DOI: 10.5061/dryad.03g3s3q
title: Data from: Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species

description: Global climate is rapidly changing and the ability for tree species to
 adapt is dependent on standing genomic variation; however the distribution
 and abundance of functional and adaptive variants are poorly understood in
 natural systems. We test key hypotheses regarding the genetics of adaptive
 variation in a foundation tree: genomic variation is associated with
 climate and genomic variation is more likely to be associated with
 temperature than precipitation or aridity. To test these hypotheses, we
 used 9,593 independent, genomic single‐nucleotide polymorphisms (SNPs)
 from 270 individuals sampled from Corymbia calophylla’s entire
 distribution in southwestern Western Australia, spanning orthogonal
 temperature and precipitation gradients. Environmental association
 analyses returned 537 unique SNPs putatively adaptive to climate. We
 identified SNPs associated with climatic variation (i.e. temperature
 (458), precipitation (75) and aridity (78)) across the landscape. Of
 these, 78 SNPs were non-synonymous (NS), while 26 SNPs were found within
 gene regulatory regions. The NS and regulatory candidate SNPs associated
 with temperature explained more deviance (27.35%) then precipitation
 (5.93%) and aridity (4.77%), suggesting that temperature provides stronger
 adaptive signals than precipitation. Genes associated with adaptive
 variants include functions important in stress responses to temperature
 and precipitation. Patterns of allelic turnover of NS and regulatory SNPs
 show small patterns of change through climate space with the exception of
 an aldehyde dehydrogenase gene variant with 80% allelic-turnover with
 temperature. Together, these findings provide evidence for the presence of
 adaptive variation to climate in a foundation species and provide critical
 information to guide adaptive management practices.
description: LFMM file for Corymbia
 calophylla.This data has 263
 individuals row wise and 9593 SNPs column wise. 0 = major homozygote, 1 =
 heterozygote, 2 = minor homozygote.Ahrens_MEC_corymbia.lfmmFile with climate data for LFMMClimate data for LFMM for each individual. column 1 = maximum temperature of the warmest month; column 2 = mean annual precipitation; column 3 = aridity index.Ahrens_lfmm_env_file.envBaypass file for Corymbia calophyllaRows are SNPs. Columns are population level allele counts. Two columns per locus. In the file, there are 27 populations and 9593 SNPs.Ahrens_baypass_corymbia.txtEnvironmental data file for Bayenv and BayPassClimate variables for populations. The climate variables are standardised following BayEnv's manual. Row 1 = maximum temperature of the warmest month; Row 2 = mean annual precipitation; Row 3 = aridity index.Ahrens_bayenv_baypass_std_env_file_corymbia.envBayenv data file for Corymbia calophyllaPopulation level allele counts for Bayenv input. Rows are SNPs, two rows per locus. Columns are populations.Ahrens_bayenv_corymbia.txtPairwise FST file for GDM inputPairwise FST for all of the SNPs for GDM analysis.Ahrens_gdm_geno_corymbia.txtClimate and geographical information for GDM inputClimate and geographical information for GDM inputAhrens_gdm_env_corymbia.txtExample gdm file for SNP j8105Pairwise FST matrix for GDM input for the SNP j8105.pw_j8105_fst.txtR code for gdm analysisReference data set and SNP j8105 for gdm analysis.Ahrens_GDM_code_reference_j8105.R