Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet plateau

Jibin Miao, Perla Farhat, Wentao Wang, Markus Rusham, Richard I. Milne, Heng Yang, Sonam Tso, Jingjing Li, Jingjing Xu, Lars Opgenoorth, Georg Miehe, Kangshan Mao

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Background and Aims
Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP).

The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow endemic junipers from the QTP that are sister to each other, was surveyed using RNA-seq data. Coalescent-based analyses were used to test speciation, migration, and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species.

Key Results
Analyses of 149,052 single nucleotide polymorphisms showed that the two species are well-differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma and only one bottleneck for J. erectopatens. The identified positive selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter.

This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in the understanding of the current distribution pattern and genetic diversity of threatened species in mountainous regions.
Original languageEnglish
Article numbermcab114
JournalAnnals of Botany
Publication statusPublished - 2 Sept 2021

Keywords / Materials (for Non-textual outputs)

  • bottleneck event
  • conservation genomics
  • demographic history
  • effective population size
  • positively selected genes
  • habitat loss
  • Juniperus microsperma
  • Juniperus erectopatens
  • speciation history


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