Data from: The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales

The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the ‘intermediate’ and ‘regional’ scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.

对于缺乏近缘参考基因组的物种，其选择相关分子特征的评估仍具挑战性，但该类研究可为解析种群响应环境信号的能力提供极具价值的基础认知。我们针对覆盖三种不同地理尺度的欧鼠李原亚种（Frangula alnus subsp. alnus，鼠李科Rhamnaceae）的25个本土种群，对183个已注释的单核苷酸多态性（single-nucleotide polymorphisms, SNPs）进行了筛选。我们将标准群体基因组学异常位点筛选方法与基于个体的多元景观基因组学方法相结合，以探究在塑造基因组变异过程中，选择相较于中性演化过程的作用强度，并识别驱动选择的主要环境因子。研究结果显示，随着地理距离增加，选择相关分子特征愈发显著，具体体现为两类SNPs的占比提升：一是表现出异常遗传多样性与分化模式的异常位点，二是与气候相关的位点。温度与降水均为塑造欧鼠李原亚种适应性基因组分化的重要选择因子，不过二者的相对重要性随空间尺度有所差异。在“中等尺度”与“区域尺度”下，观测到有限的遗传聚类与较高的种群多样性，自然选择的相关迹象表明，基因流在维持种群适应性方面可能发挥了核心作用。尤其值得关注的是，受选择位点所呈现的高遗传多样性，预示着种群具备可观的适应性潜力，但气候变化与生境破碎化的联合效应或会削弱这一潜力。