Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves

Schweizer RM, Robinson J, Harrigan R, Silva P, Galaverni M, Musiani M, Green RE, Novembre J, Wayne RK

Date Published: November 16, 2015

DOI: http://dx.doi.org/10.5061/dryad.8g0s3

 

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Title AllSamples_n107_EnvData_wLatLong
Downloaded 30 times
Description These 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)."
Download AllSamples_n107_EnvData_wLatLong_toUpload.xlsx (21.93 Kb)
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Title Variant file in VCF format
Downloaded 153 times
Description Genic variants for 107 individuals in VCF v4.1 format. For details on genotype calling and filtering, see Methods and Supplemental Information sections.
Download Filtered_variableSites_fixedSamples_9July...de.vcf (47.91 Mb)
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Title Bayenv results file for genic SNPs
Downloaded 23 times
Description This 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.
Download bayenv1_output_n107_k6_Average_10Runs_forR.txt (1.566 Mb)
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Title Bayenv output file for neutral SNPs
Downloaded 12 times
Description This 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.
Download bayenv1_output_n107_k6_Average_10Runs_NEU...rR.txt (1.793 Mb)
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Title BayeScan results file for genic SNPs
Downloaded 10 times
Description This is the output file from BayeScan run with genic SNPs for 107 wolves and 6 ecotypes.
Download bayescan_n107_Ecotypes_GenicRegions_95Cal...st.txt (692.6 Kb)
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Title BayeScan results file for neutral SNPs
Downloaded 8 times
Description This 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.
Download bayescan_n107_NeutralRegions_95CallRate_L...st.txt (657.5 Kb)
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Title Phenotype data for 47 individuals (BLACK)
Downloaded 6 times
Description 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.
Download GenicRegions_95CallRate_wKlocus_BLACK_for...pe.txt (1.978 Kb)
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Title Phenotype data for 47 individuals (WHITE)
Downloaded 8 times
Description 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.
Download GenicRegions_95CallRate_wKlocus_WHITE_for...pe.txt (1.978 Kb)
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Title Kinship matrix for EMMAX
Downloaded 13 times
Description Kinship matrix generated from LD-pruned neutral SNPs for genotype-phenotype associations in EMMAX.
Download NeutralSNPs_LDpruned_for_EmmaX.aBN.kinf (156.5 Kb)
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Title EMMAX results file (BLACK)
Downloaded 8 times
Description Results file generated from EMMAX for genotype-phenotype analysis for black coat color.
Download results_BLACK.txt (497.3 Kb)
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Title EMMAX Results file (WHITE)
Downloaded 8 times
Description Results file generated from EMMAX for genotype-phenotype analysis for white coat color.
Download results_WHITE.txt (497.7 Kb)
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Title SweeD_Report.Pop_1_WestForest_Genic_10000_chrAll
Downloaded 19 times
Description Sweed 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/
Download SweeD_Report.Pop_1_WestForest_Genic_10000...ll.txt (16.21 Mb)
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Title SweeD_Report.Pop_1_WestForest_Neutral_10000_chrAll
Downloaded 8 times
Description Sweed 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/
Download SweeD_Report.Pop_1_WestForest_Neutral_100...ll.txt (16.18 Mb)
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Title SweeD_Report.Pop_2_BorealForest_Genic_10000_chrAll
Downloaded 8 times
Description Sweed 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/
Download SweeD_Report.Pop_2_BorealForest_Genic_100...ll.txt (16.21 Mb)
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Title SweeD_Report.Pop_2_BorealForest_Neutral_10000_chrAll
Downloaded 8 times
Description Sweed 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/
Download SweeD_Report.Pop_2_BorealForest_Neutral_1...ll.txt (16.18 Mb)
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Title SweeD_Report.Pop_3_Arctic_Genic_10000_chrAll
Downloaded 8 times
Description Sweed 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/
Download SweeD_Report.Pop_3_Arctic_Genic_10000_chrAll.txt (16.21 Mb)
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Title SweeD_Report.Pop_3_Arctic_Neutral_10000_chrAll
Downloaded 7 times
Description Sweed 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/
Download SweeD_Report.Pop_3_Arctic_Neutral_10000_chrAll.txt (16.18 Mb)
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Title SweeD_Report.Pop_4_HighArctic_Genic_10000_chrAll
Downloaded 9 times
Description Sweed 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/
Download SweeD_Report.Pop_4_HighArctic_Genic_10000...ll.txt (16.21 Mb)
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Title SweeD_Report.Pop_4_HighArctic_Neutral_10000_chrAll
Downloaded 9 times
Description Sweed 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/
Download SweeD_Report.Pop_4_HighArctic_Neutral_100...ll.txt (16.18 Mb)
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Title SweeD_Report.Pop_5_BritishColumbia_Genic_10000_chrAll
Downloaded 7 times
Description Sweed 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/
Download SweeD_Report.Pop_5_BritishColumbia_Genic_...ll.txt (16.20 Mb)
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Title SweeD_Report.Pop_5_BritishColumbia_Neutral_10000_chrAll
Downloaded 6 times
Description Sweed 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/
Download SweeD_Report.Pop_5_BritishColumbia_Neutra...ll.txt (16.18 Mb)
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Title SweeD_Report.Pop_6_AtlanticForest_Genic_10000_chrAll
Downloaded 9 times
Description Sweed 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/
Download SweeD_Report.Pop_6_AtlanticForest_Genic_1...ll.txt (16.21 Mb)
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Title SweeD_Report.Pop_6_AtlanticForest_Neutral_10000_chrAll
Downloaded 9 times
Description Sweed 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/
Download SweeD_Report.Pop_6_AtlanticForest_Neutral...ll.txt (16.18 Mb)
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Title Latitude and Longitude Coordinates for 117 Wolves
Downloaded 9 times
Description These 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.
Download AllSamples_n117_wLatLong.xlsx (15.63 Kb)
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Title Output from Variant Effect Predictor
Downloaded 9 times
Description This 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.
Download variant_effect_output.txt (4.604 Mb)
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Title Capture array target regions
Downloaded 6 times
Description BED file containing annotated regions targeted for the capture array. Coordinates are provided in CanFam3.1.
Download NAwolf_capture_array_regions_Feb2012_canfam3.1.bed (610.7 Kb)
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Title NAwolf_baits_canfam3.1
Downloaded 8 times
Description Coordinates for 66937 baits covering regions targeted by capture array, in CanFam3.1.
Download NAwolf_baits_canfam3.1.bed (3.882 Mb)
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Title Information for BAM files on NCBI SRA
Description BAM files for 117 wolves, separated into genic and neutral regions. See paper text for details on alignment and mapping pipeline.
Download ../sra/?term=SRP065570 (0 bytes)
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When using this data, please cite the original publication:

Schweizer RM, Robinson J, Harrigan R, Silva P, Galaverni M, Musiani M, Green RE, Novembre J, Wayne RK (2016) Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves. Molecular Ecology 25(1): 357–379. http://dx.doi.org/10.1111/mec.13467

Additionally, please cite the Dryad data package:

Schweizer RM, Robinson J, Harrigan R, Silva P, Galaverni M, Musiani M, Green RE, Novembre J, Wayne RK (2015) Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8g0s3
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