Assemblies, supermatrices, and raw tree files of the manuscript entitled "Phylogenomics ends the two-subfamilies era in the Drosophilidae"

The family Drosophilidae is a significant and highly diverse branch in the order Diptera. In contrast, its origin and early evolutionary history remain systematically unresolved, with non-Drosophilinae subfamily taxa being roughly classified into the Steganinae subfamily for over a century. Recently released genome of <i>Braula</i> <i>coeca</i> Nitzsch, 1818(blind bee louse fly) and its close phylogenetic relationship with the Steganinae have provided new insights while also causing new confusion. In this study, we propose that certain lineages within the traditional Steganinae, characterized by longer evolutionary histories, more restricted distributions, and larval predation on specific sternorrhynchans, be divided into a new subfamily, Rhinoleucophenginae <b>subf.</b> <b>nov.</b>These lineages, along with the rest of Steganinae (defined as new Steganinae), the downgraded Braulinae <b>stat.</b> <b>nov.</b>, and the Drosophilinae, form a four-subfamily systematics framework within the Drosophilidae, with the connection forms between the surstyli and the epandrium in male terminaliaas a taxonomic diagnosis for subfamily classification. The subgenus Parastegana(Allstegana) is also elevated to the genus-level as Allstegana <b>stat.</b> <b>nov.</b> The diversification of the Drosophilidae began approximately 36.66 million years ago (mya), with early divergences primarily occurring in the early Oligocene epoch of the Paleogene period closely associated with dietary evolution. Additionally, it is highly probable that the new Steganinae originated from the Oriental region, whereas the radiation of Drosophilidae lineages during the early to mid-Neogene period is closely related to the uplift of the Hengduan Mountains and the intensification of monsoonal activities. Through an in-depth analysis of the phylogenomicswithin the superfamily Ephydroidea and the traditional Steganinae (defined as old Steganinae), we not only proposed a novel phylogenetic framework at the subfamily-level for the Drosophilidae, but also uncovered the complexity of the early evolutionary history of the Drosophilidae, where orogeny, monsoonal activities, dietary evolution, and reproductive isolation likely play crucial roles in shaping its diversity and radiation. Our findings provide new insights into the early evolutionary history, phylogenetic framework, biogeography, and evolutionary biology of the Drosophilidae, laying the groundwork for future efforts to further clarify the boundaries of the Drosophilidae and to explore the historical backgrounds and environmental factors driving the rapid radiation of the new Steganinae and the Drosophilinae.