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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

Data files

Oct 22, 2024 version files 83.08 MB

Abstract

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.