Data from: Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity

Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis-Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P

Date Published: September 26, 2017

DOI: https://doi.org/10.5061/dryad.57m0f

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Title VCF file for 6605 SNPs used in gene-environment association analyses
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Description The file Harrisson_etal_MurrayCod_6605_loci is a VCF formatted file that includes genotypes (6605 SNP loci) for 230 individuals of Maccullochella peelii used in the study by Harrisson et al "Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity" Contact Katherine Harrisson: katherine.harrisson@gmail.com
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Title CSV file with sample information
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Title Imputed SNP genotypes input file for RDA
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Download Harrisson_etal_RDA_SNP_genotypes_imputed.csv (3.092 Mb)
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Title Climate and PCNM input file for RDA
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Download Harrisson_etal_RDA_climate_pcnm.csv (42.06 Kb)
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Title Version of draft Murray cod reference genome used for read mapping
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Description A fasta file of the version of the draft reference genome used for read mapping in the the study by Harrisson et al "Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity." A final version of the genome is now published and publicly available at: http://dx.doi.org/10.5524/100329 Contact Katherine Harrisson katherine.harrisson@gmail.com
Download MurrayCodV2_02092015.fasta.gz (187.0 Mb)
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Title Input file for STRUCTURE analysis (3650 loci)
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Download Harrisson_etal_3560_loci_structure_input.txt (3.422 Mb)
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Title Input file for STRUCTURE analysis (6605 loci)
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Download Harrisson_etal_6605_loci_structure_input.txt (6.313 Mb)
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Title Candidate SNP regions sequences used in BLAST analysis
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Description Sequences for candidate SNP regions in fasta format.
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Title List of SNPs removed in LD thinning
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Description The file Harrisson_etal_ListRemovedSNPs.txt is a list of SNP loci removed during LD thinning in the study by Harrisson et al "Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity." Contact Katherine Harrisson: katherine.harrisson@gmail.com
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Title Genotype input file for LFMM analysis (6605 loci)
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Description Genotype (6605 SNP loci) input file for 230 individuals of Maccullochella peelii used in the used for LFMM analysis in the study by Harrisson et al "Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity." Contact Katherine Harrisson: katherine.harrisson@gmail.com
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Title Input file for LFMM analysis (env variables)
Downloaded 1 time
Description Contains the environmental data used in LFMM analysis in the study by Harrisson et al "Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity." Column 1 is PC1 and column 2 is PC2. Contact Katherine Harrisson: katherine.harrisson@gmail.com
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Title Genotype (6605 loci) input file for TASSEL analysis
Downloaded 6 times
Description A VCF formatted file (sorted for TASSEL) that includes genotype information (6605 SNP loci) for 230 individuals of Maccullochella peelii used in TASSEL analysis.
Download Harrisson_etal_6605loci_sorted_forTASSEL.vcf (31.72 Mb)
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Title Phenotypes and covariates input for TASSEL
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Download Harrisson_etal_phentypes_covariates_TASSEL.txt (23.56 Kb)
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When using this data, please cite the original publication:

Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis-Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P (2017) Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity. Molecular Ecology 26(22): 6253-6269. https://doi.org/10.1111/mec.14368

Additionally, please cite the Dryad data package:

Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis-Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P (2017) Data from: Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity. Dryad Digital Repository. https://doi.org/10.5061/dryad.57m0f
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