Tree of life for the genera of Chinese vascular plants
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 taxonomi...
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| Published in | Journal of systematics and evolution : JSE Vol. 54; no. 4; pp. 277 - 306 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Beijing
Blackwell Publishing Ltd
01.07.2016
Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1674-4918 1759-6831 |
| DOI | 10.1111/jse.12219 |
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| 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. |
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| AbstractList | 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. 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. 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 13695 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. |
| Author | 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 |
| AuthorAffiliation | State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen ＆ Chinese Academy of Sciences,Shenzhen 518004, China Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China College of Life Sciences, Shanxi Normal University, Linfen 041004, China The Orchid Conservation ＆ Research Center of Shenzhen, Shenzhen 518114, China Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China Department of Botany, Taiwan Forestry Research Institute, 20 Nan-Hai Road, Taipei 100, China Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA Genetics Institute, University of Florida, Gainesville, FL 32610, USA Biology Department, Hope College, Holland, MI 49423, USA University of Chinese A |
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Gainesville, FL 32611, USA – sequence: 37 givenname: Pamela S. surname: Soltis fullname: Soltis, Pamela S. organization: Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA – sequence: 38 givenname: Shi-Liang surname: Zhou fullname: Zhou, Shi-Liang organization: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China – sequence: 39 givenname: Jin-Hua surname: Ran fullname: Ran, Jin-Hua organization: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China – sequence: 40 givenname: Xiao-Quan surname: Wang fullname: Wang, Xiao-Quan organization: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China – sequence: 41 givenname: Xiao-Hua surname: Jin fullname: Jin, Xiao-Hua organization: State Key Laboratory of Systematic and 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Z.-D. Chen. . Tel.: +86-010-62836434. Fax: +86-010-62836095. A.-M. Lu. . Tel.: +86-010-62836448. Fax: +86-010-62836095. S.-Z. Zhang . Tel.: +86-755-25732477. Fax: +86-755-25734474, zhiduan@ibcas.ac.cnanmin@ibcas.ac.cnszzhang@126.com organization: Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China – sequence: 46 givenname: An-Ming surname: Lu fullname: Lu, An-Ming email: Authors for correspondence. Z.-D. Chen. . Tel.: +86-010-62836434. Fax: +86-010-62836095. A.-M. Lu. . Tel.: +86-010-62836448. Fax: +86-010-62836095. S.-Z. Zhang . Tel.: +86-755-25732477. Fax: +86-755-25734474, zhiduan@ibcas.ac.cnanmin@ibcas.ac.cnszzhang@126.com organization: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China |
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| Language | English |
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| Notes | China, DarwinTree, megaphylogeny, regional tree of life, SoTree, vascular plants. 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. 11-5779/Q Chinese Academy of Sciences Externa1 Cooperation Program of BIC - No. GJHZ201321 National Key Basic Research Program of China - No. 2014CB954100 ArticleID:JSE12219 US National Science Foundation for Open tree - No. DEB-1208428 Science and Technology Basic Work - No. 2013FY112100 Shenzhen Science and Technology Innovation Council Funding - No. KQC 201105310009A iDigBio - No. EF-1115210 ark:/67375/WNG-PQ10J2GR-N Chinese Academy of Sciences Visiting Professorship for Senior International Scientists - No. 2011T1S24 National Natural Science Foundation of China - No. 31270268; No. 31270269 Chinese Academy of Sciences International Institution Development Program - No. SAJC201315 istex:9965CC9DBBD1C1CD37048B8730E8F447B1024BFC National Natural Science Foundation of China - No. 31590822 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
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| PublicationDate | July 2016 |
| PublicationDateYYYYMMDD | 2016-07-01 |
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| PublicationDecade | 2010 |
| PublicationPlace | Beijing |
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| PublicationTitle | Journal of systematics and evolution : JSE |
| PublicationTitleAlternate | Journal of Systematics and Evolution |
| PublicationYear | 2016 |
| Publisher | Blackwell Publishing Ltd Wiley Subscription Services, Inc |
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Exploring generic delimitation within the fern family Thely 2013; 4 2013; 2 2011b; 49 1978a; 16 2011; 59 2000; 133 2000; 134 1998; 85 2013; 5 2011a; 108 2014; 22 1978 2009; 12 2004; 32 2010; 20 2004; 31 1940; 5 2000; 16 2000; 17 1990 2002; 89 2000; 97 2014; 14 2007; 7 1981 2007; 168 2007; 689 2006; 55 2015; 53 1998 2008; 57 1994 1996; 13 2001; 21 1999 2012; 195 2010; 48 2015a; 53 1997; 35 2015b; 14 2008; 46 2014; 30 2010; 52 2006; 103 2009; 106 2012; 61 1997; 84 2015; 102 2011; 11 2011; 98 1999; 86 2011; 12 2016; 181 1999; 402 2014; 5 2003; 90 2001 2002; 40 1997; 14 2005; 148 2000; 55 2009; 161 1993; 80 1999; 96 2014; 52 2012; 65 1996; 21 1950; 1 2015; 15 2013; 48 1995; 92 2000; 25 2011 2010 2002; 33 2016; 54 2009 1992; 79 2001; 409 2005 2003 2002 2004; 91 1987; 19 2007; 56 2014; 82 2008; 90 1994; 43 2006; 311 1978b; 16 2011; 108 2002; 163 2013; 30 2009; 9 2013 2007; 44 1998; 36 2014; 101 2003; 141 2014; 75 Wu ZY (e_1_2_8_115_1) 1998; 36 e_1_2_8_26_1 e_1_2_8_49_1 e_1_2_8_68_1 Hong DY (e_1_2_8_40_1) 2013 Wang ZC. (e_1_2_8_107_1) 1994 Wu ZY (e_1_2_8_112_1) 2002; 40 Cheng WC (e_1_2_8_18_1) 1978 e_1_2_8_5_1 Soltis DE (e_1_2_8_93_1) 2005 e_1_2_8_9_1 e_1_2_8_117_1 Hu HH. (e_1_2_8_43_1) 1950; 1 e_1_2_8_22_1 e_1_2_8_64_1 e_1_2_8_87_1 e_1_2_8_60_1 e_1_2_8_83_1 e_1_2_8_109_1 e_1_2_8_15_1 e_1_2_8_38_1 e_1_2_8_57_1 Huang HW (e_1_2_8_45_1) 2013 e_1_2_8_120_1 e_1_2_8_91_1 e_1_2_8_95_1 e_1_2_8_99_1 e_1_2_8_105_1 e_1_2_8_11_1 e_1_2_8_34_1 Heath TA (e_1_2_8_37_1) 2008; 46 e_1_2_8_53_1 e_1_2_8_76_1 e_1_2_8_101_1 e_1_2_8_30_1 e_1_2_8_72_1 Zhang YX (e_1_2_8_121_1) 2013 e_1_2_8_29_1 Chen ZD (e_1_2_8_17_1) 1998; 36 Wu ZY (e_1_2_8_113_1) 2003 e_1_2_8_2_1 Bayer C (e_1_2_8_6_1) 2003 e_1_2_8_110_1 Kubitzki K (e_1_2_8_48_1) 1998 e_1_2_8_67_1 e_1_2_8_86_1 e_1_2_8_118_1 e_1_2_8_63_1 e_1_2_8_82_1 e_1_2_8_14_1 e_1_2_8_79_1 Wang XQ (e_1_2_8_104_1) 1998; 36 e_1_2_8_94_1 e_1_2_8_90_1 e_1_2_8_98_1 Ching RC. (e_1_2_8_19_1) 1940; 5 Cronquist A. (e_1_2_8_23_1) 1981 e_1_2_8_10_1 e_1_2_8_56_1 e_1_2_8_106_1 e_1_2_8_75_1 e_1_2_8_52_1 e_1_2_8_102_1 e_1_2_8_71_1 e_1_2_8_28_1 e_1_2_8_24_1 e_1_2_8_47_1 Doweld A (e_1_2_8_25_1) 2008; 90 e_1_2_8_3_1 e_1_2_8_81_1 e_1_2_8_111_1 e_1_2_8_7_1 e_1_2_8_66_1 e_1_2_8_89_1 e_1_2_8_119_1 e_1_2_8_85_1 Meng Z (e_1_2_8_62_1) 2010; 20 e_1_2_8_13_1 e_1_2_8_36_1 e_1_2_8_59_1 Ge S (e_1_2_8_33_1) 1997; 35 e_1_2_8_122_1 e_1_2_8_97_1 e_1_2_8_32_1 e_1_2_8_55_1 e_1_2_8_78_1 Wu ZY (e_1_2_8_114_1) 1994 Hong DY (e_1_2_8_41_1) 2008; 46 e_1_2_8_51_1 e_1_2_8_74_1 Peng H. (e_1_2_8_70_1) 2013 e_1_2_8_46_1 e_1_2_8_27_1 e_1_2_8_69_1 e_1_2_8_80_1 e_1_2_8_4_1 Hu QM (e_1_2_8_44_1) 2013 e_1_2_8_8_1 Ching RC. (e_1_2_8_21_1) 1978; 16 e_1_2_8_42_1 e_1_2_8_88_1 e_1_2_8_116_1 e_1_2_8_65_1 e_1_2_8_84_1 e_1_2_8_61_1 e_1_2_8_39_1 e_1_2_8_35_1 Ching RC. (e_1_2_8_20_1) 1978; 16 e_1_2_8_16_1 e_1_2_8_58_1 e_1_2_8_92_1 e_1_2_8_96_1 e_1_2_8_100_1 e_1_2_8_31_1 e_1_2_8_77_1 e_1_2_8_12_1 e_1_2_8_54_1 Wang XQ (e_1_2_8_103_1) 1997; 35 e_1_2_8_108_1 e_1_2_8_73_1 e_1_2_8_50_1 |
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| Snippet | We reconstructed a phylogenetic tree of Chinese vascular plants （Tracheophyta） using sequences of the chloroplast genes atpB, matk, ndhF, and rbcL and... We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and... |
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| SubjectTerms | China chloroplasts DarwinTree Dipterocarpaceae DNA Ferns ferns and fern allies Flora Flowers & plants genes Gymnospermae megaphylogeny mitochondria monophyly nucleotide sequences paraphyly Phylogenetics Phylogeny regional tree of life Santalaceae Sapotaceae SoTree Taxonomy Tracheophyta vascular plants |
| Title | Tree of life for the genera of Chinese vascular plants |
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