Saltational episodes of reticulate evolution in the jumping pomace fly Drosophila saltans species group

Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of investigation. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. 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 whole genome data and to individual loci. We used four strategies, two of which consisted of windows from pseudo-reference genomes aligned to either an outgroup or ingroup species, and two based on our new assemblies using either conserved genes or [≥]50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed [~]7% of the blocks in the most conflicting species quartets. High incidences of low phylogenetic resolution (polytomy) were restricted to three nodes on the tree, that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.