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Phylogenomics and the rise of the angiosperms

Author

Listed:
  • Alexandre R. Zuntini

    (Royal Botanic Gardens, Kew)

  • Tom Carruthers

    (Royal Botanic Gardens, Kew)

  • Olivier Maurin

    (Royal Botanic Gardens, Kew)

  • Paul C. Bailey

    (Royal Botanic Gardens, Kew)

  • Kevin Leempoel

    (Royal Botanic Gardens, Kew)

  • Grace E. Brewer

    (Royal Botanic Gardens, Kew)

  • Niroshini Epitawalage

    (Royal Botanic Gardens, Kew)

  • Elaine Françoso

    (Royal Botanic Gardens, Kew
    Royal Holloway University of London)

  • Berta Gallego-Paramo

    (Royal Botanic Gardens, Kew)

  • Catherine McGinnie

    (Royal Botanic Gardens, Kew)

  • Raquel Negrão

    (Royal Botanic Gardens, Kew)

  • Shyamali R. Roy

    (Royal Botanic Gardens, Kew)

  • Lalita Simpson

    (James Cook University)

  • Eduardo Toledo Romero

    (Royal Botanic Gardens, Kew)

  • Vanessa M. A. Barber

    (Royal Botanic Gardens, Kew)

  • Laura Botigué

    (Campus UAB)

  • James J. Clarkson

    (Royal Botanic Gardens, Kew)

  • Robyn S. Cowan

    (Royal Botanic Gardens, Kew)

  • Steven Dodsworth

    (University of Portsmouth)

  • Matthew G. Johnson

    (Texas Tech University)

  • Jan T. Kim

    (University of Hertfordshire)

  • Lisa Pokorny

    (Royal Botanic Gardens, Kew
    Real Jardín Botánico (RJB-CSIC))

  • Norman J. Wickett

    (Clemson University)

  • Guilherme M. Antar

    (Universidade de São Paulo
    Centro Universitário Norte do Espírito Santo, Universidade Federal do Espírito Santo)

  • Lucinda DeBolt

    (Smith College)

  • Karime Gutierrez

    (Smith College)

  • Kasper P. Hendriks

    (University of Osnabrück
    Naturalis Biodiversity Center)

  • Alina Hoewener

    (Technical University Munich)

  • Ai-Qun Hu

    (Royal Botanic Gardens, Kew)

  • Elizabeth M. Joyce

    (James Cook University
    Ludwig Maximilian University of Munich)

  • Izai A. B. S. Kikuchi

    (University of British Columbia)

  • Isabel Larridon

    (Royal Botanic Gardens, Kew)

  • Drew A. Larson

    (University of Michigan)

  • Elton John Lírio

    (Universidade de São Paulo)

  • Jing-Xia Liu

    (Chinese Academy of Sciences)

  • Panagiota Malakasi

    (Royal Botanic Gardens, Kew)

  • Natalia A. S. Przelomska

    (Royal Botanic Gardens, Kew
    University of Portsmouth)

  • Toral Shah

    (Royal Botanic Gardens, Kew)

  • Juan Viruel

    (Royal Botanic Gardens, Kew)

  • Theodore R. Allnutt

    (Royal Botanic Gardens Victoria)

  • Gabriel K. Ameka

    (University of Ghana)

  • Rose L. Andrew

    (University of New England)

  • Marc S. Appelhans

    (University of Göttingen)

  • Montserrat Arista

    (Universidad de Sevilla)

  • María Jesús Ariza

    (Universidad de Sevilla)

  • Juan Arroyo

    (Universidad de Sevilla)

  • Watchara Arthan

    (Royal Botanic Gardens, Kew)

  • Julien B. Bachelier

    (Freie Universität)

  • C. Donovan Bailey

    (New Mexico State University)

  • Helen F. Barnes

    (Royal Botanic Gardens Victoria)

  • Matthew D. Barrett

    (James Cook University)

  • Russell L. Barrett

    (Botanic Gardens of Sydney)

  • Randall J. Bayer

    (University of Memphis)

  • Michael J. Bayly

    (The University of Melbourne)

  • Ed Biffin

    (Botanic Gardens and State Herbarium)

  • Nicky Biggs

    (Royal Botanic Gardens, Kew)

  • Joanne L. Birch

    (The University of Melbourne)

  • Diego Bogarín

    (Naturalis Biodiversity Center
    Universidad de Costa Rica)

  • Renata Borosova

    (Royal Botanic Gardens, Kew)

  • Alexander M. C. Bowles

    (University of Bristol)

  • Peter C. Boyce

    (University of Florence)

  • Gemma L. C. Bramley

    (Royal Botanic Gardens, Kew)

  • Marie Briggs

    (Royal Botanic Gardens, Kew)

  • Linda Broadhurst

    (National Research Collections Australia, CSIRO)

  • Gillian K. Brown

    (Brisbane Botanic Gardens)

  • Jeremy J. Bruhl

    (University of New England)

  • Anne Bruneau

    (University of Montreal)

  • Sven Buerki

    (Boise State University)

  • Edie Burns

    (Royal Botanic Gardens, Kew)

  • Margaret Byrne

    (Department of Biodiversity, Conservation and Attractions, Government of Western Australia)

  • Stuart Cable

    (Royal Botanic Gardens, Kew)

  • Ainsley Calladine

    (Botanic Gardens and State Herbarium)

  • Martin W. Callmander

    (Conservatoire et Jardin Botaniques de Genève)

  • Ángela Cano

    (Cambridge University Botanic Garden)

  • David J. Cantrill

    (Royal Botanic Gardens Victoria)

  • Warren M. Cardinal-McTeague

    (University of British Columbia)

  • Mónica M. Carlsen

    (Missouri Botanical Garden)

  • Abigail J. A. Carruthers

    (Royal Botanic Gardens, Kew)

  • Alejandra Castro Mateo

    (Universidad de Sevilla)

  • Mark W. Chase

    (Royal Botanic Gardens, Kew
    Curtin University)

  • Lars W. Chatrou

    (Ghent University)

  • Martin Cheek

    (Royal Botanic Gardens, Kew)

  • Shilin Chen

    (Chengdu University of Traditional Chinese Medicine
    Chinese Academy of Medical Sciences)

  • Maarten J. M. Christenhusz

    (Royal Botanic Gardens, Kew
    Curtin University
    Plant Gateway)

  • Pascal-Antoine Christin

    (University of Sheffield)

  • Mark A. Clements

    (National Research Collections Australia, CSIRO)

  • Skye C. Coffey

    (Government of Western Australia)

  • John G. Conran

    (The University of Adelaide)

  • Xavier Cornejo

    (Universidad de Guayaquil)

  • Thomas L. P. Couvreur

    (Université Montpellier, CIRAD IRD)

  • Ian D. Cowie

    (Northern Territory Herbarium Department of Environment Parks & Water Security, Northern Territory Government)

  • Laszlo Csiba

    (Royal Botanic Gardens, Kew)

  • Iain Darbyshire

    (Royal Botanic Gardens, Kew)

  • Gerrit Davidse

    (Missouri Botanical Garden)

  • Nina M. J. Davies

    (Royal Botanic Gardens, Kew)

  • Aaron P. Davis

    (Royal Botanic Gardens, Kew)

  • Kor-jent Dijk

    (The University of Adelaide, North Terrace Campus)

  • Stephen R. Downie

    (University of Illinois at Urbana-Champaign)

  • Marco F. Duretto

    (Botanic Gardens of Sydney)

  • Melvin R. Duvall

    (Northern Illinois University)

  • Sara L. Edwards

    (Royal Botanic Gardens, Kew)

  • Urs Eggli

    (Sukkulenten-Sammlung Zürich/ Grün Stadt Zürich)

  • Roy H. J. Erkens

    (Naturalis Biodiversity Center
    Maastricht University
    Maastricht University)

  • Marcial Escudero

    (Universidad de Sevilla)

  • Manuel Estrella

    (Universidad de Córdoba)

  • Federico Fabriani

    (Ghent University)

  • Michael F. Fay

    (Royal Botanic Gardens, Kew)

  • Paola de L. Ferreira

    (Universidade de São Paulo
    Aarhus University)

  • Sarah Z. Ficinski

    (Royal Botanic Gardens, Kew)

  • Rachael M. Fowler

    (The University of Melbourne)

  • Sue Frisby

    (Royal Botanic Gardens, Kew)

  • Lin Fu

    (Chinese Academy of Sciences)

  • Tim Fulcher

    (Royal Botanic Gardens, Kew)

  • Mercè Galbany-Casals

    (Universitat Autònoma de Barcelona)

  • Elliot M. Gardner

    (Case Western Reserve University)

  • Dmitry A. German

    (Altai State University)

  • Augusto Giaretta

    (Universidade Federal da Grande Dourados)

  • Marc Gibernau

    (Université de Corse)

  • Lynn J. Gillespie

    (Canadian Museum of Nature)

  • Cynthia C. González

    (Universidad Nacional de la Patagonia San Juan Bosco)

  • David J. Goyder

    (Royal Botanic Gardens, Kew)

  • Sean W. Graham

    (University of British Columbia)

  • Aurélie Grall

    (Royal Botanic Gardens, Kew)

  • Laura Green

    (Royal Botanic Gardens, Kew)

  • Bee F. Gunn

    (Royal Botanic Gardens Victoria)

  • Diego G. Gutiérrez

    (Museo Argentino de Ciencias Naturales (MACN-CONICET))

  • Jan Hackel

    (Royal Botanic Gardens, Kew
    Universität Marburg)

  • Thomas Haevermans

    (Muséum National d’Histoire Naturelle)

  • Anna Haigh

    (Royal Botanic Gardens, Kew)

  • Jocelyn C. Hall

    (University of Alberta)

  • Tony Hall

    (Royal Botanic Gardens, Kew)

  • Melissa J. Harrison

    (James Cook University)

  • Sebastian A. Hatt

    (Royal Botanic Gardens, Kew)

  • Oriane Hidalgo

    (Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona))

  • Trevor R. Hodkinson

    (The University of Dublin)

  • Gareth D. Holmes

    (Royal Botanic Gardens Victoria)

  • Helen C. F. Hopkins

    (Royal Botanic Gardens, Kew)

  • Christopher J. Jackson

    (Royal Botanic Gardens Victoria)

  • Shelley A. James

    (Government of Western Australia)

  • Richard W. Jobson

    (Botanic Gardens of Sydney)

  • Gudrun Kadereit

    (Botanischer Garten München-Nymphenburg)

  • Imalka M. Kahandawala

    (Royal Botanic Gardens, Kew)

  • Kent Kainulainen

    (Gothenburg Botanical Garden)

  • Masahiro Kato

    (National Museum of Nature and Science)

  • Elizabeth A. Kellogg

    (Donald Danforth Plant Science Center)

  • Graham J. King

    (Southern Cross University)

  • Beata Klejevskaja

    (Synergy SRG)

  • Bente B. Klitgaard

    (Royal Botanic Gardens, Kew)

  • Ronell R. Klopper

    (South African National Biodiversity Institute
    University of Pretoria)

  • Sandra Knapp

    (Natural History Museum)

  • Marcus A. Koch

    (Heidelberg University)

  • James H. Leebens-Mack

    (University of Georgia)

  • Frederic Lens

    (Naturalis Biodiversity Center)

  • Christine J. Leon

    (Royal Botanic Gardens, Kew)

  • Étienne Léveillé-Bourret

    (University of Montreal)

  • Gwilym P. Lewis

    (Royal Botanic Gardens, Kew)

  • De-Zhu Li

    (Chinese Academy of Sciences)

  • Lan Li

    (CSIRO)

  • Sigrid Liede-Schumann

    (University of Bayreuth)

  • Tatyana Livshultz

    (Drexel University
    Drexel University)

  • David Lorence

    (National Tropical Botanical Garden)

  • Meng Lu

    (Royal Botanic Gardens, Kew)

  • Patricia Lu-Irving

    (Botanic Gardens of Sydney)

  • Jaquelini Luber

    (Instituto de Pesquisas Jardim Botânico do Rio de Janeiro)

  • Eve J. Lucas

    (Royal Botanic Gardens, Kew)

  • Manuel Luján

    (Royal Botanic Gardens, Kew)

  • Mabel Lum

    (Bioplatforms Australia Ltd)

  • Terry D. Macfarlane

    (Government of Western Australia)

  • Carlos Magdalena

    (Royal Botanic Gardens, Kew)

  • Vidal F. Mansano

    (Instituto de Pesquisas Jardim Botânico do Rio de Janeiro)

  • Lizo E. Masters

    (Royal Botanic Gardens, Kew)

  • Simon J. Mayo

    (Royal Botanic Gardens, Kew)

  • Kristina McColl

    (Botanic Gardens of Sydney)

  • Angela J. McDonnell

    (Saint Cloud State University)

  • Andrew E. McDougall

    (The University of Adelaide, North Terrace Campus)

  • Todd G. B. McLay

    (Royal Botanic Gardens Victoria)

  • Hannah McPherson

    (Botanic Gardens of Sydney)

  • Rosa I. Meneses

    (Universidad Católica del Norte)

  • Vincent S. F. T. Merckx

    (Naturalis Biodiversity Center)

  • Fabián A. Michelangeli

    (New York Botanical Garden)

  • John D. Mitchell

    (New York Botanical Garden)

  • Alexandre K. Monro

    (Royal Botanic Gardens, Kew)

  • Michael J. Moore

    (Oberlin College)

  • Taryn L. Mueller

    (University of Minnesota)

  • Klaus Mummenhoff

    (University of Osnabrück)

  • Jérôme Munzinger

    (Université Montpellier, IRD, CIRAD, CNRS INRAE)

  • Priscilla Muriel

    (Pontificia Universidad Católica del Ecuador)

  • Daniel J. Murphy

    (Royal Botanic Gardens Victoria)

  • Katharina Nargar

    (James Cook University
    National Research Collections Australia, CSIRO)

  • Lars Nauheimer

    (James Cook University)

  • Francis J. Nge

    (Botanic Gardens and State Herbarium)

  • Reto Nyffeler

    (University of Zürich)

  • Andrés Orejuela

    (Royal Botanic Garden Edinburgh
    Instituto Tecnológico del Putumayo)

  • Edgardo M. Ortiz

    (Technical University Munich)

  • Luis Palazzesi

    (Museo Argentino de Ciencias Naturales (MACN-CONICET))

  • Ariane Luna Peixoto

    (Instituto de Pesquisas Jardim Botânico do Rio de Janeiro)

  • Susan K. Pell

    (US Botanic Garden)

  • Jaume Pellicer

    (Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona))

  • Darin S. Penneys

    (University of North Carolina Wilmington)

  • Oscar A. Perez-Escobar

    (Royal Botanic Gardens, Kew)

  • Claes Persson

    (University of Gothenburg)

  • Marc Pignal

    (Muséum National d’Histoire Naturelle)

  • Yohan Pillon

    (LSTM Université Montpellier, CIRADIRD)

  • José R. Pirani

    (Universidade de São Paulo)

  • Gregory M. Plunkett

    (New York Botanical Garden)

  • Robyn F. Powell

    (Royal Botanic Gardens, Kew)

  • Ghillean T. Prance

    (Royal Botanic Gardens, Kew)

  • Carmen Puglisi

    (Royal Botanic Gardens, Kew
    Missouri Botanical Garden)

  • Ming Qin

    (Chinese Academy of Sciences)

  • Richard K. Rabeler

    (University of Michigan)

  • Paul E. J. Rees

    (Royal Botanic Gardens, Kew)

  • Matthew Renner

    (Botanic Gardens of Sydney)

  • Eric H. Roalson

    (Washington State University)

  • Michele Rodda

    (Singapore Botanic Gardens)

  • Zachary S. Rogers

    (New Mexico State University)

  • Saba Rokni

    (Royal Botanic Gardens, Kew)

  • Rolf Rutishauser

    (University of Zürich)

  • Miguel F. Salas

    (University of Tasmania)

  • Hanno Schaefer

    (Technical University Munich)

  • Rowan J. Schley

    (University of Exeter)

  • Alexander Schmidt-Lebuhn

    (National Research Collections Australia, CSIRO)

  • Alison Shapcott

    (University Sunshine Coast)

  • Ihsan Al-Shehbaz

    (Missouri Botanical Garden)

  • Kelly A. Shepherd

    (Government of Western Australia)

  • Mark P. Simmons

    (Colorado State University)

  • André O. Simões

    (Universidade Estadual de Campinas)

  • Ana Rita G. Simões

    (Royal Botanic Gardens, Kew)

  • Michelle Siros

    (Royal Botanic Gardens, Kew
    University of California, San Francisco)

  • Eric C. Smidt

    (Universidade Federal do Paraná)

  • James F. Smith

    (Boise State University)

  • Neil Snow

    (Pittsburg State University)

  • Douglas E. Soltis

    (University of Florida)

  • Pamela S. Soltis

    (University of Florida)

  • Robert J. Soreng

    (Smithsonian Institution)

  • Cynthia A. Sothers

    (Royal Botanic Gardens, Kew)

  • Julian R. Starr

    (University of Ottawa)

  • Peter F. Stevens

    (Missouri Botanical Garden)

  • Shannon C. K. Straub

    (Hobart and William Smith Colleges)

  • Lena Struwe

    (Rutgers University)

  • Jennifer M. Taylor

    (CSIRO)

  • Ian R. H. Telford

    (University of New England)

  • Andrew H. Thornhill

    (University of New England
    Botanic Gardens and State Herbarium
    The University of Adelaide)

  • Ifeanna Tooth

    (Botanic Gardens of Sydney)

  • Anna Trias-Blasi

    (Royal Botanic Gardens, Kew)

  • Frank Udovicic

    (Royal Botanic Gardens Victoria)

  • Timothy M. A. Utteridge

    (Royal Botanic Gardens, Kew)

  • Jose C. Valle

    (Universidad de Sevilla)

  • G. Anthony Verboom

    (University of Cape Town)

  • Helen P. Vonow

    (Botanic Gardens and State Herbarium)

  • Maria S. Vorontsova

    (Royal Botanic Gardens, Kew)

  • Jurriaan M. Vos

    (University of Basel)

  • Noor Al-Wattar

    (Royal Botanic Gardens, Kew)

  • Michelle Waycott

    (Botanic Gardens and State Herbarium
    The University of Adelaide)

  • Cassiano A. D. Welker

    (Universidade Federal de Uberlândia)

  • Adam J. White

    (CSIRO)

  • Jan J. Wieringa

    (Naturalis Biodiversity Center)

  • Luis T. Williamson

    (The University of Adelaide, North Terrace Campus)

  • Trevor C. Wilson

    (Botanic Gardens of Sydney)

  • Sin Yeng Wong

    (Universiti Malaysia Sarawak)

  • Lisa A. Woods

    (Botanic Gardens of Sydney)

  • Roseina Woods

    (Royal Botanic Gardens, Kew)

  • Stuart Worboys

    (James Cook University)

  • Martin Xanthos

    (Royal Botanic Gardens, Kew)

  • Ya Yang

    (University of Minnesota-Twin Cities)

  • Yu-Xiao Zhang

    (Southwest Forestry University)

  • Meng-Yuan Zhou

    (Chinese Academy of Sciences)

  • Sue Zmarzty

    (Royal Botanic Gardens, Kew)

  • Fernando O. Zuloaga

    (Instituto de Botánica Darwinion)

  • Alexandre Antonelli

    (Royal Botanic Gardens, Kew
    University of Gothenburg
    University of Gothenburg
    University of Oxford)

  • Sidonie Bellot

    (Royal Botanic Gardens, Kew)

  • Darren M. Crayn

    (James Cook University)

  • Olwen M. Grace

    (Royal Botanic Gardens, Kew
    Royal Botanic Garden Edinburgh)

  • Paul J. Kersey

    (Royal Botanic Gardens, Kew)

  • Ilia J. Leitch

    (Royal Botanic Gardens, Kew)

  • Hervé Sauquet

    (Botanic Gardens of Sydney)

  • Stephen A. Smith

    (University of Michigan)

  • Wolf L. Eiserhardt

    (Royal Botanic Gardens, Kew
    Aarhus University)

  • Félix Forest

    (Royal Botanic Gardens, Kew)

  • William J. Baker

    (Royal Botanic Gardens, Kew
    Aarhus University)

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 origins5–7. 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.

Suggested Citation

  • Alexandre R. Zuntini & Tom Carruthers & Olivier Maurin & Paul C. Bailey & Kevin Leempoel & Grace E. Brewer & Niroshini Epitawalage & Elaine Françoso & Berta Gallego-Paramo & Catherine McGinnie & Raque, 2024. "Phylogenomics and the rise of the angiosperms," Nature, Nature, vol. 629(8013), pages 843-850, May.
  • Handle: RePEc:nat:nature:v:629:y:2024:i:8013:d:10.1038_s41586-024-07324-0
    DOI: 10.1038/s41586-024-07324-0
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    1. Xiao-Xiao Wang & Chien-Hsun Huang & Diego F. Morales-Briones & Xiang-Yu Wang & Ying Hu & Na Zhang & Pu-Guang Zhao & Xiao-Mei Wei & Kun-Hua Wei & Xinya Hemu & Ning-Hua Tan & Qing-Feng Wang & Ling-Yun C, 2024. "Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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