J Syst Evol ›› 2016, Vol. 54 ›› Issue (4): 277-306.doi: 10.1111/jse.12219

• Research Articles • Previous Articles     Next Articles

Tree of life for the genera of Chinese vascular plants

Zhi-Duan Chen1*, Tuo Yang1,12, Li Lin1,12, Li-Min Lu1, Hong-Lei Li1,2, Miao Sun1, Bing Liu1, Min Chen1,12, Yan-Ting Niu1,12, Jian-Fei Ye1,12, Zhi-Yong Cao1, Hong-Mei Liu2, Xiao-Ming Wang2, Wei Wang1, Jing-Bo Zhang1,12, Zhen Meng3, Wei Cao3, Jian-Hui Li3, Sheng-Dan Wu4, Hui-Ling Zhao4,Zhong-Jian Liu5, Zhi-Yuan Du6, Qing-Feng Wang6, Jing Guo4, Xin-Xin Tan4, Jun-Xia Su4, Lin-Jing Zhang4, Lei-Lei Yang2, Yi-Ying Liao2, Ming-He Li5, Guo-Qiang Zhang5, Shih-Wen Chung7, Jian Zhang1, Kun-Li Xiang1,12, Rui-Qi Li1, Douglas E. Soltis8,9,10, Pamela S. Soltis9,10, Shi-Liang Zhou1, Jin-Hua Ran1, Xiao-Quan Wang1, Xiao-Hua Jin1, You-Sheng Chen1, Tian-Gang Gao1, Jian-Hua Li11, Shou-Zhou Zhang2*, An-Ming Lu1*, and China Phylogeny Consortium#   

  1. 1State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
    2Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China
    3Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
    4College of Life Sciences, Shanxi Normal University, Linfen 041004, Shanxi, China
    5The Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China
    6Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
    7Department of Botany, Taiwan Forestry Research Institute, 20 Nan-Hai Road, Taipei 100, China
    8Department of Biology, University of Florida, Gainesville, FL 32611, USA
    9Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
    10Genetics Institute, University of Florida, Gainesville, FL 32610, USA  11Biology Department, Hope College, Holland, MI 49423, USA  12University of Chinese Academy of Sciences, Beijing 100049, China
  • Received:2016-05-22 Online:2016-06-23 Published:2016-07-25
  • Contact: # Members of China Phylogeny Consortium are listed in the Appendix 1.

Abstract: We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13?695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.

Key words: China, DarwinTree, megaphylogeny, regional tree of life, SoTree, vascular plants

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