Modeling compositional heterogeneity resolves deep phylogeny of flowering plants

doi:10.1016/j.pld.2024.07.007

Plant Diversity ›› 2025, Vol. 47 ›› Issue (01): 13-20.DOI: 10.1016/j.pld.2024.07.007

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Modeling compositional heterogeneity resolves deep phylogeny of flowering plants

Yongli Wang^a, Yan-Da Li^b,c, Shuo Wang^d, Erik Tihelka^b,c, Michael S. Engel^e,f,g, Chenyang Cai^b

a. Biofuels Institute, School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, China;
b. Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China;
c. School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom;
d. College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China;
e. Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024-5192, USA;
f. Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru;
g. Departamento de Entomología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 15072, Peru

Received:2024-02-08 Revised:2024-07-17 Online:2025-02-15 Published:2025-01-25
Contact: Chenyang Cai,E-mail:cycai@nigpas.ac.cn
Supported by:
The work has been supported by the National Natural Science Foundation of China (42222201, 42288201).

Modeling compositional heterogeneity resolves deep phylogeny of flowering plants

Yongli Wang^a, Yan-Da Li^b,c, Shuo Wang^d, Erik Tihelka^b,c, Michael S. Engel^e,f,g, Chenyang Cai^b

a. Biofuels Institute, School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, China;
b. Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China;
c. School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom;
d. College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China;
e. Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024-5192, USA;
f. Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru;
g. Departamento de Entomología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 15072, Peru

通讯作者: Chenyang Cai,E-mail:cycai@nigpas.ac.cn
基金资助:
The work has been supported by the National Natural Science Foundation of China (42222201, 42288201).

Abstract

Abstract: 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.

Key words: Angiosperms, Ceratophyllales, Phylogenomics, Radiation, Methodological factors, CAT model

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.

关键词: Angiosperms, Ceratophyllales, Phylogenomics, Radiation, Methodological factors, CAT model

Yongli Wang, Yan-Da Li, Shuo Wang, Erik Tihelka, Michael S. Engel, Chenyang Cai. Modeling compositional heterogeneity resolves deep phylogeny of flowering plants[J]. Plant Diversity, 2025, 47(01): 13-20.

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Modeling compositional heterogeneity resolves deep phylogeny of flowering plants

Modeling compositional heterogeneity resolves deep phylogeny of flowering plants

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