Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite Toad (Anaxyrus canorus)
Data files
Nov 29, 2022 version files 283.64 MB
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README.txt
38.31 KB
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YOTOAD_CLIMATE_ADAPTATION.zip
283.60 MB
Abstract
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.
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 < 30 km apart
- Aggregated FST 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