Biodiv Sci ›› 2017, Vol. 25 ›› Issue (6): 675-682.  DOI: 10.17520/biods.2017042

Special Issue: 物种形成与系统进化

• Original Papers • Previous Articles     Next Articles

The complex reticulate evolutionary relationships of early terrestrial plants as revealed by phylogenomics analysis

Jiangping Shu1,2, Li Liu1,2, Hui Shen2, Xiling Dai1, Quanxi Wang1,4, Yuehong Yan2,3,4,*()   

  1. 1 College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234
    2 Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences; Shanghai Chenshan Botanical Garden, Shanghai 201602
    3 East China Wild Endangered Resources Plant Conservation Center, State Forestry Administration, Shanghai 201602
    4 Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai 201602
  • Received:2017-02-18 Accepted:2017-06-20 Online:2017-06-20 Published:2017-07-10
  • Contact: Yan Yuehong


Plants from aquatic to terrestrial ecosystems have undergone a very complex evolution, and their evolutionary pathways of large numbers of genes may be different from one another, so that traditional phylogenetic trees cannot show true evolutionary relationships. The phylogenetic network graph is a good solution to show the complex relationships of reticulate evolution, including vertical evolution and horizontal evolution. In this paper, we selected Chlamydomonas reinhardtii and four terrestrial plants, and screened 1,668 one-to-one orthologous genes to reconstruct the phylogenetic relationship of terrestrial plants based on phylogenomics. Results showed that phylogenetic trees were different based on different analysis strategies. The 1,668 genes were analyzed separately and 15 different topologies were found. The phylogenetic network of the orthologous genes obtained from the five species was analyzed, and the results showed that in a very robust phylogenetic network map, only five species have nine different split branches, suggesting a very complex evolutionary relationship network. Futhermore, the difference in split branches between algae and bryophytes or lycophytes is very small, which may be one of the reasons influencing the phylogenetic tree conflict, and implies that early terrestrial plants underwent a complex radiate evolution.

Key words: reticulate evolution, gene tree conflict, phylogenomics, terrestrial plant evolution, de novo transcriptome