Evolutionary history of Ridge-nosed Rattlesnakes (Crotalus willardi): A specialized and diverse montane species

Mountain organisms often exhibit complex distributions, patterns of variation, and evolutionary histories due to the topographical, climatic, and orogenic complexity of the areas in which they occur. Many montane taxa, however, lack the detailed sampling across space and the genome required to characterize diversity or estimate key evolutionary parameters. Here, we leverage comprehensive sampling, genome-wide data, and a draft genome assembly to investigate patterns of diversity and evolutionary history within a widespread but poorly studied snake, the Ridge-nosed Rattlesnake (Crotalus willardi), that inhabits the montane pine-oak woodlands in the Sierra Madre Occidental and Madrean Archipelago. We test for population genetic structure, measure gene flow and admixture between populations, and estimate phylogenetic history and divergence times among groups. We find substantial genetic structure, with up to seven differentiated populations, only three of which correspond with existing subspecific taxonomy. We identify one putative recent admixture event as well as evidence of historical gene flow among populations. We find that southern populations are generally older than those currently occurring in the Madrean Archipelago, which diverged within the last 0.6 million years. Together, our results reveal that current taxonomy fails to capture the substantial diversity and complex evolutionary processes at work in this species of montane snake and suggest that high-resolution sampling is crucial to understanding the biotic history of complex montane regions.