Fig 1. Cladogram of drosophilid species with whole-genome data, with some groups collapsed (gray triangles).

Species relationships were inferred from 1,000 orthologs (see Methods). Node values are the local posterior probabilities reported by ASTRAL-MP [26]. Counts of described species for each group were obtained from the TaxoDros database [22]. Values in the colored boxes indicate, as of August 2023, the number of species with whole-genome sequences for each taxon. The count of short-read and long-read datasets, and data available before this study (including [8]) and new genomes presented here are shown separately. *Note that Scaptodrosophila, Hirtodrosophila, Zaprionus, immigrans, and histrio groups are potentially rendered polyphyletic by these samples. The positions of nigrosparsa and pinicola groups are currently considered to be uncertain. The data underlying this figure can be found in https://doi.org/10.5281/zenodo.11200891.