Divergence and introgression among the virilis group of Drosophila

Abstract

Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains 12 species that are geographically widespread and show varying levels of prezygotic and postzygotic isolation. Here, we use de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and desiccation tolerance, and may be related to the evolution of sexual isolation and adaptation. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and more recent gene flow between closely related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome as has been found in other systems. Our results show how ancient and recent introgressions confuse phylogenetic reconstruction, but may play an important role during early radiation of a group.

Saltational episodes of reticulate evolution in theDrosophila saltansspecies group

“…Both approaches helped us to define signals of reticulate evolution that were not homogeneously distributed across the subgroups. (Mai et al 2020;Khallaf et al 2021;Suvorov et al 2022;Yusuf et al 2022) Perhaps the most striking outcome of our synteny-based analysis is the low incidence of interspecific introgression compared to recent analyses across the genus Drosophila suggesting introgression to be widespread (Suvorov et al 2022). Whether this discrepancy is due to the size of the analyzed loci or reflect genuine differences between the saltans group and other Drosophila clades would require the extension of the 2A2B test to these clades.…”

“…A large number of Drosophila genomes have been sequenced and used in phylogenetic analyses (Suvorov et al 2022; Khallaf et al 2021; Kim et al 2021; Li et al 2022), but studies with comprehensive sampling of nearly all species in a group remain relatively uncommon (Mai et al 2020; Conner et al 2021; Yusuf et al 2022; Moreyra et al 2023). Despite minor inconsistencies, our phylogenomic analysis of 15 species of the Drosophila saltans species group produced a consistent picture of the relationships between the five subgroups of this clade.…”

“…Both approaches helped us to define signals of reticulate evolution that were not homogeneously distributed across the subgroups. (Mai et al 2020; Khallaf et al 2021; Suvorov et al 2022; Yusuf et al 2022)…”

Characterization of clock‐related proteins and neuropeptides in Drosophila littoralis and their putative role in diapause

“…(a) Simplified phylogenetic tree demonstrating the relationship of the virilis group to D. melanogaster after Yusuf et al. (2022). (b) Expression of selected neuropeptides in the brain of D. melanogaster .…”

“…F I G U R E 1 Phylogeny of the virilis group, and neuropeptide expression in clock-and diapause-related cells in D. melanogaster brain. (a) Simplified phylogenetic tree demonstrating the relationship of the virilis group to D. melanogaster after Yusuf et al (2022). (b) Expression of selected neuropeptides in the brain of D. melanogaster.…”