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: English
• Published: Dryad 2019
• Subjects: FOS Biological sciences; Ice Sheet
• Online Access: https://dx.doi.org/10.5061/dryad.xsj3tx99h; http://datadryad.org/stash/dataset/doi: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 throughout its range. Recent phylogeographic work has demonstrated that Pleistocene toad lineages diverged and then admixed to differing extents across an elevational gradient. Although lineage divisions may have significant effects on evolutionary trajectories over large spatial and temporal scales, present-day population dynamics must be delineated in order to manage and conserve the species effectively. In this study, we used a double-digest RADseq dataset to address three primary questions: (1) Are single meadows or neighborhoods of nearby meadows most correlated with population boundaries? (2) Does asymmetrical migration occur among neighborhoods of nearby meadows? (3) What topographic or hydrological variables predict such asymmetrical migration in these meadow neighborhoods? Hierarchical STRUCTURE and AMOVA analyses suggested that populations are typically circumscribed by a single meadow, although 84% of meadows exist in neighborhoods of at least two meadows connected by low levels of migration, and over half (53%) of neighborhoods examined display strong asymmetrical migration. Meadow neighborhoods often contain one or more large and flat “hub” meadows that experience net immigration, surrounded by smaller and topographically rugged “satellite” meadows with net emigration. Hubs tend to contain more genetic diversity and could be prioritized for conservation and habitat management and as potential sources for reestablishment efforts. ** Note: Multiple articles are associated with this dataset : Note: the python script fasta2genotype.py was used for converting raw data (STACKS fasta file) into genotype data of many formats, which were subsequently analyzed. This includes the "micro-haplotype" and phylogenetic data described in the article. GitHub repository link for the fasta2genotype.py script:https://github.com/paulmaier/fasta2genotype Please consult the README.pdf for all usage information.