Data from: Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders

Closely related taxa with dissimilar morphologies are often considered to
have diverged via natural selection favoring different phenotypes.
However, some studies have found these scenarios to be paired with limited
or no genetic differentiation. Desmognathus quadramaculatus and D.
marmoratus are sympatric salamander species thought to represent a case of
ecological speciation based on distinct morphologies, but the results of
previous studies have not resolved corresponding patterns of lineage
divergence. Here, we use genome-wide data to test this hypothesis of
ecological speciation. Population structure analyses partitioned
individuals geographically, but not morphologically, into two adjacent
regions of western North Carolina: Pisgah and Nantahala. Phylogenetic
analyses confirmed the nominal species are non-monophyletic and resolved
deep divergence between the two geographic clusters. Model-testing
overwhelmingly supported the hypothesis that lineage divergence followed
geography. Finally, ecological niche modeling showed that Pisgah and
Nantahala individuals occupy different climatic niches, and geographic
boundaries for the two lineages correspond to a difference in
precipitation regimes across southern Appalachia. Overall, we reject the
previous hypothesis of ecological speciation based on microhabitat
partitioning. Instead, our results suggest that there are two cryptic
lineages, each containing the same pair of morphotypes.