中国科学院南京地质古生物研究所机构知识库

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	Modeling compositional heterogeneity resolves deep phylogeny of flowering plants
通讯作者	Cai, Chenyang([email protected])
	Wang, Yongli1; Li, Yan-Da2,3; Wang, Shuo4; Tihelka, Erik2,3; Engel, Michael S.5,6,7; Cai, Chenyang2
	2025
发表期刊	PLANT DIVERSITY
ISSN	2096-2703
卷号	47期号:1页码:13-20
摘要	Angiosperms experienced one of the most remarkable radiations of land plants and are now the dominant autotrophs in terrestrial ecosystems. Recent phylogenomic studies based on large-scale data from plastid, mitochondrial, or nuclear transcriptomes/genomes and increased taxon sampling have provided unprecedent resolution into the phylogeny of flowering plants. However, owing to ancient rapid radiations, the interrelationships among the five lineages of Mesangiospermae, the vast majority of angiosperms, remain contentious. Here we show that, although plastid and mitochondrial genomes lack sufficient phylogenetic signal for resolving deeper phylogeny, the relationships among five mesangiosperm lineages can be confidently resolved under better-fitting models using genome-scale data. According to our Bayesian cross-validation and model test in a maximum likelihood framework, site- heterogeneous models (e.g., CAT-GTR + G4, LG + C20 + F + G) outperform site-homogeneous or partition models often used in previous studies. Under site-heterogeneous models, the approximately unbiased test favored our preferred tree recovered from various datasets: Ceratophyllales (coontails) are robustly recovered as sister to monocots, and they together are sister to the clade comprising magnoliids, Chloranthales, and eudicots. Our phylogenomic analyses resolve the last enigma of the deeper phylogeny of angiosperms and emphasize the efficacy of modeling compositional heterogeneity in resolving rapid radiations of plants. Copyright (c) 2024 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY- NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
关键词	Angiosperms Ceratophyllales Phylogenomics Radiation Methodological factors CAT model
DOI	10.1016/j.pld.2024.07.007
收录类别	SCI
语种	英语
关键词[WOS]	LAND PLANTS ; TREE ; EVOLUTION ; ORIGIN ; GENOME ; BRYOPHYTES
资助项目	National Natural Science Foundation of China[42222201] ; National Natural Science Foundation of China[42288201]
WOS研究方向	Plant Sciences
WOS类目	Plant Sciences
WOS记录号	WOS:001426916200001
项目资助者	National Natural Science Foundation of China
出版者	KEAI PUBLISHING LTD
文献类型	期刊论文
条目标识符	http://ir.nigpas.ac.cn/handle/332004/44926
专题	中国科学院南京地质古生物研究所
通讯作者	Cai, Chenyang
作者单位	1.Jiangsu Univ, Biofuels Inst, Sch Environm & Safety Engn, Zhenjiang 212013, Peoples R China 2.Chinese Acad Sci, Nanjing Inst Geol & Palaeontol, Key Lab Palaeobiol & Petr Stratig, Nanjing 210008, Peoples R China 3.Univ Bristol, Sch Earth Sci, Life Sci Bldg,Tyndall Ave, Bristol BS8 1TQ, England 4.Qingdao Univ Sci & Technol, Coll Marine Sci & Biol Engn, Qingdao 266042, Peoples R China 5.Amer Museum Nat Hist, Div Invertebrate Zool, New York, NY 10024 USA 6.Univ Nacl Mayor San Marcos, Fac Ciencias Biol, Lima 15081, Peru 7.Univ Nacl Mayor San Marcos, Dept Entomol, Museo Hist Nat, Lima 15072, Peru
推荐引用方式 GB/T 7714	Wang, Yongli,Li, Yan-Da,Wang, Shuo,et al. Modeling compositional heterogeneity resolves deep phylogeny of flowering plants[J]. PLANT DIVERSITY,2025,47(1):13-20.
APA	Wang, Yongli,Li, Yan-Da,Wang, Shuo,Tihelka, Erik,Engel, Michael S.,&Cai, Chenyang.(2025).Modeling compositional heterogeneity resolves deep phylogeny of flowering plants.PLANT DIVERSITY,47(1),13-20.
MLA	Wang, Yongli,et al."Modeling compositional heterogeneity resolves deep phylogeny of flowering plants".PLANT DIVERSITY 47.1(2025):13-20.

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