DOI: 10.5061/dryad.57m0f
title: Data from: Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity

description: Adaptive differences across species’ ranges can have important
 implications for population persistence and conservation management
 decisions. Despite advances in genomic technologies, detecting adaptive
 variation in natural populations remains challenging. Key challenges in
 gene-environment association studies involve distinguishing the effects of
 drift from those of selection, and identifying subtle signatures of
 polygenic adaptation. We used paired-end restriction-site associated-DNA
 sequencing data (6605 biallelic single nucleotide polymorphisms; SNPs) to
 examine population structure and test for signatures of adaptation across
 the geographic range of an iconic Australian endemic freshwater fish
 species, the Murray cod Maccullochella peelii. Two univariate
 gene-association methods identified 61 genomic regions associated with
 climate variation. We also tested for subtle signatures of polygenic
 adaptation using a multivariate method (redundancy analysis; RDA). The RDA
 analysis suggested that climate (temperature- and precipitation-related
 variables) and geography had similar magnitudes of effect in shaping the
 distribution of SNP genotypes across the sampled range of Murray cod.
 Although there was poor agreement among the candidate SNPs identified by
 the univariate methods, the top 5% of SNPs contributing to significant RDA
 axes included 67% of the SNPs identified by univariate methods. We discuss
 the potential implications of our findings for the management of Murray
 cod and other species generally, particularly in relation to informing
 conservation actions such as translocations to improve evolutionary
 resilience of natural populations. Our results highlight the value of
 using a combination of different approaches, including polygenic methods,
 when testing for signatures of adaptation in landscape genomics studies.
description: VCF file for 6605 SNPs
 used in gene-environment association analysesThe 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.comHarrisson_etal_MurrayCod_6605_loci.vcfCSV file with sample informationHarrisson_etal_sample_info.csvImputed SNP genotypes input file for RDAHarrisson_etal_RDA_SNP_genotypes_imputed.csvClimate and PCNM input file for RDAHarrisson_etal_RDA_climate_pcnm.csvVersion of draft Murray cod reference genome used for read mappingA 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.comMurrayCodV2_02092015.fasta.gzInput file for STRUCTURE analysis (3650 loci)Harrisson_etal_3560_loci_structure_input.txtInput file for STRUCTURE analysis (6605 loci)Harrisson_etal_6605_loci_structure_input.txtCandidate SNP regions sequences used in BLAST analysisSequences for candidate SNP regions in fasta format.Harrisson_etal_candidate_SNP_regions_sequences.fastaList of SNPs removed in LD thinningThe 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.comHarrisson_etal_ListRemovedSNPs.txtGenotype input file for LFMM analysis (6605 loci)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.comHarrisson_etal_6605genotypes.lfmmInput file for LFMM analysis (env variables)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.comHarrisson_etal_LFMM_PCvariables.envGenotype (6605 loci) input file for TASSEL analysisA VCF formatted file (sorted for TASSEL) that includes genotype information (6605 SNP loci) for 230 individuals of Maccullochella peelii used in TASSEL analysis.Harrisson_etal_6605loci_sorted_forTASSEL.vcfPhenotypes and covariates input for TASSELHarrisson_etal_phentypes_covariates_TASSEL.txt