Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

• Main Authors: Maier, Paul A., Vandergast, Amy G., Ostoja, Steven M., Aguilar, Andres, Bohonak, Andrew J.
• Format: Dataset
• Language: unknown
• Published: 2022
• Subjects: Bufo canorus; Anaxyrus; Phylogeography; fastsimcoal2; lineage discovery; lineage introgression; Pleistocene; population genetics; gene pools; hierarchical structure; asymmetrical gene flow; Isolation By Distance (IBD); landscape genetics; climate change; range shift; machine learning; Random Forests; ResistanceGA; least cost path; Least-cost corridor; gene flow; emigration; immigration; Ice Sheet
• Online Access: https://zenodo.org/record/4989342; https://doi.org/10.5061/dryad.xsj3tx99h

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus) Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this "glacial pulse" model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including novel admixed ("fused") lineages. We tested for patterns of glacial pulse lineage diversification in the Yosemite toad (Anaxyrus [Bufo] canorus), an alpine endemic tied to glacially influenced meadow environments. Using double-digest RADseq on populations densely sampled from a portion of the species range, we identified nine distinct lineages with divergence times ranging from 18–724 ka, coinciding with multiple Sierra Nevada glacial events. Three lineages have admixed origins, and demographic models suggest these fused lineages have persisted throughout past glacial cycles. Directionality indices supported the hypothesis that some lineages recolonized Yosemite from east of the ice sheet, whereas other lineages remained in western refugia. Finally, refugial niche reconstructions suggest that low- and high-elevation lineages have convergently adapted to similar climatic niches. Our results suggest glacial cycles and refugia may be important crucibles of adaptive diversity across deep evolutionary time. Gene pool boundaries for the Yosemite toad (Anaxyrus canorus) reveal asymmetrical migration within meadow neighborhoods The Yosemite toad (Anaxyrus [Bufo] canorus) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well documented, and is reputed to remain in low abundance ...