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Journal of Systematics and Evolution  2016, Vol. 54 Issue (4): 277-306    DOI: 10.1111/jse.12219
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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#
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
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#
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
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摘要: 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.
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 wordsChina;    DarwinTree;    megaphylogeny;    regional tree of life;    SoTree;    vascular plants;
收稿日期: 2016-05-22      suppinfo 出版日期: 2016-06-23
通讯作者: # Members of China Phylogeny Consortium are listed in the Appendix 1.   
Corresponding author: # Members of China Phylogeny Consortium are listed in the Appendix 1.   
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Zhi-Duan Chen
Tuo Yang
Li Lin
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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
引用本文:

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. . Journal of Systematics and Evolution, 2016, 54(4): 277-306.
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. Chinese Journal of Plant Ecology, 2016, 54(4): 277-306.

链接本文:

http://www.jse.ac.cn/CN/10.1111/jse.12219      或      http://www.jse.ac.cn/CN/Y2016/V54/I4/277

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