Organization of genetic and reproductive behavioral diversity in the two-lined salamander (<i>Eurycea bislineata</i>) species complex

Describing the mechanisms that generate and maintain genetic and phenotypic diversity is a central goal of evolutionary biology. This is dependent upon accurate reconstructions of evolutionary histories, which have traditionally been inferred as simple, bifurcating phylogenies. However, speciation is often neither instantaneous nor permanent, and genomic data have revealed the ubiquity of reticulate evolutionary histories across diverse organisms. This revelation has underscored the importance of understanding the causes and outcomes of ancient and modern hybridization. Here, I examine these themes by studying the distribution of genetic and reproductive behavioral diversity in the two-lined salamander (Eurycea bislineata) species complex—a group of plethodontid salamanders. First, I use a phylogenomic methods with dataset of > 2 million SNPs from > 120 individuals to demonstrate the importance of river drainage reorganization in the reticulate evolutionary history of the group. Next, I use population genomic methods and a dataset of > 9,000 SNPs from 330 individuals in replicate contact zones to demonstrate reproductive isolation and fine-scale ecological segregation between two sympatric species. Finally, I use a genomic, behavioral, and field observational data to demonstrate the existence of alternative reproductive tactics within three putative species in the group and comment more broadly on variation in reproductive behavior. Together, these results demonstrate previously unrecognized genetic and behavioral variation in the E. bislineata species complex and describe the mechanisms—from large-scale geologic change to fine-scale ecological gradients—responsible for its organization.