Data from: Evidence of intraspecific adaptive variation in the American pika (Ochotona princeps) on a continental scale using a target enrichment and mitochondrial genome skimming approach

Montane landscapes present an array of abiotic challenges that drive
adaptive evolution among organisms. These adaptations can promote habitat
specialization, which may heighten the risk of extirpation from
environmental change. For example, higher metabolic rates in an
endothermic species may contribute to heightened cold tolerance, while
simultaneously limiting heat tolerance. Here, using the climate-sensitive
American pika (Ochotona princeps), we test for evidence of intraspecific
adaptive variation among environmental gradients across the Intermountain
West of North America. We leveraged results from previous studies on pika
adaptation to generate a custom nuclear target enrichment design to
sequence several hundred candidate genes related to cold, hypoxia, and
dietary detoxification. We also applied a ‘genome skimming’ approach to
sequence mitochondrial DNA. Using genotype-environment association tests,
we identified rare genomic variants associated with elevation and
temperature variation among populations. Among mitochondrial genes, we
identified intraspecific variation in selective signals and significant
changes to the amino acid property equilibrium constant, which may relate
to electron transport chain efficiency. These results illustrate a complex
dynamic of adaptive variation among O. princeps where lineages and
populations have adapted to unique regional conditions. Some of the
clearest signals of selection were in a genetic lineage that includes
pikas of the Great Basin region, which is also where recent localized
extirpations have taken place and highlights the risk of losing adaptive
alleles during environmental change.