinae, rendering Drosophilidae nonmonophyletic and underscoring the need for taxonomic revision. Relationships within Steganinae (including Braula) were fully resolved, whereas the position of some Drosophilinae lineages (eg Scaptodrosophila) remains uncertain, likely due to extensive gene tree heterogeneity. Divergence time estimates suggest that the family originated near the Cretaceous-Paleogene boundary (67.3 Ma; 95% highest posterior density: 83 to 52 Ma), with subfamilies diversifying primarily during the Eocene (56 to 34 Ma). The neutral evolutionary rate, estimated from fossil calibrations and third codon positions, aligns with previous biogeographically calibrated estimates but is lower than mutation-derived rates, likely reflecting the action of purifying selection and uncertainty about generation times across lineages.