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Journal article
Phylogenomics and the rise of the angiosperms
Nature, Vol.629, pp.843-850
2024
Abstract
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5,6,7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
Details
- Title
- Phylogenomics and the rise of the angiosperms
- Authors
- Alexandre R Zuntini - Royal Botanic Gardens, KewTom Carruthers - Royal Botanic Gardens, KewOlivier Maurin - Royal Botanic Gardens, KewPaul C Bailey - Royal Botanic Gardens, KewKevin Leempoel - Royal Botanic Gardens, KewGrace Brewer - Royal Botanic Gardens, KewNiroshini Epitawalage - Royal Botanic Gardens, KewElaine Françoso - Royal Botanic Gardens, KewBerta Gallego-Paramo - Royal Botanic Gardens, KewCatherine McGinnie - Royal Botanic Gardens, KewRaquel Negrão - Royal Botanic Gardens, KewShyamali R Roy - Royal Botanic Gardens, KewLalita Simpson - James Cook UniversityEduardo Toledo Romero - Royal Botanic Gardens, KewVanessa M A Barger - Royal Botanic Gardens, KewLaura Botigué - Center for Research in Agricultural GenomicsJames J Clarkson - Royal Botanic Gardens, KewRobyn S Cowan - Royal Botanic Gardens, KewSteven Dodsworth - Texas Tech UniversityMatthew G Johnson - Texas Tech UniversityJan T Kim - University of HertfordshireLisa Pokorny - Royal Botanic Gardens, KewNorman J Wickett - Clemson UniversityGuilherme M Antar - University of Sao PauloLucinda DeBolt - Smith CollegeKarmie Gutierrez - Smith CollegeKasper P Hendriks - University of OsnabrückAlina Hoewener - Technical University MunichAi-Qun Hu - Royal Botanic Gardens, KewElizabeth M Joyce - James Cook UniversityIzai A B S Kikuchi - University of British ColumbiaIsabel Larridon - Royal Botanic Gardens, KewDrew A Larson - University of MichiganElton John de Lirio - University of Sao PauloJing-Zia Liu - Kunming Institute of BotanyPanagiota Malakasi - Royal Botanic Gardens, KewNatalia A S Przelomska - Royal Botanic Gardens, KewToral Shah - Royal Botanic Gardens, KewJuan Viruel - Royal Botanic Gardens, KewTheodore R Allnutt - Royal Botanic Gardens VictoriaGabriel K Ameka - University of GhanaRose L Andrew - University of New EnglandMarc S Appelhans - University of GöttingenMontserrat Arista - Universidad de SevillaMaría Jesús Ariza - Universidad de SevillaJuan Arroyo - Universidad de SevillaWatchara Arthan - Royal Botanic Gardens, KewSee article text for complete list of authors (Author)Alison Shapcott - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
- Publication details
- Nature, Vol.629, pp.843-850
- Publisher
- Nature Publishing Group
- Date published
- 2024
- DOI
- 10.1038/s41586-024-07324-0
- ISSN
- 1476-4687; 0028-0836
- Copyright note
- This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
- Data Availability
- All raw DNA sequence data generated for this study are deposited in the European Nucleotide Archive under the following bioprojects PRJNA478314, PRJEB35285, PRJEB49212 and PRJNA678873. All analysed data and metadata are available in Zenodo at https://doi.org/10.5281/zenodo.10778206 (ref. 55). The resulting trees and metadata are also available in GBIF (https://doi.org/10.15468/4njn8b) and Open Tree of Life (https://tree.opentreeoflife.org/curator/study/view/ot_2304). The names used in this work match the World Checklist of Vascular Plants (https://doi.org/10.34885/jdh2-dr22).
- Organisation Unit
- School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 991022796302621
- Output Type
- Journal article
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