Data from: Genetic subdivision and candidate genes under selection in North American gray wolves

Schweizer RM, vonHoldt BM, Harrigan R, Knowles JC, Musiani M, Coltman D, Novembre J, Wayne RK

Date Published: September 2, 2015

DOI: http://dx.doi.org/10.5061/dryad.c9b25

 

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Title Environmental Data for 94 wolves in 6 populations
Downloaded 35 times
Description These data represent latitude and longitude coordinates for the 94 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 EnvironmentalData_6pops_94indiv.xlsx (20.52 Kb)
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Title nacanids_111indiv_unrel_noYNP_42Ksnps.tped
Downloaded 18 times
Description The set of all 42,587 SNPs for 111 unrelated wolves, in PLINK .tped format. (http://pngu.mgh.harvard.edu/~purcell/plink/)
Download nacanids_111indiv_unrel_noYNP_42Ksnps.tped (20.10 Mb)
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Title nacanids_111indiv_unrel_noYNP_42Ksnps.tfam
Downloaded 17 times
Description The .tfam file, in PLINK format, that corresponds to nacanids_111indiv_unrel_noYNP_42Ksnps.tped. This file has the sample names for 111 unrelated wolves.
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Title nonAdmix_nacanids_94indiv_unrel_noYNP_42Ksnps_wEcotypes.tped
Downloaded 8 times
Description The set of all 42,587 SNPs for 94 unrelated wolves, with >50% assignment in structure, in PLINK .tped format.(http://pngu.mgh.harvard.edu/~purcell/plink/)
Download nonAdmix_nacanids_94indiv_unrel_noYNP_42Ks....tped (17.21 Mb)
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Title nonAdmix_nacanids_94indiv_unrel_noYNP_42Ksnps_wEcotypes.tfam
Downloaded 7 times
Description The corresponding TFAM file for the set of 94 unrelated individuals showing >50% assignment in structure. The first column of each line is the ecotype designation for each sample.
Download nonAdmix_nacanids_94indiv_unrel_noYNP_42Ks....tfam (3.863 Kb)
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Title BayeScan results with prior odds of 10
Downloaded 12 times
Description This is the results (fst) file from running BayeScan with prior odds of 10, with 94 non-admixed individuals and the 42K snp set. Each row represents a different SNP, with the order of the SNPs the same as in the nonAdmix_nacanids_94indiv_unrel_noYNP_42Ksnps_wEcotypes.tped file.
Download 94indiv_42Ksnps_BayeScan_pr_odd_10_output_fst.txt (2.150 Mb)
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Title BayeScan results file with prior odds of 1000
Downloaded 13 times
Description This is the results (fst) file from running BayeScan with prior odds of 1000, with 94 non-admixed individuals and the 42K snp set. Each row represents a different SNP, with the order of the SNPs the same as in the nonAdmix_nacanids_94indiv_unrel_noYNP_42Ksnps_wEcotypes.tped file.
Download 94indiv_42Ksnps_BayeScan_pr_odd_1000_outp...st.txt (2.277 Mb)
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Title BayeScan results with prior odds of 10000
Downloaded 6 times
Description This is the results (fst) file from running BayeScan with prior odds of 10000, with 94 non-admixed individuals and the 42K snp set. Each row represents a different SNP, with the order of the SNPs the same as in the nonAdmix_nacanids_94indiv_unrel_noYNP_42Ksnps_wEcotypes.tped file.
Download 94indiv_42Ksnps_BayeScan_pr_odd_10000_out...st.txt (2.082 Mb)
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Title Bayenv output file
Downloaded 11 times
Description Results file from Bayenv for 94 individuals in six populations for 12 environmental variables. File is the matrix of bayes factors after averaging across ten independent runs. Each row represents a SNP, and each column contains the bayes factor for each environmental variable. BIO1: annual mean temp., BIO2: mean diurnal temp. range, BIO4: temp. seasonality, BIO5: max. temp. of warmest month, BIO6: min. temp. of coldest month), BIO12: annual precipitation, BIO15: precipitation seasonality, BIO19: precipitation of coldest quarter, LC: land cover metric, NDVIM: normalized difference vegetation index, TREE: percentage tree cover, and SRTM: shuttle radar topography metric.
Download bf_output_94indiv_12Var_Jan2015_average_forR.txt (5.064 Mb)
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Title Genetic distance matrix for Mantel and spatial autocorrelation tests
Downloaded 10 times
Description This date file is a square matrix of genetic distance as measured using 42K SNPs and the 111 individual data set. Genetic distance was calculated in PLINK using the '--cluster --distance-matrix' command options. The order of individuals is the same as in the nacanids_111indiv_unrel_noYNP_42Ksnps.tfam file.
Download nacanids_111indiv_unrel_noYNP_42Ksnps.mdist (108.8 Kb)
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Title Geographic distance matrix for Mantel and spatial autocorrelation tests
Downloaded 11 times
Description This file is a square matrix of geographic distance, in kilometers, between 111 wolves. Genalex was used to calculate these distances, using the options 'Genalex --> distance --> geographic --> decimal lat/long, square matrix'. Individuals are in the same order as in the nacanids_111indiv_unrel_noYNP_42Ksnps.tfam file.
Download nacanids_111indiv_geogDistInKiloMeters.txt (107.8 Kb)
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Title nacanids_unrel_42Ksnps_CoatColor_wYNP_n33.tped
Downloaded 8 times
Description PLINK formatted genotypes of 33 individuals used for coat color association test, gentoyped at 42K SNPs. This data set includes 10 Yellowstone wolves which were not included in the main analysis for the paper, but were included for the coat color association.
Download nacanids_123indiv_unrel_42Ksnps_CoatColor_....tped (6.820 Mb)
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Title nacanids_unrel_42Ksnps_CoatColor_wYNP_n33_white.tfam
Downloaded 6 times
Description PLINK formatted TFAM file with coat color genotype for each of 33 wolves. Individuals coded as a 2 are white, individuals coded as a 1 are not white (can be black or gray).
Download nacanids_123indiv_unrel_42Ksnps_CoatColor_....tfam (1.403 Kb)
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Title nacanids_123indiv_unrel_42Ksnps_CoatColor_wYNP_n33_black.tfam
Downloaded 6 times
Description PLINK formatted TFAM file with coat color genotype for each of 33 wolves. Individuals coded as a 2 are black, individuals coded as a 1 are not black (can be white or gray).
Download nacanids_123indiv_unrel_42Ksnps_CoatColor_....tfam (1.403 Kb)
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When using this data, please cite the original publication:

Schweizer RM, vonHoldt BM, Harrigan R, Knowles JC, Musiani M, Coltman D, Novembre J, Wayne RK (2016) Genetic subdivision and candidate genes under selection in North American gray wolves. Molecular Ecology 25(1): 380–402. http://dx.doi.org/10.1111/mec.13364

Additionally, please cite the Dryad data package:

Schweizer RM, vonHoldt BM, Harrigan R, Knowles JC, Musiani M, Coltman D, Novembre J, Wayne RK (2015) Data from: Genetic subdivision and candidate genes under selection in North American gray wolves. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.c9b25
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