Understanding how the environment shapes genetic variation provides critical insight about the evolution of local adaptation in natural populations. At multiple spatial scales and multiple geographic contexts within a single species, such information could address a number of fundamental questions about the scale of local adaptation and whether or not the same loci are involved at different spatial scales or geographic contexts. We used landscape genomic approaches from three local elevational transects and rangewide sampling to (a) identify genetic variation underlying local adaptation to environmental gradients in the California endemic oak, Quercus lobata; (b) examine whether putatively adaptive SNPs show signatures of selection at multiple spatial scales; and (c) map putatively adaptive variation to assess the scale and pattern of local adaptation. Of over 10 k single‐nucleotide polymorphisms (SNPs) generated with genotyping‐by‐sequencing, we found signatures of natural selection by climate or local environment at over 600 SNPs (536 loci), some at multiple spatial scales across multiple analyses. Candidate SNPs identified with gene–environment tests (LFMM) at the rangewide scale also showed elevated associations with climate variables compared to the background at both rangewide and elevational transect scales with gradient forest analysis. Some loci overlap with those detected in other oak species, raising the question of whether the same loci might be involved in local climate adaptation in different congeneric species that inhabit different geographic contexts. Mapping landscape patterns of adaptive versus background genetic variation identified regions of marked local adaptation and suggests nonlinear association of candidate SNPs and environmental variables. Taken together, our results offer robust evidence for novel candidate genes for local climate adaptation at multiple spatial scales.

中文翻译：

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阔叶栎的景观基因组学揭示了在多个空间尺度上参与局部气候适应的基因

了解环境如何影响遗传变异可提供有关自然种群中局部适应性进化的重要见解。在单个物种内的多个空间尺度和多个地理环境下，此类信息可以解决一些有关局部适应规模以及是否在不同的空间尺度或地理环境下涉及同一基因座的基本问题。我们使用了来自三个局部高程样线的景观基因组学方法，并进行了范围广泛的采样，以（a）确定加利福尼亚地方性栎类栎（Quercus lobata）局部适应环境梯度的遗传变异; （b）检查假定的自适应SNP是否在多个空间尺度上显示选择的特征；（c）映射假定的适应性变化，以评估局部适应的规模和模式。在通过基因分型测序产生的超过10 k单核苷酸多态性（SNP）中，我们发现了600多个SNP（536个基因座）的气候或当地环境的自然选择特征，其中一些在多个分析的多个空间尺度上。通过基因环境测试（LFMM）在范围范围内鉴定出的候选SNPs也显示出与气候变量的关联性高于通过梯度森林分析在范围范围内和高程横断面范围内与背景相比的背景。一些位点与其他橡树物种中发现的位点重叠，提出了一个问题，即同一个基因座是否可能参与居住在不同地理环境中的不同同类物种的当地气候适应。绘制适应性与背景性遗传变异的景观格局可识别出明显的局部适应性区域，并暗示候选SNP与环境变量之间的非线性关联。综上所述，我们的结果为多种空间尺度上的局部气候适应新候选基因提供了有力的证据。