DOI: 10.5061/dryad.8g0s3
title: Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves

description: In an era of ever-increasing amounts of whole genome sequence data for
 individuals and populations, the utility of traditional single nucleotide
 polymorphisms (SNPs) array-based genome scans is uncertain. We previously
 performed a SNP array-based genome scan to identify candidate genes under
 selection in six distinct gray wolf (Canis lupus) ecotypes. Using this
 information, we designed a targeted capture array for 1040 genes,
 including all exons and flanking regions, as well as 5000 1 kb non-genic
 neutral regions and resequenced these regions in 107 wolves. Selection
 tests revealed striking patterns of variation within candidate genes
 relative to non-candidate regions and identified potentially functional
 variants related to local adaptation. We found 27% and 47% of candidate
 genes from the previous SNP array study had functional changes that were
 outliers in SweeD and Bayenv analyses, respectively. This result verifies
 the use of genome wide SNP surveys to tag genes that contain functional
 variants between populations. We highlight non-synonymous variants in
 APOB, LIPG, and USH2A that occur in functional domains of these proteins,
 and that demonstrate high correlation with precipitation seasonality and
 vegetation. We find Arctic and High Arctic wolf ecotypes have higher
 numbers of genes under selection, which highlight their conservation value
 and heightened threat due to climate change. This study demonstrates that
 combining genome wide genotyping arrays with large scale resequencing and
 environmental data provides a powerful approach to discern candidate
 functional variants in natural populations.
description: AllSamples_n107_EnvData_wLatLongThese data represent latitude and longitude coordinates for the 107 wolves used in this study for selection tests. The 12 environmental variables for each coordinate were downloaded within ArcGIS from various WORLDCLIM databases (http://www.worldclim.org/). Please see descriptions on website for information on what each variable measures. From the website: "Please note that the temperature data are in °C * 10. This means that a value of 231 represents 23.1 °C. This does lead to some confusion, but it allows for much reduced file sizes which is important as for many downloading large files remains difficult. The unit used for the precipitation data is mm (millimeter)."Variant file in VCF formatGenic variants for 107 individuals in VCF v4.1 format. For details on genotype calling and filtering, see Methods and Supplemental Information sections.Filtered_variableSites_fixedSamples_9July2014_minDP10noMissing_ecotypesOnly_n107_GenicRegions_95CallRate.recode.vcfBayenv results file for genic SNPsThis is the output averaged from 10 independent runs of Bayenv for genic SNPs in 107 wolves and 6 ecotypes. Column headers are provided in the file.bayenv1_output_n107_k6_Average_10Runs_forR.txtBayenv output file for neutral SNPsThis is the output averaged across 10 runs of Bayenv using neutral SNPs, in 107 wolves and 6 ecotypes. The results in this file were used as a null for determining empirical significance for the genic SNPs. See paper text for details.bayenv1_output_n107_k6_Average_10Runs_NEUTRAL_forR.txtBayeScan results file for genic SNPsThis is the output file from BayeScan run with genic SNPs for 107 wolves and 6 ecotypes.bayescan_n107_Ecotypes_GenicRegions_95CallRate_wEcotypes_output_prior_odds_1000_fst.txtBayeScan results file for neutral SNPsThis is the output file from BayeScan for neutral SNPs in 107 wolves and 6 ecotypes. Results within this file were used to assess null background for assigning significance to genic SNPs. See main text for details.bayescan_n107_NeutralRegions_95CallRate_LDpruned_output_prior_odds_10000_fst.txtPhenotype data for 47 individuals (BLACK)Phenotype data for 47 individuals, coded so that black individuals are 2, and non-black individuals are 1. Input file was used for running EMMAX phenotype genotype analysis.GenicRegions_95CallRate_wKlocus_BLACK_forEmma_phenotype.txtPhenotype data for 47 individuals (WHITE)Phenotype data for 47 individuals, coded so that white individuals are 2, and non-white individuals are 1. Input file was used for running EMMAX phenotype genotype analysis.GenicRegions_95CallRate_wKlocus_WHITE_forEmma_phenotype.txtKinship matrix for EMMAXKinship matrix generated from LD-pruned neutral SNPs for genotype-phenotype associations in EMMAX.NeutralSNPs_LDpruned_for_EmmaX.aBN.kinfEMMAX results file (BLACK)Results file generated from EMMAX for genotype-phenotype analysis for black coat color.results_BLACK.txtEMMAX Results file (WHITE)Results file generated from EMMAX for genotype-phenotype analysis for white coat color.results_WHITE.txtSweeD_Report.Pop_1_WestForest_Genic_10000_chrAllSweed Output file for West Forest Wolves & Genic sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_1_WestForest_Neutral_10000_chrAllSweed Output file for West Forest Wolves & neutral sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_2_BorealForest_Genic_10000_chrAllSweed Output file for Boreal Forest Wolves & genic sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_2_BorealForest_Neutral_10000_chrAllSweed Output file for Boreal Forest Wolves & neutral sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_3_Arctic_Genic_10000_chrAllSweed Output file for Arctic Wolves & genic sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_3_Arctic_Neutral_10000_chrAllSweed Output file for Arctic Wolves & neutral sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_4_HighArctic_Genic_10000_chrAllSweed Output file for High Arctic Wolves & genic sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_4_HighArctic_Neutral_10000_chrAllSweed Output file for High Arctic Wolves & neutral sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_5_BritishColumbia_Genic_10000_chrAllSweed Output file for British Columbia Wolves & genic sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_5_BritishColumbia_Neutral_10000_chrAllSweed Output file for British Columbia Wolves & neutral sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_6_AtlanticForest_Genic_10000_chrAllSweed Output file for Atlantic Forest Wolves & genic sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/SweeD_Report.Pop_6_AtlanticForest_Neutral_10000_chrAllSweed Output file for Atlantic Forest Wolves & neutral sites. Columns are chromosome, position, likelihood, and alpha. See SweeD details at http://sco.h-its.org/exelixis/web/software/sweed/Latitude and Longitude Coordinates for 117 WolvesThese are the latitude and longitude coordinates for all 117 wolves initially sampled in this study. Ten individuals were not included in any selection tests for the reason indicated in the "Ecotype or Status" column, i.e. they were admixed in Structure or related to another individual and dropped.AllSamples_n117_wLatLong.xlsxOutput from Variant Effect PredictorThis file is the output file of Ensembl's Variant Effect Predictor run on genic variants observed in 107 wolves at a minimum call rate of 95%. See main text for more details.variant_effect_output.txtCapture array target regionsBED file containing annotated regions targeted for the capture array. Coordinates are provided in CanFam3.1.NAwolf_capture_array_regions_Feb2012_canfam3.1.bedNAwolf_baits_canfam3.1Coordinates for 66937 baits covering regions targeted by capture array, in CanFam3.1.Information for BAM files on NCBI SRABAM files for 117 wolves, separated into genic and neutral regions. See paper text for details on alignment and mapping pipeline.