DOI: 10.5061/dryad.1ns1rn90b
title: Data from: Phylogenomics of American pika (Ochotona princeps) lineage diversification

description: 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.
description: 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.
description: # 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:
 [michael.russello@ubc.ca](mailto:michael.russello@ubc.ca) 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 phylogenetic relationships across the 7 included pikas species. * 12pika_21565_nomiss.nex: Nexus formatted file used as input for the SVDquartets analysis performed on the interspecific dataset * 363_25244.recode.vcf: vcf file of the 25244 neutral SNPs identified across the 363 American pika iindividuals retained in this study for use in population genomic analyses. * 366_2401.nex: nexus format file used as input for the intraspecific phylogenetic analysis run on the 363 American pika individuals and 3 collared pika samples included in this dataset * paup_block_exhaustive.txt: paup block commands for the SVDquartets analysis for the initial instrapscific phylogeny reconstruction. * paup_block_exhaustive_1rep.txt: paup bloack commands for boostrap replicates of the SVDquartets analysis. This file was used for 10 runs of 100 bootstrap replicates * 366_2401.recode.vcf: vcf file containing the 2401 SNPs across the 363 American pika and 3 collared pika samples for the intraspecific phylogenomic analyses. * Treemix_366_pruned_2401.tremix.frq: Input file for the Treemix analysis as generated from the vcf2treemix.sh script * Treemix_366_2401.clust: cluster file for use in generating the Treemix analysis input file * jointSFS.tar.gz: gzipped folder for the jointSFS generated for the fastsimcoal2.6 analysis with the ProcessVCF_bootstrap.sh script located within the "block bootstrap and model choice.zip" file * 24bp_dist2_ind5_5_5_5_5_5_3.est: Prior parameters and rules files designated for the fastsimcoal2.6 analysis. * 24bp_dist2_ind5_5_5_5_5_5_3.tpl: Coalescent modeling parameters specified for the fastsimcoal2.6 simulations for model 1, which reflect the phylogenomic relationships reconstructed from the SNP data in the current study. Note: the mutation rate was estimated using the mammalian mutation rate as estimated in Kumar and Subramanian (2002) [2.2x10-9 per base per year] and correcting for a generation time of 2 years per generation. * sfs_24bp_dist2_ind5_5_5_5_5_5_3.pv: file of point estimates for the fastsimcoal nonparametric bootstrap analyses. These values are from the fastsimcoal run of model 1 with the overall highest composite log likelihood.