Data from: Genomic signatures of climate adaptation in bank voles

Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species’ ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect footprints of climate mediated selection in natural populations. Here we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association (GEA) methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis (RDA), we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.

景观尺度上的歧化选择与适应性变异证据，可为解析物种适应不同环境的能力提供重要见解。然而，尽管基因组学领域近年取得显著进展，在自然种群中检测气候介导选择的分子印记仍颇具难度。本研究针对分布于欧洲的12个欧洲棕背䶄（Clethrionomys glareolus）种群，结合地理气候变异分析双酶切限制性位点相关DNA测序（ddRAD sequencing）数据（涵盖21892个单核苷酸多态性（Single Nucleotide Polymorphism，SNPs）位点），以探寻适应性分化的分子特征。为鉴定受气候变异相关选择作用的基因位点，我们采用了多种基因型-环境关联（GEA）分析方法，包含2种单变量方法与1种多变量方法，并对种群结构的影响进行了控制。最终共鉴定出213个适应性候选位点，其中74个位于基因内部。尤为值得关注的是，我们在与脂质代谢及免疫系统功能相关的候选基因中发现了选择作用的分子特征。借助冗余分析（RDA）的结果，我们证实种群历史与气候对泛欧洲集合种群的遗传变异存在联合影响。进一步仅针对候选位点开展分析后发现，年平均气温是塑造欧洲棕背䶄适应性遗传变异的关键驱动因子。本研究结合景观基因组学研究手段，揭示了欧洲棕背䶄全基因组范围内的适应性分化，以及受局地气候调控的适应性变异相关变异体的空间分布格局。