Data from: Phylogenomics of American pika (Ochotona princeps) lineage diversification

Here, we paired genome-wide data (25,244 SNPs) with range-wide sampling to re-examine the number and distribution of intra-specific lineages, and investigate patterns of within- and among-lineage divergence and diversity. Our results provide genomic evidence of O. princeps monophyly, reconstructing six distinct lineages that underwent multiple rounds of divergence (0.809-2.81mya), including a new Central Rocky Mountain lineage.

We further found evidence for population differentiation across multiple spatial scales, and reconstructed levels of standing variation comparable to those found in other small mammals. Overall, our findings demonstrate the influence of past glacial cycles on O. princeps lineage diversification, suggest that current subspecific taxonomy may need to be revisited, and provide an important framework for investigations of American pika adaptive potential in the face of anthropogenic climate change.

Methods

Date of data collection: 2014-2020. Restriction site-associated DNA sequencing (RADseq) following Baird et al. (2008) processed using the Stacks workflow. Short-read DNA sequencing data can be accessed via Genbank SRA Bioproject PRJNA1075342.