J Syst Evol ›› 2020, Vol. 58 ›› Issue (3): 282-294.DOI: 10.1111/jse.12546

• Research Articles • Previous Articles     Next Articles

Nucleotide diversity and demographic history of Pinus bungeana, an endangered conifer species endemic in China

Yi-Xin Yang1,2†, Li-Qiang Zhi3†, Yun Jia1†, Qiu-Yi Zhong1, Zhan-Lin Liu1, Ming Yue1, and Zhong-Hu Li1*   

  1. 1Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
    2Medical Experiment Center, Shaanxi University of Chinese Medicine, Xianyang 712046, Shaanxi, China
    3Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, China
  • Received:2018-11-30 Accepted:2019-10-03 Online:2019-10-17 Published:2020-05-01


Orographic and climatic oscillations have played crucial roles in shaping the nucleotide diversity and evolutionary history of many species across the Northern Hemisphere. In this study, based on 10 nuclear loci and a chloroplast DNA marker, we analyzed the nucleotide polymorphisms and demographic history of the endangered conifer species Pinus bungeana in Northwest China and investigated the phylogenetic relationships between P. bungeana and two related species, that is, Pinus gerardiana and Pinus squamata. We found that P. bungeana exhibited an extremely low level of nucleotide diversity (πsil = 0.00159). Demographic simulations based on DIYABC analysis showed that P. bungeana underwent demographic expansion and contraction during the Miocene. According to ecological niche modeling, we found that this species survived in situ during the glacial period and was not restricted to southern refugia. We speculate that P. bungeana may have experienced widespread population shrinkage from the Last Interglacial to the Last Glacial Maximum due to geological or climatic events. Isolation‐with‐migration analysis revealed that the divergence (~2.4–4.2 Ma) among P. bungeana and its related species was significantly associated with the Qinghai–Tibetan Plateau uplift events in the mid‐to‐late Tertiary period. Species tree analyses suggested that these three related Pinus species formed a monophyletic clade with high bootstrap support. These results suggest that the Miocene–Pliocene and Pleistocene geological and climatic fluctuations might have profoundly affected the nucleotide diversity and demography of this psychrotolerant conifer species in western China.

Key words: climate fluctuation, ecological niche model, evolutionary history, nucleotide polymorphism, Pinus bungeana