Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling
Angiosperms (flowering plants) are the most diverse and species-rich group of plants. The vast majority (∼99.95%) of angiosperms form a clade called Mesangiospermae, which is subdivided into five major groups: eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales. The relationships amon...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-03-01
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| Series: | Plant Communications |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2590346220300080 |
| _version_ | 1819058520140546048 |
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| author | Lingxiao Yang Danyan Su Xin Chang Charles S.P. Foster Linhua Sun Chien-Hsun Huang Xiaofan Zhou Liping Zeng Hong Ma Bojian Zhong |
| author_facet | Lingxiao Yang Danyan Su Xin Chang Charles S.P. Foster Linhua Sun Chien-Hsun Huang Xiaofan Zhou Liping Zeng Hong Ma Bojian Zhong |
| author_sort | Lingxiao Yang |
| collection | DOAJ |
| description | Angiosperms (flowering plants) are the most diverse and species-rich group of plants. The vast majority (∼99.95%) of angiosperms form a clade called Mesangiospermae, which is subdivided into five major groups: eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales. The relationships among these Mesangiospermae groups have been the subject of long debate. In this study, we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa, including representatives of all five lineages, to investigate the phylogeny of major angiosperm lineages under both coalescent- and concatenation-based methods. We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny. We further removed the genes with weak phylogenetic signal and showed that eudicots, Ceratophyllales, and Chloranthales form a clade, with magnoliids and monocots being the next successive sister lineages. Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny. Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms. Meanwhile, we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago, and Mesangiospermae diversified into the five extant groups in a short time span (∼27 million years) at the Early to Late Jurassic. |
| first_indexed | 2024-12-21T13:56:30Z |
| format | Article |
| id | doaj.art-f71b3ee3d0e14100928e43f77b9cddbb |
| institution | Directory Open Access Journal |
| issn | 2590-3462 |
| language | English |
| last_indexed | 2024-12-21T13:56:30Z |
| publishDate | 2020-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Plant Communications |
| spelling | doaj.art-f71b3ee3d0e14100928e43f77b9cddbb2022-12-21T19:01:32ZengElsevierPlant Communications2590-34622020-03-0112Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene SamplingLingxiao Yang0Danyan Su1Xin Chang2Charles S.P. Foster3Linhua Sun4Chien-Hsun Huang5Xiaofan Zhou6Liping Zeng7Hong Ma8Bojian Zhong9College of Life Sciences, Nanjing Normal University, Nanjing, ChinaCollege of Life Sciences, Nanjing Normal University, Nanjing, ChinaCollege of Life Sciences, Nanjing Normal University, Nanjing, ChinaSchool of Life and Environmental Sciences, University of Sydney, Sydney, AustraliaPeking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, ChinaState Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, ChinaInstitute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USADepartment of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USACollege of Life Sciences, Nanjing Normal University, Nanjing, China; Corresponding authorAngiosperms (flowering plants) are the most diverse and species-rich group of plants. The vast majority (∼99.95%) of angiosperms form a clade called Mesangiospermae, which is subdivided into five major groups: eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales. The relationships among these Mesangiospermae groups have been the subject of long debate. In this study, we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa, including representatives of all five lineages, to investigate the phylogeny of major angiosperm lineages under both coalescent- and concatenation-based methods. We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny. We further removed the genes with weak phylogenetic signal and showed that eudicots, Ceratophyllales, and Chloranthales form a clade, with magnoliids and monocots being the next successive sister lineages. Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny. Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms. Meanwhile, we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago, and Mesangiospermae diversified into the five extant groups in a short time span (∼27 million years) at the Early to Late Jurassic.http://www.sciencedirect.com/science/article/pii/S2590346220300080Mesangiospermaegene tree conflictphylogenomicsphylogenetic signaldivergence times |
| spellingShingle | Lingxiao Yang Danyan Su Xin Chang Charles S.P. Foster Linhua Sun Chien-Hsun Huang Xiaofan Zhou Liping Zeng Hong Ma Bojian Zhong Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling Plant Communications Mesangiospermae gene tree conflict phylogenomics phylogenetic signal divergence times |
| title | Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling |
| title_full | Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling |
| title_fullStr | Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling |
| title_full_unstemmed | Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling |
| title_short | Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling |
| title_sort | phylogenomic insights into deep phylogeny of angiosperms based on broad nuclear gene sampling |
| topic | Mesangiospermae gene tree conflict phylogenomics phylogenetic signal divergence times |
| url | http://www.sciencedirect.com/science/article/pii/S2590346220300080 |
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