Suda Ryo A, Kubota Shosei, Kumar Vinod, Castric Vincent, Krämer Ute, Morinaga Shin-Ichi, Tsuchimatsu Takashi
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan.
Fasmac Co., Ltd., 3088 Okada, Atsugi, Kanagawa, 243-0021 Japan.
Plant Cell Physiol. 2025 May 17;66(4):529-541. doi: 10.1093/pcp/pcae113.
Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (∼50, 000 years ago). The ecological niche modeling predicted the geographic or distribution range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.
第四纪的气候振荡迫使物种发生重大的纬度或海拔范围变化。有人认为，与范围变化相伴的适应在气候振荡期间物种的响应中起着关键作用，但针对气候变化的局部适应选择的作用在很大程度上仍未得到探索。在此，我们基于141个日本南芥个体的全基因组多态性数据，并以外群欧洲个体为参照，研究了种群结构、种群历史以及气候驱动选择的特征。基于溯祖理论的分析表明，自末次冰期（LGP）以来日本亚种群之间存在遗传分化，这可能促成了当前种群结构模式的形成。种群动态分析揭示了末次冰期种群数量的波动，自亚种群开始分化（约5万年前）以来这种波动尤为显著。生态位模型预测了地理分布范围可能从南部沿海地区向北部沿海和山区转移，这可能与种群数量波动有关。通过对生物气候变量的全基因组关联分析和选择扫描，我们研究了与气候相关的基因座是否在选择扫描的极端尾部富集，并证明了选择的主要特征，特别是南部亚种群朝向温暖气候以及北部亚种群朝向干燥环境的选择，这可能发生在末次冰期期间或之后。我们的研究强调了整合气候关联、选择扫描和种群动态分析对于识别种群特异性适应的基因组特征的重要性，这也将有助于我们预测对未来气候变化的进化响应。
