Data from: Genomic vulnerability of a sentinel mammal under climate change

We collected genome-wide data (29,709 SNPs) from 363 individuals spanning the entire range in western North America and employed genotype-environment association analyses to identify 938 robust outlier SNPs, several of which were linked to genes previously associated with high elevation and hypoxia responses in various pika species (Ochotonidae). Adaptive genomic variation was most strongly influenced by mean warmest month temperature, followed by precipitation of the coldest quarter.

Spatial patterns of genomic offset were heterogeneous, significantly predicted by levels of adaptive genetic variation, elevation and latitude. Sites within the Northern Rocky Mountains exhibited the highest genomic offset under projected climate change despite possessing high levels of adaptive genetic variation. As such, while our study provides an example of how genomic data can be used to explore the potential consequences of climate change, it further highlights the need for careful consideration of genomic offset values within their proper ecological context.

Methods

VCF: folder of VCF files of the full dataset used for outlier detection (363_29709.vcf), the robust outlier dataset of 924 SNPs (363_924.recode.vcf), and the shuffled dataset of 924 robust outlier SNPs (363_924_shuffled.vcf) indv_info_update.txt: Text file of individual metadata used in R analyses site_info.txt: Text file of site metadata used in the R analyses Rcode_SchmidtRussello: R code used for data analysis