Tree of life for the genera of Chinese vascular plants

doi:10.1111/jse.12219

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 Chen^1*, Tuo Yang^1,12, Li Lin^1,12, Li-Min Lu¹, Hong-Lei Li^1,2, Miao Sun¹, Bing Liu¹, Min Chen^1,12, Yan-Ting Niu^1,12, Jian-Fei Ye^1,12, Zhi-Yong Cao¹, Hong-Mei Liu², Xiao-Ming Wang², Wei Wang¹, Jing-Bo Zhang^1,12, 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 Xiang^1,12, Rui-Qi Li¹, Douglas E. Soltis^8,9,10, Pamela S. Soltis^9,10, Shi-Liang Zhou¹, Jin-Hua Ran¹, Xiao-Quan Wang¹, Xiao-Hua Jin¹, You-Sheng Chen¹, Tian-Gang Gao¹, Jian-Hua Li¹¹, Shou-Zhou Zhang^2*, An-Ming Lu^1*, and China Phylogeny Consortium^#

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 Published:2016-07-25
Contact: # Members of China Phylogeny Consortium are listed in the Appendix 1.

Abstract

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

Zhi-Duan Chen, Tuo Yang, Li Lin, Li-Min Lu, Hong-Lei Li, Miao Sun, Bing Liu, Min Chen, Yan-Ting Niu, Jian-Fei Ye, Zhi-Yong Cao, Hong-Mei Liu, Xiao-Ming Wang, Wei Wang, Jing-Bo Zhang, Zhen Meng, Wei Cao, Jian-Hui Li, Sheng-Dan Wu, Hui-Ling Zhao, Zhong-Jian Liu, Zhi-Yuan Du, Qing-Feng Wang, Jing Guo, Xin-Xin Tan, Jun-Xia Su, Lin-Jing Zhang, Lei-Lei Yang, Yi-Ying Liao, Ming-He Li, Guo-Qiang Zhang, Shih-Wen Chung, Jian Zhang, Kun-Li Xiang, Rui-Qi Li, Douglas E. Soltis, Pamela S. Soltis, Shi-Liang Zhou, Jin-Hua Ran, Xiao-Quan Wang, Xiao-Hua Jin, You-Sheng Chen, Tian-Gang Gao, Jian-Hua Li, Shou-Zhou Zhang, An-Ming Lu, China Phylogeny Consortium. Tree of life for the genera of Chinese vascular plants[J]. J Syst Evol, 2016, 54(4): 277-306.

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Tree of life for the genera of Chinese vascular plants

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