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

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 (pi(sil) = 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 (similar to 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.