Modeling compositional heterogeneity resolves deep phylogeny of flowering plants
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...
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KeAi Communications Co., Ltd.
2025-01-01
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| Series: | Plant Diversity |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468265924001240 |
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| author | Yongli Wang Yan-Da Li Shuo Wang Erik Tihelka Michael S. Engel Chenyang Cai |
| author_facet | Yongli Wang Yan-Da Li Shuo Wang Erik Tihelka Michael S. Engel Chenyang Cai |
| author_sort | Yongli Wang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-99aec914227e4b5c98605f546e0f0b6e |
| institution | Kabale University |
| issn | 2468-2659 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Plant Diversity |
| spelling | doaj-art-99aec914227e4b5c98605f546e0f0b6e2025-02-12T05:31:31ZengKeAi Communications Co., Ltd.Plant Diversity2468-26592025-01-014711320Modeling compositional heterogeneity resolves deep phylogeny of flowering plantsYongli Wang0Yan-Da Li1Shuo Wang2Erik Tihelka3Michael S. Engel4Chenyang Cai5Biofuels Institute, School of Environmental and Safety Engineering, Jiangsu University, Zhenjiang 212013, ChinaKey Laboratory of Palaeobiology and Petroleum Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United KingdomCollege of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, ChinaKey Laboratory of Palaeobiology and Petroleum Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United KingdomDivision of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024-5192, USA; Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru; Departamento de Entomología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 15072, PeruKey Laboratory of Palaeobiology and Petroleum Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China; Corresponding author.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.http://www.sciencedirect.com/science/article/pii/S2468265924001240AngiospermsCeratophyllalesPhylogenomicsRadiationMethodological factorsCAT model |
| spellingShingle | Yongli Wang Yan-Da Li Shuo Wang Erik Tihelka Michael S. Engel Chenyang Cai Modeling compositional heterogeneity resolves deep phylogeny of flowering plants Plant Diversity Angiosperms Ceratophyllales Phylogenomics Radiation Methodological factors CAT model |
| title | Modeling compositional heterogeneity resolves deep phylogeny of flowering plants |
| title_full | Modeling compositional heterogeneity resolves deep phylogeny of flowering plants |
| title_fullStr | Modeling compositional heterogeneity resolves deep phylogeny of flowering plants |
| title_full_unstemmed | Modeling compositional heterogeneity resolves deep phylogeny of flowering plants |
| title_short | Modeling compositional heterogeneity resolves deep phylogeny of flowering plants |
| title_sort | modeling compositional heterogeneity resolves deep phylogeny of flowering plants |
| topic | Angiosperms Ceratophyllales Phylogenomics Radiation Methodological factors CAT model |
| url | http://www.sciencedirect.com/science/article/pii/S2468265924001240 |
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