River drainage reorganization, ancient hybridization, and the phylogeography of the two-lined salamander (Eurycea bislineata) species complex

Genome-scale data have revealed the ubiquity of reticulate evolutionary histories across diverse organisms. Especially for species with weak dispersal abilities, the repeated origin and loss of major biogeographic barriers may create alternating periods of isolation and secondary contact, enabling gene flow between previously independently evolving metapopulations. Previous research on the two-lined salamander (Eurycea bislineata) species complex demonstrated the strong correspondence between paleodrainage basins and mitochondrial DNA gene trees. However, due to the limitations imposed by a single-locus dataset, the role of drainage reorganization in initiating secondary contact and gene flow could not be assessed. Here, we generate triple-enzyme restriction site-associated DNA sequencing (3RAD) data for >100 individuals representing all major mtDNA lineages and use a suite of complementary phylogenomic methods to demonstrate that discordance among earlier morphological, allozyme, and mitochondrial DNA datasets is best explained by a reticulate evolutionary history in the E. bislineata species complex. Most of the ancient hybridization events that we infer occurred in regions with particularly dynamic histories of river drainage reorganization, and we cautiously discuss how specific hypotheses of drainage evolution may be concordant with our results.