DOI: 10.5061/dryad.6m905qg3r
title: Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite Toad (Anaxyrus canorus)

description: An essential goal in conservation biology is delineating population units
 that maximize the probability of species persisting into the future and
 adapting to future environmental change. However, future-facing
 conservation concerns are often addressed using retrospective patterns
 that could be irrelevant. We recommend a novel landscape genomics
 framework for delineating future “Geminate Evolutionary Units” (GEUs) in a
 focal species: (1) identify loci under environmental selection, (2) model
 and map adaptive conservation units that may spawn future lineages, (3)
 forecast relative selection pressures on each future lineage, and (4)
 estimate their fitness and likelihood of persistence using geo-genomic
 simulations. Using this process, we delineated conservation units for the
 Yosemite toad (Anaxyrus canorus), a U.S. federally threatened species that
 is highly vulnerable to climate change. We used a genome-wide dataset,
 redundancy analysis, and Bayesian association methods to identify 24
 candidate loci responding to climatic selection (R2 ranging from
 0.09–0.52), after controlling for demographic structure. Candidate loci
 included genes such as MAP3K5, involved in cellular response to
 environmental change. We then forecasted future genomic response to
 climate change using the multivariate machine learning algorithm Gradient
 Forests. Based on all available evidence, we found three GEUs in Yosemite
 National Park, reflecting contrasting adaptive optima: YF-North (high
 winter snowpack with moderate summer rainfall), YF-East (low to moderate
 snowpack with high summer rainfall), and YF-Low-Elevation (low snowpack
 and rainfall). Simulations under the RCP 8.5 climate change scenario
 suggest that the species will decline by 29% over 90 years, but the highly
 diverse YF-East lineage will be least impacted for two reasons: (1)
 geographically it will be sheltered from the largest climatic selection
 pressures, (2) its standing genetic diversity will promote a faster
 adaptive response. Our approach provides a comprehensive strategy for
 protecting imperiled non-model species with genomic data alone and has
 wide applicability to other declining species.
description: scripts All R and bash scripts necessary to
 perform the analyses, including: 
 Bioinformatic genotype filtering
 Environmental raster processing
 Genetic-environment association (GEA) analyses: bayenv2,
 RDA Annotating gene function of outlier loci using
 Yosemite toad transcriptome Modeling future natural
 selection with Gradient Forests GEU
 delimitation Predictions of future selective pressure
 by climate change Estimated levels of neutral and
 adaptive genetic diversity (including NeEstimator2)
 Geo-genomic simulations to model future lineage fitness and
 persistence Follow the primary R script,
 ToadClimateAdaptation.R data
 Directory for input data, including: 
 VCF file of 43k SNPs for 653 toads (644 Yosemite
 toad) STACKS haplotype output for 653 toads (644
 Yosemite toad) Locus length for each RAD locus (96 bp
 = R1, 101 bp = R2) List of 2039 loci
 PED/MAP format of 644 Yosemite toads with 2039 SNP
 loci Bayenv2 format of 102 Yosemite toad meadows with
 2039 loci Covariance matrix from first phase of
 bayenv2 analysis STACKS haplotype and pi summary info
 for 102 Yosemite toad meadows NeEstimator2
 input/output at meadow and meadow neigborhood scales
 Environmental data for 102 Yosemite toad populations
 rasters Current and
 future climate rasters, from WorldClim and California Basin
 Characterization Model (BCM) 
 vectors ESRI Shapefiles for the
 two national parks (YOSE and KICA), and the Yosemite toad species
 boundary hierarchy 
 Hierarchy of parks, lineages, meadow neighborhoods, meadows, and
 individuals lcp 
 Pairwise least cost paths (LCPs) between meadows &lt; 30 km
 apart Aggregated F<sub>ST</sub> surface,
 from Maier et al. 2022, Heredity 
 bayenv2 Covariance matrix from
 first phase of bayenv2 analysis Output from 10
 replicates of bayenv2 analysis (second phase) 
 blast FASTA format of RADseq
 loci FASTA format of Yosemite toad
 transcriptome Results of blasting RAD to RAD (R1/R2
 to R1+R2), and RAD to transcriptome 
 annotation Trinotate table
 containing Yosemite toad transcriptome info 
 geonomics Rasters for natural
 selection, migration, and suitability in geo-genomic
 simulations