Table_1_Population Genomics Reveals Demographic History and Genomic Differentiation of Populus davidiana and Populus tremula.docx

Forest trees can increase our understanding of how evolutionary processes drive the genomic landscape and understand speciation due to the majority of forest trees being distributed widely and able to adapt to different climates and environments. Populus davidiana and Populus tremula are among the most geographically widespread and ecologically important tree species in Northern Hemisphere. Whole-genome resequencing data of 41 individuals of P. davidiana and P. tremula throughout Eurasia was conducted, finding that genetic differentiation was evident between the two species, the FST values between P. davidiana and P. tremula was 0.3625. The ancestors of the two aspen diverged into P. davidiana and P. tremula species approximately 3.60 million years ago (Mya), which was in accordance with the rapid uplift of Qinghai–Tibet Plateau (QTP) around the Miocene/Pliocene boundary. The two species experienced a considerable long-term bottleneck after divergence, with population expansion beginning approximately 20,000 years ago after the end of the last glacial maximum. Although the majority of regions of genomic differentiation between the two species can be explained by neutral evolutionary processes, some outlier regions have also been tested that are significantly influenced by natural selection. We found that the highly differentiated regions of the two species exhibited significant positive selection characteristics, and also identified long-term balancing selection in the poorly differentiated regions in both species. Our results provide strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between P. davidiana and P. tremula. These results provide the detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in P. davidiana and P. tremula.

林木多数类群分布广泛且可适应多样气候与环境条件，其研究有助于解析进化过程如何塑造基因组分化格局，并深化对物种形成机制的认知。山杨（Populus davidiana）与欧洲山杨（Populus tremula）是北半球地理分布最广、生态重要性最高的林木物种之一。本研究对欧亚大陆分布的41个山杨与欧洲山杨个体开展了全基因组重测序分析，结果显示两物种间存在显著的遗传分化，二者的群体分化系数（Fixation Index, FST）值为0.3625。这两个杨属物种的共同祖先约在360万年前（Mya，百万年前）分化为山杨与欧洲山杨，这一时间节点与中新世-上新世交界时期青藏高原（Qinghai–Tibet Plateau, QTP）的快速隆升事件相吻合。两物种在分化后经历了长期且显著的种群瓶颈事件，并在末次冰盛期结束后约2万年前开始种群扩张。尽管两物种间多数基因组分化区域可通过中性进化过程解释，但本研究也检测到部分异常分化区域受到了自然选择的显著作用。研究发现，两物种间的高分化区域呈现显著的正选择（positive selection）特征，同时在二者的低分化区域中也检测到了长期平衡选择（balancing selection）的信号。本研究结果为连锁选择（linked selection）在塑造山杨与欧洲山杨间异质性基因组分化格局中的作用提供了有力支撑。本研究结果为解析山杨与欧洲山杨的遗传多样性、种群历史动态（demography）、遗传负荷（genetic burden）及适应性演化机制提供了详实全面的基因组层面认知。