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

Quaternary climate oscillations have profoundly influenced current species
distributions. For many montane species, these fluctuations were a
prominent driver in species range shifts, often resulting in intraspecific
diversification, as has been the case for American pikas (Ochotona
princeps). Range shifts and population declines in this
thermally-sensitive lagomorph have been linked to historical and
contemporary environmental changes across its western North American
range, with previous research reconstructing five mitochondrial DNA
lineages. 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.