BACKGROUND AND AIMS The biogeographic patterns of the East-Asia-endemic shrub Magnolia sieboldii, in which the range of the subsp. sieboldii is intervened by the disjunct distribution of subsp. japonica, implies a complex evolutionary history, involving rapid speciation and hybridization. Here, we aim to reveal the evolutionary and phylogeographic histories of the species with a particular focus on the time of subspecies divergence, the hypothesis of secondary hybridization, and the Pleistocene survival of each subspecies, using a combination of genetic analyses and ecological niche modelling. METHODS Genetic variation, genetic structures, and phylogenetic relationships were elucidated based on nuclear low-copy genes, chloroplast DNA, and nuclear SSRs. A scenario selection analysis and divergence time estimation were performed using coalescent simulation in DIYABC and *BEAST . Ecological niche modelling and a test of niche differentiation were performed using Maxent and ENMTools. KEY RESULTS All marker types showed deep, but pronouncedly incongruent, west-east genetic divergences, with the subspecies being delineated only by the nuclear low-copy genes. Phylogenetic tree topologies suggested that ancient hybridization and introgression were likely to have occurred; however, this scenario did not receive significant support in the DIYABC analysis. The subspecies differentiated their niches, but both showed a dependence on high humidity and were predicted to have persisted during the last glacial cycle by maintaining a stable latitudinal distribution via migration to lower altitudes. CONCLUSIONS We found a deep genetic divergence and a pronounced phylogenetic incongruence among the two subspecies of M. sieboldii, which may have been driven by major paleogeographic and paleoclimatic events that occurred since the Neogene in East Asia, including global cooling, climate oscillations and the formation of land bridges. Both subspecies were, however, considered to persist in situ in stable climatic conditions during the late Pleistocene.

中文翻译：

---

东亚地方性灌木 Magnolia sieboldii 的亚种分化和明显的系统发育不一致

背景和目的东亚地方性灌木 Magnolia sieboldii 的生物地理模式，其中亚种的范围。sieboldii 被 subsp 的分离分布所干预。japonica，意味着复杂的进化历史，涉及快速的物种形成和杂交。在这里，我们旨在通过遗传分析和生态位建模的组合，揭示物种的进化和系统地理学历史，特别关注亚种分化的时间、二次杂交的假设和每个亚种的更新世存活。方法基于核低拷贝基因、叶绿体DNA和核SSRs阐明遗传变异、遗传结构和系统发育关系。使用 DIYABC 和 *BEAST 中的聚结模拟进行场景选择分析和发散时间估计。使用 Maxent 和 ENMTools 进行生态位建模和生态位分化测试。主要结果 所有标记类型都显示出深度但明显不一致的东西向遗传差异，亚种仅由核低拷贝基因描述。系统发育树拓扑结构表明可能发生了古代杂交和基因渗入；然而，这种情景在 DIYABC 分析中并未得到显着支持。这些亚种区分了它们的生态位，但两者都表现出对高湿度的依赖，并且通过迁移到低海拔来维持稳定的纬度分布，预计它们会在最后一个冰川周期中持续存在。结论 我们发现 M. sieboldii 的两个亚种之间存在深刻的遗传差异和明显的系统发育不一致，这可能是由东亚新近纪以来发生的主要古地理和古气候事件驱动的，包括全球变冷、气候振荡和形成的陆桥。然而，这两个亚种都被认为在晚更新世期间在稳定的气候条件下原地存在。