Data from: Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations

Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus 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, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes factors over many possible phase reconstructions. Epistatic selection offers a realistic multilocus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Overall 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 signals arose between an FST outlier and a nonsynonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low elevations and northern or southern populations. Several haplotypes contained nonsynonymous mutations situated in genes with known functional importance for adaptation to climatic factors.检测受气候变化威胁的林木种群的选择印记，是当前的核心研究重点。本研究以法国东南部文图山南北坡的两个种群对共96株欧洲山毛榉（Fagus sylvatica L.）个体为材料，探究了小空间尺度下的局部适应印记。本研究基于包含546个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点的53个气候相关候选基因，开展了单基因座与多基因座的选择分析。在SNP水平上，基于固定指数（Fixation Index, FST）的离群值检测方法仅发现微弱的选择信号，北方种群中存在3个边缘显著的离群位点。以单倍型（haplotype）作为等位基因进行基因水平分析时，又额外检测到2个边缘显著的离群基因，南北坡各1个。为规避单倍型推断的不确定性，本研究对多种可能的相位重构结果的贝叶斯因子（Bayes factor）取平均值。上位性选择（epistatic selection）为自然种群提供了贴合实际的多基因座选择模型，本研究采用了大野木（Ohta）基于连锁不平衡方差分解提出的检验方法。在所有种群中，0.23%的SNP位点对（单倍型）呈现上位性选择信号，其中近80%位于基因内部。其中1个基因间上位性选择信号出现在一个FST离群位点与一个抗旱响应基因中的非同义突变之间。此外，本研究还鉴定出了携带选择性优势等位基因组合的单倍型，这类单倍型仅存在于高/低海拔以及南北坡种群中。部分单倍型携带的非同义突变位于已知对气候适应具有关键功能的基因中。