J Syst Evol ›› 2019, Vol. 57 ›› Issue (6): 633-645.DOI: 10.1111/jse.12543

• Research Articles • Previous Articles     Next Articles

Genomic insight into “sky island” species diversification in a mountainous biodiversity hotspot

Dan Zhang1†, Guo-Qian Hao1,2†, Xin-Yi Guo1,3†, Quan-Jun Hu1, and Jian-Quan Liu1,4*   

  1. 1Key Laboratory of Bio‐Resource and Eco‐Environment, College of Life Sciences and State Key Laboratory of Hydraulics & Mountain River Engineering, Ministry of Education, Sichuan University, Chengdu 610065, China
    2Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan 614000, Sichua, China
    3CEITEC—Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
    4State Key Laboratory of Grassland Agro‐Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, China
  • Received:2019-05-15 Accepted:2019-09-17 Published:2019-11-01


“Sky island” species diversification contributes greatly to mountainous biodiversity. However, the underlying genomic divergence and the inferred drivers remain largely unknown. In this study, we examined the diversification history of five diploid species with three exclusively endemic to the sky islands (mountains) of the Himalaya–Hengduan Mountains biodiversity hotspot. All of them together comprise a clade of the genus Eutrema (Brassicaceae). We resequenced genomes of multiple individuals of the found populations for each species. We recovered the inconsistent phylogenetic relationships between plastome and nuclear‐genome trees for one species. Based on nuclear population genomic data, we detected high genetic divergence between five species with limited gene flow. Four species seemed to diverge mainly through geographical isolation, whereas one arose through hybrid origin. The origins of the sampled five species were dated to within the late Miocene when mountains were uplifted and climates oscillated. All species decreased their population sizes since the inferred origin of each species initially, but only two of them expanded after the Last Glacial Maximum. Together, these findings suggest that geographic isolation plays an important role in driving the sky island species diversification of the sampled species in addition to the occasional gene flow that might have led to the hybrid origin of some sky island species, similar to the species diversification of sea islands.

Key words: Eutrema, evolutionary history, population genomics, sky island