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 ..., 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., , # README: Data from: Phylogenomics of American pika (*Ochotona princeps*) lineage diversification

1. **Author Information:**
Name: Danielle Schmidt
Institution: The University of British Columbia, Kelowna, British Columbia, Canada

Name: Dr Kurt Galbreath
Institution: Northern Michigan University, Marquette, MI, USA

Name: Dr Michael Russello
Institution: The University of British Columbia, Kelowna, British Columbia, Canada
Email: [[e-mail]](mailto:[e-mail])

2. **Suggested citation:** Schmidt, Danielle; Galbreath, Kurt; Russello, Michael (2023), Data from: Phylogenomics of American pika (*Ochotona princeps*) lineage diversification, Dryad, Dataset, [https://doi.org/10.5061/dryad.vq83bk3vs](https://doi.org/10.5061/dryad.vq83bk3vs)

#### File List/Information

* 12pika_21565_nomiss.recode.vcf: vcf file of the 21565 SNPs identified across the 12 individual samples in the interspecific dataset used to rconstruct the phylogeneti...