DOI: 10.5061/dryad.f1vhhmgtk
title: Data from: Contrasted patterns of local adaptation to climate change across the range of an evergreen oak, Quercus aquifolioides

description: Long-lived tree species are genetically differentiated and locally adapted
 with respect to fitness-related traits, but the genetic basis of local
 adaptation remains largely unresolved. Recent advances in population
 genetics and landscape genomic analyses enable identification of putative
 adaptive loci and specific selective pressures acting on local adaptation.
 Here we sampled 60 evergreen oak (Quercus aquifolioides) populations
 throughout the species’ range and pool-sequenced 587 individuals at
 drought stress candidate genes. We analyzed patterns of genetic diversity
 and differentiation for 381 single nucleotide polymorphisms (SNPs) from 65
 candidate genes and eight microsatellites. Outlier loci were identified by
 genetic differentiation analysis and genome–environment associations. The
 response pattern of genetic variation to environmental gradient was
 assessed by linear isolation by distance/environment tests, redundancy
 analysis and non-linear methods. SNPs and microsatellites revealed two
 genetic lineages: Tibet and Hengduan Mountains-Western Sichuan Plateau
 (HDM-WSP), with reduced genetic diversity in Tibet lineage. More outlier
 loci were detected in HDM-WSP lineage than Tibet lineage. Among these,
 three SNPs in two genes responded to dry season precipitation in the
 HDM-WSP lineage but not in Tibet. By contrast, genetic variation in the
 Tibet lineage was related to geographic distance instead of the
 environment. Furthermore, Risk of Non-Adaptedness (RONA) analyses
 suggested HDM-WSP lineage will have a better capacity to adapt in the
 predicted future climate compared to the Tibet lineage. We detected
 genetic imprints consistent with natural selection and molecular
 adaptation to drought on the Qinghai-Tibet Plateau (QTP) over a range of
 long-lived and widely distributed oak species in a changing environment.
 Our results suggest that different within-species adaptation processes
 occur in species occurring in heterogeneous environments.Long-lived tree
 species are genetically differentiated and locally adapted with respect to
 fitness-related traits, but the genetic basis of local adaptation remains
 largely unresolved. Recent advances in population genetics and landscape
 genomic analyses enable identification of putative adaptive loci and
 specific selective pressures acting on local adaptation. Here we sampled
 60 evergreen oak (Quercus aquifolioides) populations throughout the
 species’ range and pool-sequenced 587 individuals at drought stress
 candidate genes. We analyzed patterns of genetic diversity and
 differentiation for 381 single nucleotide polymorphisms (SNPs) from 65
 candidate genes and eight microsatellites. Outlier loci were identified by
 genetic differentiation analysis and genome–environment associations. The
 response pattern of genetic variation to environmental gradient was
 assessed by linear isolation by distance/environment tests, redundancy
 analysis and non-linear methods. SNPs and microsatellites revealed two
 genetic lineages: Tibet and Hengduan Mountains-Western Sichuan Plateau
 (HDM-WSP), with reduced genetic diversity in Tibet lineage. More outlier
 loci were detected in HDM-WSP lineage than Tibet lineage. Among these,
 three SNPs in two genes responded to dry season precipitation in the
 HDM-WSP lineage but not in Tibet. By contrast, genetic variation in the
 Tibet lineage was related to geographic distance instead of the
 environment. Furthermore, Risk of Non-Adaptedness (RONA) analyses
 suggested HDM-WSP lineage will have a better capacity to adapt in the
 predicted future climate compared to the Tibet lineage. We detected
 genetic imprints consistent with natural selection and molecular
 adaptation to drought on the Qinghai-Tibet Plateau (QTP) over a range of
 long-lived and widely distributed oak species in a changing environment.
 Our results suggest that different within-species adaptation processes
 occur in species occurring in heterogeneous environments.
description: <b>SNP calls for all samples in VCF format (before
 filtering)</b> SNP call data for all samples
 across in Southwest China, produced by GATK in VCF format, before final
 filtering steps. SNP_All.vcf SNP
 calls for all samples, final in table format SNP calls
 in tab-separated format with columns as individual samples and rows as
 loci as inferred from GATK. These are the final data that were filtered
 such that the minor allele frequency is greater than 0.025 and there is no
 more than 50% missing data at a locus. This file contains all samples
 of<i> Quercus aquifolioides</i>.
 SNP_All_MAF_2.5_Mis50.xlsx SNP calls for
 Tibet samples, final in table format SNP calls in
 tab-separated format with columns as individual samples and rows as loci
 as inferred from GATK. These are the final data that were filtered such
 that the minor allele frequency is greater than 0.025 and there is no more
 than 50% missing data at a locus. This file contains Tibet samples
 of<i> Quercus aquifolioides</i>.
 SNP_Tibet_MAF_2.5_Mis50.xlsx SNP calls for
 HDM-WSP samples, final in table format SNP calls in
 tab-separated format with columns as individual samples and rows as loci
 as inferred from GATK. These are the final data that were filtered such
 that the minor allele frequency is greater than 0.025 and there is no more
 than 50% missing data at a locus. This file contains HDM-WSP samples
 of<i> Quercus aquifolioides</i>.
 SNP_HDM-WSP_MAF_2.5_Mis50.xlsx SSR for All
 samples, final in table format SSR data in
 tab-separated format with columns as neutral nuclear microsatellite
 markers and rows as individual samples as obtained from FlexiBinv2.
 Missing data is represented by “?”. This file contains all samples
 of<i> Quercus aquifolioides</i>.
 SSR_All.xlsx