IHB OpenIR  > 藻类生物学及应用研究中心  > 期刊论文
Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models
Fang, Ling1; Leliaert, Frederik2,3; Novis, Phil4; Zhang, Zhenhua1; Zhu, Huan5; Liu, Guoxiang5; Penny, David6; Zhong, Bojian1
Corresponding AuthorZhong, Bojian(bjzhong@gmail.com)
2018-10-01
Source PublicationMOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN1055-7903
Volume127Pages:248-255
AbstractPhylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve. The core Chlorophyta include Chlorophyceae, Ulvophyceae, Trebouxiophyceae, Pedinophyceae and Chlorodendrophyceae, but the relationships among these classes remain unresolved and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial. We analyzed a dataset of 101 green algal species and 73 protein-coding genes sampled from complete and partial chloroplast genomes, including six newly sequenced ulvophyte genomes (Blidingia minima NIES-1837, Ulothrix zonata, Halochlorococcum sp. NIES-1838, Scotinosphaera sp. NIES-154, Caulerpa brownii and Cephaleuros sp. HZ-2017). We applied the Tree Certainty (TC) score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets, and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites. With removing the most GC-heterogeneous sites, our chloroplast phylogenomic analyses using heterogeneous models consistently support monophyly of the Chlorophyceae and of the Trebouxiophyceae, but the Ulvophyceae was resolved as polyphyletic. Our analytical framework provides an efficient approach to reconstruct the optimal phylogenetic relationships by minimizing conflicting signals.
KeywordGreen algae Phylogenomics GC-heterogeneous sites Heterogeneous models Phylogenetic signals
DOI10.1016/j.ympev.2018.06.006
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand
Indexed BySCI ; SCI
Language英语
Funding ProjectNational Natural Science Foundation of China[31570219] ; Natural Science Foundation of Jiangsu Province[BK20150971] ; Jiangsu Province Key Project for Scientific Research[16KJA180002] ; Six Talent Peaks Projects of Jiangsu Province[2016-XNY-035] ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand
WOS Research AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS IDWOS:000446021300021
WOS KeywordNONCANONICAL GENETIC-CODE ; COCCOID GREEN-ALGAE ; LAND PLANTS ; ORIGIN ; TREBOUXIOPHYCEAE ; GENUS ; ROOT ; NOV. ; TREE ; 18S
PublisherACADEMIC PRESS INC ELSEVIER SCIENCE
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Natural Science Foundation of Jiangsu Province ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Jiangsu Province Key Project for Scientific Research ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Six Talent Peaks Projects of Jiangsu Province ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; Qing Lan Project ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand ; SSIF funding for Crown Research Institutes from the Ministry of Business, Innovation and Employment's Science and Innovation Group, New Zealand
Citation statistics
Cited Times:3[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/28952
Collection藻类生物学及应用研究中心_期刊论文
中科院水生所知识产出(2009年前)
Corresponding AuthorZhong, Bojian
Affiliation1.Nanjing Normal Univ, Coll Life Sci, Nanjing 210023, Jiangsu, Peoples R China
2.Bot Garden Meise, B-1860 Meise, Belgium
3.Univ Ghent, Phycol Res Grp, Biol Dept, B-9000 Ghent, Belgium
4.Manaaki Whenua Landcare Res, Allan Herbarium, Lincoln 7640, New Zealand
5.Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China
6.Massey Univ, Inst Fundamental Sci, Palmerston North 4442, New Zealand
Recommended Citation
GB/T 7714
Fang, Ling,Leliaert, Frederik,Novis, Phil,et al. Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2018,127:248-255.
APA Fang, Ling.,Leliaert, Frederik.,Novis, Phil.,Zhang, Zhenhua.,Zhu, Huan.,...&Zhong, Bojian.(2018).Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models.MOLECULAR PHYLOGENETICS AND EVOLUTION,127,248-255.
MLA Fang, Ling,et al."Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models".MOLECULAR PHYLOGENETICS AND EVOLUTION 127(2018):248-255.
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