Shahzad Khurram, Liu Mi-Li, Zhao Yu-He, Zhang Ting-Ting, Liu Jian-Ni, Li Zhong-Hu
Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education College of Life Sciences Northwest University Xi'an China.
Department of Geology Early Life Institute State Key Laboratory of Continental Dynamics Northwest University Xi'an China.
Ecol Evol. 2020 Nov 11;10(24):14052-14066. doi: 10.1002/ece3.6996. eCollection 2020 Dec.
Geological and climatic events are considered to profoundly affect the evolution and lineage divergence of plant species. However, the evolutionary histories of tree species that have responded to past geological and climate oscillations in central China's mountainous areas remain mostly unknown. In this study, we assessed the evolutionary history of the endangered and relict tree species in the Qinling Mountains (QM) and adjacent areas in East Asia based on variations in the complete chloroplast genomes (cpDNA) and reduced-genomic scale single nucleotide polymorphisms (SNPs). Population structure and phylogenetic analysis based on the cpDNA variations suggested that could be divided into two intraspecific genetic lineages in the eastern and western sides of the QM (EQM and WQM, respectively) in East Asia. Molecular dating suggested that the intraspecific divergence of occurred approximately 39.2 million years ago during the later Paleogene. It was significantly correlated with the orogeny of the QM, where the formation of this significant geographic barrier in the region may have led to the divergence of independent lineages. Bayesian clustering and demographic analysis showed that intraspecific gene flow was restricted between the EQM and WQM lineages. Isolation-with-migration analysis indicated that the two genetic lineages experienced significant demographic expansions after the Pleistocene ice ages. However, the genetic admixture was determined in some populations between the two lineages by the large scale of SNP variations due to DNA incompatibility, the large significant population size, and rapid gene flow of nuclear DNA markers. Our results suggest that two different conservation and management units should be constructed for in the EQM and WQM areas. These findings provide novel insights into the unprecedented effects of tectonic changes and climatic oscillations on lineage divergence and plant population evolution in the QM and adjacent areas in East Asia.
地质和气候事件被认为对植物物种的进化和谱系分化有深远影响。然而，在中国中部山区对过去地质和气候振荡做出响应的树种的进化历史大多仍不为人知。在本研究中，我们基于完整叶绿体基因组（cpDNA）变异和简化基因组规模单核苷酸多态性（SNP），评估了秦岭及东亚邻近地区濒危和残遗树种的进化历史。基于cpDNA变异的种群结构和系统发育分析表明，该树种在东亚可分为秦岭东西两侧的两个种内遗传谱系（分别为东秦岭和西秦岭）。分子定年表明，该树种的种内分化发生在古近纪晚期约3920万年前。这与秦岭的造山运动显著相关，该地区这一重要地理屏障的形成可能导致了独立谱系的分化。贝叶斯聚类和种群统计学分析表明，东秦岭和西秦岭谱系之间的种内基因流受到限制。隔离迁移分析表明，这两个遗传谱系在更新世冰期后经历了显著的种群扩张。然而，由于DNA不兼容性导致的大规模SNP变异、大量显著的种群规模以及核DNA标记的快速基因流，在两个谱系的一些种群中确定了遗传混合现象。我们的结果表明，应在东秦岭和西秦岭地区为该树种构建两个不同的保护和管理单元。这些发现为构造变化和气候振荡对东亚秦岭及邻近地区谱系分化和植物种群进化的前所未有的影响提供了新的见解。
