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（local adaptation）是动植物种群普遍具备的特征。适应性表型性状（adaptive phenotypic traits）沿环境梯度（environmental gradient）发生遗传分化，但这类适应的遗传基础迄今仍不甚明晰。针对局部适应的遗传关联研究（genetic association studies）会整合多个种群的数据。此类研究中校正种群结构（population structure）往往存在难点：选择作用与中性种群历史事件（neutral demographic events）均可导致种群间出现相似的等位基因频率（allele frequency）差异。采用传统方法校正种群历史影响，可能会剔除部分真实的关联信号。本研究开发了一种全新的贝叶斯方法（Bayesian approach），可在种群分层（population stratification）与适应作用可能引发双重混杂（double confounding）的多种群场景下，识别适应性性状背后的基因座（loci，为locus的复数形式）。借助该方法，我们针对欧洲赤松（Pinus sylvestris）种群的局部适应相关性状——芽形成时间（年度生长停止时间的替代指标）的遗传基础展开了研究。芽形成时间的种群均值与纬度呈现高度相关性。多数单个基因座的效应较为微弱。有趣的是，我们在该渐变群（cline）的北欧与中欧区域间发现了遗传异质性（genetic heterogeneity）——即与该性状相关的基因集存在显著差异。此外，我们在该物种分布范围的北部区域发现了更强的稳定选择（stabilizing selection）信号。北部严苛的环境条件可能对生长停止时间施加更强的选择压力，而用于感知季节变化的不同环境信号（environmental cues）的相对重要性，也可能随原产地纬度的不同而存在差异。