DOI: 10.5061/dryad.2bvq83bzf
title: Data from: Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

description: Improved understanding of the genetic basis of adaptation to climate
 change is necessary for maintaining global biodiversity moving forward.
 Studies to date have largely focused on sequence variation, yet there is
 growing evidence that suggests that changes in genome structure may be an
 even more significant source of adaptive potential. The American pika
 (Ochotona princeps) is an alpine specialist that shows some evidence of
 adaptation to climate along elevational gradients, but previous work has
 been limited to single nucleotide polymorphism (SNP)-based analyses within
 a fraction of the species range. Here, we investigated the role of copy
 number variation underlying patterns of local adaptation in the American
 pika using genome-wide data previously collected across the entire species
 range. We identified 37-193 putative copy number variants (CNVs)
 associated with environmental variation (temperature, precipitation, solar
 radiation) within each of the six major American pika lineages, with
 patterns of divergence largely following elevational and latitudinal
 gradients. Genes associated (n=158) with independent annotations across
 lineages, variables, and/or CNVs had functions related to mitochondrial
 structure/function, immune response, hypoxia, olfaction, and DNA repair,
 some of which have been previously linked to putative high elevation
 and/or climate adaptation that may serve as important targets in future
 studies.
description: This research made use of previously archived short-read
 sequencing data deposited in the NCBI sequence read archive (BioProject
 ID: PRJNA1075342).
description: # Data from: Putative climate adaptation in American pikas (*Ochotona
 princeps*) is associated with copy number variation across environmental
 gradients Suggested citation: Sjodin, Bryson; Schmidt, Danielle;
 Galbreath, Kurt; Russello, Michael (2024), Data from: Putative climate
 adaptation in American pikas (*Ochotona princeps*) is associated with copy
 number variation across environmental gradients, Dryad, Dataset,
 [https://doi.org/10.5061/dryad.2bvq83bzf](https://doi.org/10.5061/dryad.2bvq83bzf) ## FILE LIST/INFORMATION **NRM_filtered.vcf.gz:** gzipped VCF file of 150978 SNPs (post-filtering) identified across 76 individual samples in the Northern Rocky Mountains (NRM) lineage. Individual IDs follow the format of SampleSite_SampleID. **NRM_snp_categorization.csv:** comma-separated file of summary statistics and categorizations of 150978 SNPs identified across 76 individual samples in the Northern Rocky Mountains (NRM) lineage. **NRM_cnv_normalized.txt:** tab-delimited file of normalized read counts for 2208 putative CNVs identified across 76 individual samples in the Northern Rocky Mountains (NRM) lineage. Headers indicate sample (format: SampleSite_SampleID) and the first column indicates CNVs (format: ChromosomeID_Position_RADtagID). **CRM_filtered.vcf.gz:** gzipped VCF file of 60383 SNPs (post-filtering) identified across 78 individual samples in the Central Rocky Mountains (CRM) lineage. Individual IDs follow the format of SampleSite_SampleID. **CRM_snp_categorization.csv:** comma-separated file of summary statistics and categorizations of 60383 SNPs identified across 78 individual samples in the Central Rocky Mountains (CRM) lineage. **CRM_cnv_normalized.txt:** tab-delimited file of normalized read counts for 2729 putative CNVs identified across 78 individual samples in the Central Rocky Mountains (CRM) lineage. Headers indicate sample (format: SampleSite_SampleID) and the first column indicates CNVs (format: ChromosomeID_Position_RADtagID). **SRM_filtered.vcf.gz:** gzipped VCF file of 95387 SNPs (post-filtering) identified across 48 individual samples in the Southern Rocky Mountains (SRM) lineage. Individual IDs follow the format of SampleSite_SampleID. **SRM_snp_categorization.csv:** comma-separated file of summary statistics and categorizations of 95387 SNPs identified across 48 individual samples in the Southern Rocky Mountains (SRM) lineage. **SRM_cnv_normalized.txt:** tab-delimited file of normalized read counts for 3550 putative CNVs identified across 48 individual samples in the Southern Rocky Mountains (SRM) lineage. Headers indicate sample (format: SampleSite_SampleID) and the first column indicates CNVs (format: ChromosomeID_Position_RADtagID). **CSC_filtered.vcf.gz:** gzipped VCF file of 64181 SNPs (post-filtering) identified across 68 individual samples in the Cascades (CSC) lineage. Individual IDs follow the format of SampleSite_SampleID. **CSC_snp_categorization.csv:** comma-separated file of summary statistics and categorizations of 64184 SNPs identified across 68 individual samples in the Cascades (CSC) lineage. **CSC_cnv_normalized.txt:** tab-delimited file of normalized read counts for 3092 putative CNVs identified across 68 individual samples in the Cascades (CSC) lineage. Headers indicate sample (format: SampleSite_SampleID) and the first column indicates CNVs (format: ChromosomeID_Position_RADtagID). **SN_filtered.vcf.gz:** gzipped VCF file of 130119 SNPs (post-filtering) identified across 50 individual samples in the Sierra Nevada (SN) lineage. Individual IDs follow the format of SampleSite_SampleID. **SN_snp_categorization.csv:** comma-separated file of summary statistics and categorizations of 130119 SNPs identified across 50 individual samples in the Sierra Nevada (SN) lineage. **SN_cnv_normalized.txt:** tab-delimited file of normalized read counts for 9585 putative CNVs identified across 50 individual samples in the Sierra Nevada (SN) lineage. Headers indicate sample (format: SampleSite_SampleID) and the first column indicates CNVs (format: ChromosomeID_Position_RADtagID). **CU_filtered.vcf.gz:** gzipped VCF file of 65521 SNPs (post-filtering) identified across 28 individual samples in the Central Utah (CU) lineage. Individual IDs follow the format of SampleSite_SampleID. **CU_snp_categorization.csv:** comma-separated file of summary statistics and categorizations of 65521 SNPs identified across 28 individual samples in the Central Utah (CU) lineage. **CU_cnv_normalized.txt:** tab-delimited file of normalized read counts for 5058 putative CNVs identified across 28 individual samples in the Central Utah (CU) lineage. Headers indicate sample (format: SampleSite_SampleID) and the first column indicates CNVs (format: ChromosomeID_Position_RADtagID).