Folkertsma Remco, Charbonnel Nathalie, Henttonen Heikki, Heroldová Marta, Huitu Otso, Kotlík Petr, Manzo Emiliano, Paijmans Johanna L A, Plantard Olivier, Sándor Attila D, Hofreiter Michael, Eccard Jana A
Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of Science University of Potsdam Potsdam Germany.
Comparative Cognition Unit, Messerli Research Institute University of Veterinary Medicine Vienna Vienna Austria.
Ecol Evol. 2024 Mar 7;14(3):e10886. doi: 10.1002/ece3.10886. eCollection 2024 Mar.
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 the 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 () distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association 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, 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.
整个分布区域内趋异选择和适应性变异的证据能够为了解一个物种适应不同环境的能力提供线索。然而，尽管基因组学最近取得了进展，但在自然种群中仍难以检测到气候介导选择的痕迹。在这里，我们结合地理气候变异分析了12个分布于欧洲各地的小林姬鼠种群的ddRAD测序数据（21,892个单核苷酸多态性），以寻找适应性分化的特征。为了识别与气候变异相关的受选择位点，我们应用了多种基因型 - 环境关联方法，包括两种单变量方法和一种多变量方法，并控制了种群结构的影响。我们总共鉴定出213个适应性候选位点，其中74个位于基因内。特别是，我们在与脂质代谢和免疫系统相关功能的候选基因中鉴定出了选择特征。利用冗余分析的结果，我们证明了种群历史和气候对泛欧集合种群的遗传变异具有联合效应。此外，仅通过检查候选位点，我们发现年平均温度是塑造小林姬鼠适应性遗传变异的一个重要因素。通过结合景观基因组学方法，我们的研究揭示了全基因组适应性分化以及受当地气候影响的适应性变异基础变体的空间分布情况。
