DOI: 10.5061/dryad.f4qrfj73x
title: Data from: Evidence of intraspecific adaptive variation in the American pika (Ochotona princeps) on a continental scale using a target enrichment and mitochondrial genome skimming approach

description: Montane landscapes present an array of abiotic challenges that drive
 adaptive evolution among organisms. These adaptations can promote habitat
 specialization, which may heighten the risk of extirpation from
 environmental change. For example, higher metabolic rates in an
 endothermic species may contribute to heightened cold tolerance, while
 simultaneously limiting heat tolerance. Here, using the climate-sensitive
 American pika (Ochotona princeps), we test for evidence of intraspecific
 adaptive variation among environmental gradients across the Intermountain
 West of North America. We leveraged results from previous studies on pika
 adaptation to generate a custom nuclear target enrichment design to
 sequence several hundred candidate genes related to cold, hypoxia, and
 dietary detoxification. We also applied a ‘genome skimming’ approach to
 sequence mitochondrial DNA. Using genotype-environment association tests,
 we identified rare genomic variants associated with elevation and
 temperature variation among populations. Among mitochondrial genes, we
 identified intraspecific variation in selective signals and significant
 changes to the amino acid property equilibrium constant, which may relate
 to electron transport chain efficiency. These results illustrate a complex
 dynamic of adaptive variation among O. princeps where lineages and
 populations have adapted to unique regional conditions. Some of the
 clearest signals of selection were in a genetic lineage that includes
 pikas of the Great Basin region, which is also where recent localized
 extirpations have taken place and highlights the risk of losing adaptive
 alleles during environmental change.
description: # Evidence of intraspecific adaptive variation in the American pika
 (*Ochotona princeps*) on a continental scale using a target enrichment and
 mitochondrial genome skimming approach.
 [https://doi.org/10.5061/dryad.f4qrfj73x](https://doi.org/10.5061/dryad.f4qrfj73x) This datset contains vcfs generated from target enrichment of nuclear candidate genes and genome skimming of mitochondrial genes from six American pika lineages across the species range. The mitochondrial vcf was used to generate consensus fasta files, which are also included. Finally, the linux and R code used to process and analyze these data are included, along with additional input files for the R code. ## Description of the data and file structure Fasta files in **mtDNA_geneAlignments.zip** are consensus fasta files of the 13 mitochondrial protein coding genes from 118 *O. princeps* samples. These were generated from a vcf file and the OchPri4.0 reference genome using bcftools consensus. Missing data are coded as "N". For additional information on fasta file format, see: [https://www.ncbi.nlm.nih.gov/genbank/fastaformat](https://www.ncbi.nlm.nih.gov/genbank/fastaformat) Three vcf files are included. For information about vcf file format, see: [https://samtools.github.io/hts-specs/VCFv4.3.pdf](https://samtools.github.io/hts-specs/VCFv4.3.pdf) **120_FinalAnnotate_80LDpruned.vcf.gz** consists of 17407 nuclear bi-allelic SNPs, annotated by gene ID, from 120 *O. princeps* samples, which were used for population structure and nuclear selection tests. **mt_118_dp3.recode.vcf.gz** is the vcf used in generating the mitochondrial fasta files. **118_filter1.recode.vcf.gz** is the vcf used in generating a SNP phylogenetic tree, which was used in downstream mitochondrial selection tests with the fasta files. **120_80LDpruned.ped** is a ped file, which was the input for snmf population structuring and imputation for downstream analyses. For additional information on ped file format, see: [https://zzz.bwh.harvard.edu/plink/data.shtml#ped](https://zzz.bwh.harvard.edu/plink/data.shtml#ped) Two code files are included: **linux_code.txt** consists of code for raw data processing and analyses performed in bash. **R_code.R** consists of code for analyses performed in R. Additional R input files are in **Extra_R_inputs.zip**: **120_FinalAnnotate_SNPnames.txt** was used for annotating SNP matrix with SNP names which are labeled with the Chromosome_Position_Consequence, **120_names.csv** was used for annotating SNP matrix with sample names, and **lfmm_env.csv** is the environmental data and lineage name inputs for nuclear analyses, where ID1 is sample ID, lineage is snmf-derived lineage, elevation is elevation in meters, and MCMT is mean coldest month temperature in degrees C. Additional folders within **Extra_R_inputs.zip** are as follows: * **BayeScan**: * **bayescan_pop.txt** was used for generating the BayeScan input file. ID1 refers to sample ID and lineage refers to snmf-derived lineage. * **positive_FinalAnnotation.csv** has significant BayeScan results (see BayeScan user manual for explanation of variables: [https://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.1_manual.pdf](https://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.1_manual.pdf)). Final variable, SNP, contains annotated SNP names derived from SNP genotype matrix in R. * **bayescan100_pos_FinalAnnotation_forpca.csv** is the input file for generating the BayeScan significant loci pca. Sample refers to sample ID and lineage refers to snmf-derived lineage. The rest of the fields are genotypes (0,1,2) at each SNP and SNP names have placeholders ("_") removed for compatibility with R package. * **climNA**: **climNA_input1_test.csv** and **climNA_input2.csv** are input files for climNA, **climNA_mt_input1.csv** and **climNA_mt_input2.csv** are input files for climNA for just the samples used in mtDNA analyses. In each file, ID1 refers to sample ID, ID2 refers to subspecies, lat refers to latitude, lon refers to longitude, and el refers to elevation in meters. - **lfmm**: **LFMMintersect_candlist_FinalAnnotate_forpca.csv**, **LFMMlasso_candlist_FinalAnnotate_forpca.csv**, and **LFMMridge_candlist_FinalAnnotate_forpca.csv** are input files for running pca on significant loci from LFMM. For each file, sample refers to sample ID and lineage refers to snmf-derived lineage. The rest of the fields are genotypes (0,1,2) at each SNP and SNP names have placeholders ("_") removed for compatibility with R package. * **TreeSAAP**: * **COOH_env.csv** is an input file for analyzing TreeSAAP results. Sample refers to sample ID, MAT refers to mean annual temperature (degrees C), MWMT refers to mean warmest month temperature (degrees C), MCMT refers to mean coldest month temperature (degrees C), Elevation (m) is elevation in meters, Latitude and Longitude are provided, Lineage refers to snmf-derived lineage, location refers to US state, and Sum_change refers to the sum change of pK' for all mitochondrial protein-coding genes, which derives from TableS11 in Molecular Ecology publication. * **COOH_env_sitename.csv** is an input file for analyzing additional aspects of TreeSAAP results. Variables are the same as COOH_env.csv, except Location now has country, state, and location description, ComplexI_Sum is the sum change in pK' for OXPHOS Complex I genes, ComplexII_Sum is the sum change in pK' for OXPHOS Complex II genes.