DOI: 10.5061/dryad.xsj3tx99h
title: Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

description: 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.   Landscape genetics of a
 sub-alpine toad: Climate change predicted to induce upward range shifts
 via asymmetrical migration corridors Climate change is expected to have a
 major hydrological impact on the core breeding habitat and migration
 corridors of many amphibians in the 21st century. The Yosemite toad
 (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic
 to the high-elevation Sierra Nevada Mountains of California. Despite
 living entirely on federal lands, it has recently faced severe
 extirpations, yet our understanding of climatic influences on population
 connectivity is limited. In this study, we used a previously published
 double-digest RADseq dataset along with numerous remotely sensed habitat
 features in a landscape genetics framework to answer two primary questions
 in Yosemite National Park: (1) Which fine-scale climate, topographic,
 soil, and vegetation features most facilitate meadow connectivity? (2) How
 is climate change predicted to influence both the magnitude and net
 asymmetry of genetic migration? We developed an approach for
 simultaneously modeling multiple toad migration paths, akin to circuit
 theory, except raw environmental features can be separately considered.
 Our workflow identified the most likely migration corridors between
 meadows and used the unique cubist machine learning approach to fit and
 forecast environmental models of connectivity. We identified the permuted
 modeling importance of numerous snowpack-related features, such as runoff
 and groundwater recharge. Our results highlight the importance of
 considering phylogeographic structure, and asymmetrical migration in
 landscape genetics. We predict an upward elevational shift for this
 already high elevation species, as measured by the net vector of
 anticipated genetic movement, and a north-eastward shift in species
 distribution via the network of genetic migration corridors across the
 park.   ** Note: Multiple articles are associated with this
 dataset
description: 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:<br>https://github.com/paulmaier/fasta2genotype
 Please consult the README.pdf for all usage
 information.