DOI: 10.5061/dryad.56j8vq8
title: Data from: Evaluating genomic data for management of local adaptation in a changing climate: a lodgepole pine case study

description: We evaluate genomic data, relative to phenotypic and climatic data, as a
 basis for assisted gene flow and genetic conservation. Using a common
 garden trial of 281 lodgepole pine (Pinus contorta) provenances from
 across western Canada, we compare genomic data to phenotypic and climatic
 data to assess their effectiveness in characterizing the climatic drivers
 and spatial scale of local adaptation in this species. We find that
 phenotype-associated loci are equivalent or slightly superior to climate
 data for describing local adaptation in seedling traits, but that climate
 data is superior to bulk genomic data that have not been selected for
 phenotypic associations. We also find agreement between the climate
 variables associated with genomic variation and with 20-year heights from
 a long-term provenance trial, suggesting that genomic data may be a viable
 option for identifying climatic drivers of local adaptation where
 phenotypic data are unavailable. Genetic clines associated with the
 experimental traits occur at broad spatial scales, suggesting that
 standing variation of adaptive alleles for this and similar species does
 not require management at scales finer than are indicated by phenotypic
 data. This study demonstrates that genomic data are most useful when
 paired with phenotypic data, but can also fill some of the traditional
 roles of phenotypic data in management of species for which phenotypic
 trials are not feasible.
description: Pine_AllNatural_GCandTotemIndivs_GWAS_SNPs_June8th2019Alleles of 31634 SNPs for 3500 lodgepole pine seedlings from 281 provenances across British Columbia and Alberta. Individual seedling IDs are the row names (all files in the same order), and column names are the SNP identities. SNP IDs for the array are the concatenation of the genomic contig name (gcontig) and the position of a SNP on the gcontig (pos), separated by a double underscore.Pine_AllNatural_GCandTotemIndivs_ControlSNPs_June8th20194750 intergenic SNPs used to control for population structure in GPA and GEA analyses. individual seedling IDs are the row names (all files in the same order), and column names are the SNP identities. SNP IDs for the array are the concatenation of the genomic contig name (gcontig) and the position of a SNP on the gcontig (pos), separated by a double underscore.PlSeedlotsGeographic locations of the 281 lodgepole pine provenances. This file is structured as an input file for batch generation of climate data from ClimateNA.Pine_TotemField_AllNaturalSeedling_FinalPhenoData2014_Sept11th2018Raw phenotypic data for the totem field (Vancouver) common garden trial. There are about 100 more seedlings in the raw data than the residual data because the residual data was subsetted to contain only the seedlings that genotyped successfully.Pine_TotemField_AllNaturalIndivResiduals_Jan20th2017Residual phenotypic data for the totem field (Vancouver) common garden trial. There are about 100 more seedlings in the raw data than the residual data because the residual data was subsetted to contain only the seedlings that genotyped successfully.