Data from: Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

Hecht BC, Matala AP, Hess JE, Narum SR

Date Published: October 8, 2015

DOI: http://dx.doi.org/10.5061/dryad.0g6hq

 

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Title Allele Frequencies
Downloaded 24 times
Description Allele Frequencies - The frequency of the major allele (P) is indicated for each of 19,703 SNP loci for each population (indicated by abbreviation as described in Table 1), including the global average MAF, and the global average genotype success rate (GSR).
Download Hecht_OtsLandscapeGenomics_Dryad-AlleleFre....xlsx (8.226 Mb)
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Title Genotypes
Downloaded 15 times
Description Genotypes: Individual genotypes for each sample at each of the 19,703 loci. Sample ID is population abbreviation (see Table 1) followed by "xXXX", where XXX is a three digit numerical identifier.
Download Hecht_OtsLandscapeGenomics_Dryad-Genotypes....xlsx (140.3 Mb)
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Title Hardy Weinberg equilibrium
Downloaded 13 times
Description Hardy Weinberg equilibrium: Locus summary by population including estimates of the genotyping success rate (GSR), the P-value from a chi-square test of the deviation from Hardy-Weinberg Equilibrium (HWE, * reported is the raw uncorrected p-value, the Bonferroni threshold p-value for 19,703 comparisons at α=0.05 level is 0.05/19703 = 0.00000254), the observed heterozygosity (Ho), the expected heterozygosity based on HWE (He), and the minor allele (Q) frequency (MAF). Populations are numbered according to Table 1, and the colored font corresponds to the lineage of the population (blue, North Coastal Lineage; red, South Coastal Lineage; green, Interior Columbia River Stream-Type Lineage).
Download Hecht_OtsLandscapeGenomics_Dryad-HWE_061915.xlsx (47.18 Mb)
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Title GENEPOP-Rangewide_NeutralSNPs
Downloaded 6 times
Description Input file for GENEPOP
Download GENEPOP-Rangewide_NeutralSNPs.txt (49.05 Mb)
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Title LOSITAN-Rangewide
Downloaded 8 times
Description Input file for Lositan for all populations, 19,703 SNPs
Download LOSITAN-Rangewide.txt (193.0 Mb)
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Title Ots_RADcatalog_21504SNPs
Downloaded 16 times
Description Pre-filtered RAD catalog of 21,504 SNPs
Download Ots_RADcatalog_21504SNPs.xlsx (39.37 Mb)
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Title Mantel-Hecht-Moran FST full matrices
Downloaded 15 times
Description Input files for Mantel test between Hecht Fst values and Moran et al. (2013) Fst values. Each set of Fst values are included in full matrix format in separate tabs of the Excel file. See Table S2 for corresponding triangular matrices and results of Mantel tests.
Download Mantel-Hecht-MoranFSTfullmatrices.xlsx (26.87 Kb)
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Title PCA-adegenet_neutralSNPs
Downloaded 9 times
Description Input file for PCA in adgenet for all populations; 5,007 putatively adaptive SNPs
Download PCA-adegenet_neutralSNPs.txt (1.671 Mb)
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Title RDA_BIOCLIMDATA
Downloaded 12 times
Description Input file of environmental factors included for RDA
Download RDA_BIOCLIMDATA.txt (12.90 Kb)
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Title RDA_AlleleFreq
Downloaded 10 times
Description Input file of allele frequencies for 19,703 SNPs for RDA
Download RDA_AlleleFreq.txt (4.779 Mb)
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When using this data, please cite the original publication:

Hecht BC, Matala AP, Hess JE, Narum SR (2015) Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range. Molecular Ecology 24(22): 5573-5595. http://dx.doi.org/10.1111/mec.13409

Additionally, please cite the Dryad data package:

Hecht BC, Matala AP, Hess JE, Narum SR (2015) Data from: Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.0g6hq
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