Data from: Influence of range position on locally adaptive gene-environment associations in Populus flowering time genes

Local adaptation is pervasive in forest trees, which are characterized by large effective population sizes spanning broad climatic gradients. In addition to having relatively contiguous populations, many species also form isolated populations along the rear edge of their range. These rear-edge populations may contain unique adaptive diversity reflecting a history of selection in marginal environments. Thus, discovering genomic regions conferring local adaptation in rear edge populations is a key priority for landscape genomics to ensure conservation of genetic resources under climate change. Here, we report on adaptive gene-environment associations in SNPs from 27 genes in the Populus flowering time gene network, analyzed on a range-wide collection of >1000 balsam poplar trees, including dense sampling of the southern range edge. We use a combined approach of local adaptation scans to identify candidate SNPs, followed by modeling the compositional turnover of adaptive SNPs along multivariate climate gradients using Gradient Forests (GF). Flowering time candidate genes contained extensive evidence of climate adaptation, namely outlier population structure and gene-environment associations, along with allele frequency divergence between the core and edge of the range. GF showed strong allele frequency turnover along gradients of elevation and diurnal temperature variability, as well as threshold responses to summer temperature and precipitation, with turnover especially strong in edge populations that occur at high elevation but southerly latitudes. We discuss these results in light of how climate may disrupt locally adaptivegene-environment relationships, and suggest that rear edge populations hold climate-adaptive variants that should be targeted for conservation.

本地适应在林木中普遍存在，这类植物的特征是拥有庞大的有效种群规模，且分布横跨广泛的气候梯度。除了拥有相对连续的种群外，许多物种还会在其分布范围的后缘形成孤立种群。这些后缘种群可能蕴含独特的适应性多样性，反映了其在边缘环境中历经选择的演化历史。因此，发掘后缘种群中赋予本地适应性的基因组区域，是景观基因组学（landscape genomics）在气候变化背景下保障遗传资源保育的核心要务。本研究针对杨属（Populus）开花时间基因调控网络中27个基因的单核苷酸多态性位点（Single Nucleotide Polymorphisms，SNPs）展开分析，报道其中的适应性基因-环境关联；我们的分析样本覆盖了全分布范围的1000余株香脂杨（balsam poplar），其中包括对分布范围南缘的高密度采样。我们采用联合分析策略：先通过本地适应扫描鉴定候选SNPs，随后借助梯度森林（Gradient Forests，GF）模型，探究适应性SNPs沿多变量气候梯度的组成更替模式。候选开花时间基因展现出大量气候适应的证据，具体包括异常种群结构、基因-环境关联，以及分布范围核心区与边缘区间的等位基因频率分化。梯度森林分析显示，等位基因频率沿海拔梯度与昼夜温度变异性梯度呈现显著更替，同时对夏季温度与降水存在阈值响应；在高海拔但处于偏南纬度的边缘种群中，这种更替尤为显著。我们结合气候变化如何破坏本地适应性基因-环境关联的视角讨论了本研究结果，并提出后缘种群蕴含气候适应性变异，应将其列为保育优先目标。