J Syst Evol ›› 2023, Vol. 61 ›› Issue (1): 11-21.DOI: 10.1111/jse.12828

• Research Articles • Previous Articles     Next Articles

Phylogenomics and rapid diversification of the genus Eutrema on the Qinghai–Tibet Plateau and adjacent regions

Yi Wang1†, Guo-Qian Hao1,2†, Xin-Yi Guo1,3†, Dan Zhang1, Quan-Jun Hu1, and Jian-Quan Liu1*   

  1. 1 Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
    2 Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644007, Sichuan, China
    3 Central European Institute of Technology (CEITEC), Masaryk University, Brno 625 00, Czech Republic

    These authors contributed equally to this work.
    *Author for correspondence. E‐mail: liujq@nwipb.cas.cn
  • Received:2021-10-24 Accepted:2022-01-03 Online:2022-01-11 Published:2023-01-01


Both geographic isolation and polyploidization are assumed to play an important role in driving species diversification. However, this is rarely illustrated through phylogenomic analyses. The genus Eutrema (Brassicaceae), which also includes the salt-resistant species, are distributed mainly in Asia with extensive species diversification in the Qinghai–Tibet Plateau (QTP) and adjacent regions. In this study, we revealed almost fully resolved backbone relationships of the genus with genome re-sequencing data for genomes of 168 individuals from 28 species. Phylogenetic analyses of both plastomes and single-copy nuclear genes from the whole genome recovered six well-supported clades with almost consistent relationships. The first two clades are mainly distributed in central China and central Asia, while the other four in the QTP and adjacent regions. All of them diversified within 12 million years. Within each clade, we recovered numerous conflicts in the interspecific relationships between nuclear and plastome phylogenies, likely suggesting hybridization and incomplete lineage sorting during species diversification. Our estimation of genome size and comparison of the number of the single-copy nuclear genes demonstrated frequent occurrences of polyploids in the genus. Except for an establishment of the backbone phylogeny, our phylogenomic analyses suggest that in addition to strong geographic isolation, polyploidization may have played an important role in species diversification of this genus.

Key words: Eutrema, hybridization, polyploidy, species diversification, whole‐genome phylogeny