Saltational episodes of reticulate evolution in the jumping pomace flyDrosophila saltansspecies group

Abstract

AbstractPhylogenomics revealed reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power (soft polytomy) or true evolutionary patterns (hard polytomy) remains a field of investigation. Here, we investigate the phylogeny and quantify reticulation in theDrosophila saltansspecies group, a Neotropical clade of the subgenusSophophoracomprising 23 species arranged in five subgroups, namelycordata,elliptica,parasaltans,saltansandsturtevanti, whose relationships have long been problematic. We sequenced and assembled the genomes of 15 species. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no “true” species tree could be inferred, and applied our new test (called 2A2B) to ≥50 kb-long 1,797 syntenic blocks with conserved collinearity across NeotropicalSophophora. High incidences of reticulation (sometimes up to 90% of the blocks) were restricted to three nodes on the tree, at the split between thecordata-elliptica-saltanssubgroups and at the origin of thesturtevantiandsaltanssubgroups. By contrast, cases with asymmetric discordances, which are often interpreted as evidence for interspecific introgression, did not exceed ∼5% of the blocks. Historical biogeography analysis revealed that short inter-speciational times and greater overlap of ancestral geographical ranges partly explain cases with predominant reticulation. Therefore, episodic rapid radiations have played a major role in the evolution of this largely understudied Neotropical clade.