Data from: Genetic differentiation despite high gene flow along elevational gradients in Fagus sylvatica at stress and phenology candidate genes

Detecting the signature of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two population pairs on the north and south slopes of Mont Ventoux (Southern France). We performed both single and multi-locus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP-level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene-level, with haplotypes considered alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty due to haplotype inference, we proposed averaging the Bayes Factors in FST outlier methods over many possible phase reconstructions. Epistatic selection offers a more realistic multi-locus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Over all populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signal arose between an FST outlier and a non-synonymous mutation in a drought response gene. Haplotypes containing selectively advantageous allele combinations and unique to high or low-elevation, and, northern or southern populations were additionally discovered. Several of them contained non-synonymous mutations situated in genes of demonstrated functional importance for adaptation to climate.