Data from: Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis

Local adaptation is a common feature of plant and animal populations. Adaptive phenotypic traits are genetically differentiated along environmental gradients, but the genetic basis of such adaptation is still poorly known. Genetic association studies of local adaptation combine data over populations. Correcting for population structure in these studies can be problematic since both selection and neutral demographic events can create similar allele frequency differences between populations. Correcting for demography with traditional methods may lead to eliminating some true associations. We developed a new Bayesian approach for identifying the loci underlying an adaptive trait in a multipopulation situation in the presence of possible double confounding due to population stratification and adaptation. With this method we studied the genetic basis of timing of bud set, a surrogate trait for timing of yearly growth cessation that confers local adaptation to the populations of Scots pine (Pinus sylvestris). Population means of timing of bud set were highly correlated with latitude. Most effects at individual loci were small. Interestingly, we found genetic heterogeneity (that is, different sets of loci associated with the trait) between the northern and central European parts of the cline. We also found indications of stronger stabilizing selection toward the northern part of the range. The harsh northern conditions may impose greater selective pressure on timing of growth cessation, and the relative importance of different environmental cues used for tracking the seasons might differ depending on latitude of origin.

局部适应是动植物种群的普遍特征。适应性表型性状沿环境梯度发生遗传分化，但此类适应的遗传基础仍未得到充分解析。针对局部适应的遗传关联研究通常会整合多个种群的数据集，此类研究中对种群结构（population structure）进行校正往往存在难点，因为选择作用与中性群体历史事件均可导致种群间出现相似的等位基因频率（allele frequency）差异，采用传统方法校正群体历史甚至可能误删部分真实的遗传关联信号。本研究开发了一种全新的贝叶斯方法（Bayesian approach），可在种群分层与适应作用可能带来双重混杂的多种群场景下，识别适应性性状背后的基因座（loci）。利用该方法，本研究解析了欧洲赤松（Pinus sylvestris）种群局部适应相关的芽封顶时序的遗传基础，该性状是年度生长停止时序的替代性状，可反映种群的局部适应能力。各种群的芽封顶时序均值与纬度呈现高度显著相关，多数单个基因座的效应微弱。有趣的是，本研究发现该渐变群（cline）的北欧与中欧区域间存在遗传异质性，即与该性状相关的基因座集合各不相同。同时，研究还发现分布区北部存在更强的稳定选择（stabilizing selection）信号。严苛的北部环境可能对生长停止时序施加了更强的选择压力，而用于感知季节变化的不同环境线索的相对重要性，可能会因种群的原产地纬度而异。