Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite Toad (Anaxyrus canorus)

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 can..., , 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 phas...