Phylogenomics and the rise of the angiosperms

Alexandre Zuntini; Tom Carruthers; Olivier Maurin; Paul Bailey; Kevin Leempoel; Grace Brewer; Niroshini Epitawalage; Elaine Françoso; Berta Gallego-Paramo; Catherine Mcginnie; Raquel Negrão; Shyamali Roy; Lalita Simpson; Eduardo Toledo Romero; Vanessa Barber; Laura Botigué; James Clarkson; Robyn Cowan; Steven Dodsworth; Matthew Johnson; Jan Kim; Lisa Pokorny; Norman Wickett; Guilherme Antar; Lucinda Debolt; Karime Gutierrez; Kasper Hendriks; Alina Hoewener; Ai-Qun Hu; Elizabeth Joyce; Izai Kikuchi; Isabel Larridon; Drew Larson; Elton John de Lírio; Jing-Xia Liu; Panagiota Malakasi; Natalia Przelomska; Toral Shah; Juan Viruel; Theodore Allnutt; Gabriel Ameka; Rose Andrew; Marc Appelhans; Montserrat Arista; María Jesús Ariza; Juan Arroyo; Watchara Arthan; Julien Bachelier; C. Donovan Bailey; Helen Barnes; Matthew Barrett; Russell Barrett; Randall Bayer; Michael Bayly; Ed Biffin; Nicky Biggs; Joanne Birch; Diego Bogarín; Renata Borosova; Alexander Bowles; Peter Boyce; Gemma Bramley; Marie Briggs; Linda Broadhurst; Gillian Brown; Jeremy Bruhl; Anne Bruneau; Sven Buerki; Edie Burns; Margaret Byrne; Stuart Cable; Ainsley Calladine; Martin Callmander; Ángela Cano; David Cantrill; Warren Cardinal-Mcteague; Mónica Carlsen; Abigail Carruthers; Alejandra de Castro Mateo; Mark Chase; Lars Chatrou; Martin Cheek; Shilin Chen; Maarten Christenhusz; Pascal-Antoine Christin; Mark Clements; Skye Coffey; John Conran; Xavier Cornejo; Thomas Couvreur; Ian Cowie; Laszlo Csiba; Iain Darbyshire; Gerrit Davidse; Nina Davies; Aaron Davis; Kor-Jent van Dijk; Stephen Downie; Marco Duretto; Melvin Duvall; Sara Edwards; Urs Eggli; Roy Erkens; Marcial Escudero; Manuel de la Estrella; Federico Fabriani; Michael Fay; Paola de L. Ferreira; Sarah Ficinski; Rachael Fowler; Sue Frisby; Lin Fu; Tim Fulcher; Mercè Galbany-Casals; Elliot Gardner; Dmitry German; Augusto Giaretta; Marc Gibernau; Lynn Gillespie; Cynthia González; David Goyder; Sean Graham; Aurélie Grall; Laura Green; Bee Gunn; Diego Gutiérrez; Jan Hackel; Thomas Haevermans; Anna Haigh; Jocelyn Hall; Tony Hall; Melissa Harrison; Sebastian Hatt; Oriane Hidalgo; Trevor Hodkinson; Gareth Holmes; Helen Hopkins; Christopher Jackson; Shelley James; Richard Jobson; Gudrun Kadereit; Imalka Kahandawala; Kent Kainulainen; Masahiro Kato; Elizabeth Kellogg; Graham King; Beata Klejevskaja; Bente Klitgaard; Ronell Klopper; Sandra Knapp; Marcus Koch; James Leebens-Mack; Frederic Lens; Christine Leon; Étienne Léveillé-Bourret; Gwilym Lewis; De-Zhu Li; Lan Li; Sigrid Liede-Schumann; Tatyana Livshultz; David Lorence; Meng Lu; Patricia Lu-Irving; Jaquelini Luber; Eve Lucas; Manuel Luján; Mabel Lum; Terry Macfarlane; Carlos Magdalena; Vidal Mansano; Lizo Masters; Simon Mayo; Kristina Mccoll; Angela Mcdonnell; Andrew Mcdougall; Todd Mclay; Hannah Mcpherson; Rosa Meneses; Vincent Merckx; Fabián Michelangeli; John Mitchell; Alexandre Monro; Michael Moore; Taryn Mueller; Klaus Mummenhoff; Jérôme Munzinger; Priscilla Muriel; Daniel Murphy; Katharina Nargar; Lars Nauheimer; Francis Nge; Reto Nyffeler; Andrés Orejuela; Edgardo Ortiz; Luis Palazzesi; Ariane Luna Peixoto; Susan Pell; Jaume Pellicer; Darin Penneys; Oscar Perez-Escobar; Claes Persson; Marc Pignal; Yohan Pillon; José Pirani; Gregory Plunkett; Robyn Powell; Ghillean Prance; Carmen Puglisi; Ming Qin; Richard Rabeler; Paul Rees; Matthew Renner; Eric Roalson; Michele Rodda; Zachary Rogers; Saba Rokni; Rolf Rutishauser; Miguel de Salas; Hanno Schaefer; Rowan Schley; Alexander Schmidt-Lebuhn; Alison Shapcott; Ihsan Al-Shehbaz; Kelly Shepherd; Mark Simmons; André Simões; Ana Rita G. Simões; Michelle Siros; Eric Smidt; James Smith; Neil Snow; Douglas Soltis; Pamela Soltis; Robert Soreng; Cynthia Sothers; Julian Starr; Peter Stevens; Shannon Straub; Lena Struwe; Jennifer Taylor; Ian Telford; Andrew Thornhill; Ifeanna Tooth; Anna Trias-Blasi; Frank Udovicic; Timothy Utteridge; Jose del Valle; G. Anthony Verboom; Helen Vonow; Maria Vorontsova; Jurriaan de Vos; Noor Al-Wattar; Michelle Waycott; Cassiano Welker; Adam White; Jan Wieringa; Luis Williamson; Trevor Wilson; Sin Yeng Wong; Lisa Woods; Roseina Woods; Stuart Worboys; Martin Xanthos; Ya Yang; Yu-Xiao Zhang; Meng-Yuan Zhou; Sue Zmarzty; Fernando Zuloaga; Alexandre Antonelli; Sidonie Bellot; Darren Crayn; Olwen Grace; Paul Kersey; Ilia Leitch; Hervé Sauquet; Stephen Smith; Wolf Eiserhardt; Félix Forest; William Baker

doi:10.1038/s41586-024-07324-0

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Phylogenomics and the rise of the angiosperms

Journal article

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Phylogenomics and the rise of the angiosperms

Alexandre Zuntini, Tom Carruthers, Olivier Maurin, Paul Bailey, Kevin Leempoel, Grace Brewer, Niroshini Epitawalage, Elaine Françoso, Berta Gallego-Paramo, Catherine Mcginnie, …

Nature, Vol.629, pp.843-850

24/04/2024

DOI: https://doi.org/10.1038/s41586-024-07324-0

Abstract

Phylogenetics

Phylogenomics

Plant evolution

Speciation

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods 1,2 . 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 genome 3,4 . Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins 5–7 . 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 genes 8 . This 15-fold increase in genus-level sampling relative to comparable nuclear studies 9 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.

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Title: Phylogenomics and the rise of the angiosperms
Creators - without role: Alexandre Zuntini - Royal Botanic Gardens, Kew
Tom Carruthers - Royal Botanic Gardens, Kew
Olivier Maurin - Royal Botanic Gardens, Kew
Paul Bailey - Royal Botanic Gardens, Kew
Kevin Leempoel - Royal Botanic Gardens, Kew
Grace Brewer - Royal Botanic Gardens, Kew
Niroshini Epitawalage - Royal Botanic Gardens, Kew
Elaine Françoso - Royal Botanic Gardens, Kew
Berta Gallego-Paramo
Catherine Mcginnie - Royal Botanic Gardens, Kew
Raquel Negrão - Royal Botanic Gardens, Kew
Shyamali Roy - Royal Botanic Gardens, Kew
Lalita Simpson - Australian Institute of Tropical Health and Medicine
Eduardo Toledo Romero
Vanessa Barber - Royal Botanic Gardens, Kew
Laura Botigué - Center for Research in Agricultural Genomics
James Clarkson - Royal Botanic Gardens, Kew
Robyn Cowan - Royal Botanic Gardens, Kew
Steven Dodsworth - University of Portsmouth
Matthew Johnson - Texas Tech University
Jan Kim - University of Hertfordshire
Lisa Pokorny - Royal Botanic Gardens, Kew
Norman Wickett - Clemson University
Guilherme Antar - Instituto de Botânica
Lucinda Debolt - Smith College
Karime Gutierrez - Smith College
Kasper Hendriks - Osnabrück University
Alina Hoewener
Ai-Qun Hu
Elizabeth Joyce - Australian Institute of Tropical Health and Medicine
Izai Kikuchi
Isabel Larridon - Royal Botanic Gardens, Kew
Drew Larson - University of Michigan–Ann Arbor
Elton John de Lírio - Instituto de Botânica
Jing-Xia Liu
Panagiota Malakasi - Royal Botanic Gardens, Kew
Natalia Przelomska
Toral Shah - Royal Botanic Gardens, Kew
Juan Viruel - Royal Botanic Gardens, Kew
Theodore Allnutt - Royal Botanic Garden Sydney
Gabriel Ameka - University of Ghana
Rose Andrew - University of New England
Marc 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 Bachelier - Freie Universität Berlin
C. Donovan Bailey - New Mexico State University
Helen Barnes - Royal Botanic Garden Sydney
Matthew Barrett - Australian Institute of Tropical Health and Medicine
Russell Barrett - Royal Botanic Garden Sydney
Randall Bayer - University of Memphis
Michael Bayly - University of Melbourne
Ed Biffin - State Herbarium of South Australia
Nicky Biggs - Royal Botanic Gardens, Kew
Joanne Birch - University of Melbourne
Diego Bogarín - Naturalis Biodiversity Center
Renata Borosova - Royal Botanic Gardens, Kew
Alexander Bowles
Peter Boyce - University of Florence
Gemma Bramley
Marie Briggs - Royal Botanic Gardens, Kew
Linda Broadhurst - ACT Government
Gillian Brown
Jeremy Bruhl - University of New England
Anne Bruneau - Université de Montréal
Sven Buerki - Boise State University
Edie Burns - Royal Botanic Gardens, Kew
Margaret Byrne - Government of Western Australia
Stuart Cable - Royal Botanic Gardens, Kew
Ainsley Calladine - State Herbarium of South Australia
Martin Callmander - Conservatory and Botanical Garden of the City of Geneva
Ángela Cano - University of Cambridge
David Cantrill - Royal Botanic Gardens Victoria
Warren Cardinal-Mcteague - University of British Columbia
Mónica Carlsen - Missouri Botanical Garden
Abigail Carruthers
Alejandra de Castro Mateo - Universidad de Sevilla
Mark Chase - Royal Botanic Gardens, Kew
Lars Chatrou - Ghent University
Martin Cheek - Royal Botanic Gardens, Kew
Shilin Chen - Chengdu University of Traditional Chinese Medicine
Maarten Christenhusz
Pascal-Antoine Christin
Mark Clements - Centre for Australian National Biodiversity Research
Skye Coffey - Government of Western Australia
John Conran - University of Adelaide
Xavier Cornejo - University of Guayaquil
Thomas Couvreur
Ian Cowie - Government of the Northern Territory
Laszlo Csiba - Royal Botanic Gardens, Kew
Iain Darbyshire - Royal Botanic Gardens, Kew
Gerrit Davidse - Missouri Botanical Garden
Nina Davies - Royal Botanic Gardens, Kew
Aaron Davis - Royal Botanic Gardens, Kew
Kor-Jent van Dijk
Stephen Downie - University of Illinois Urbana-Champaign
Marco Duretto - Royal Botanic Garden Sydney
Melvin Duvall - Northern Illinois University
Sara Edwards - Royal Botanic Gardens, Kew
Urs Eggli - Sukkulenten-Sammlung Zürich
Roy Erkens
Marcial Escudero - Universidad de Sevilla
Manuel de la Estrella - University of Córdoba
Federico Fabriani - Ghent University
Michael Fay - Royal Botanic Gardens, Kew
Paola de L. Ferreira
Sarah Ficinski - Royal Botanic Gardens, Kew
Rachael Fowler - University of Melbourne
Sue Frisby - Royal Botanic Gardens, Kew
Lin Fu - South China Botanical Garden
Tim Fulcher - Royal Botanic Gardens, Kew
Mercè Galbany-Casals - Universitat Autònoma de Barcelona
Elliot Gardner - Case Western Reserve University
Dmitry German - Altai State University
Augusto Giaretta - Universidade Federal da Grande Dourados
Marc Gibernau - Université de Corse Pascal Paoli
Lynn Gillespie - Canadian Museum of Nature
Cynthia González - National University of Patagonia San Juan Bosco
David Goyder - Royal Botanic Gardens, Kew
Sean Graham - University of British Columbia
Aurélie Grall - Royal Botanic Gardens, Kew
Laura Green - Royal Botanic Gardens, Kew
Bee Gunn - Royal Botanic Garden Sydney
Diego Gutiérrez - Bernardino Rivadavia Natural Sciences Museum
Jan Hackel - Philipps University of Marburg
Thomas Haevermans - Institut de Systématique, Évolution, Biodiversité
Anna Haigh - Royal Botanic Gardens, Kew
Jocelyn Hall - University of Alberta
Tony Hall - Royal Botanic Gardens, Kew
Melissa Harrison - Australian Institute of Tropical Health and Medicine
Sebastian Hatt - Royal Botanic Gardens, Kew
Oriane Hidalgo - Institut Botànic de Barcelona
Trevor Hodkinson - Trinity College Dublin
Gareth Holmes - Royal Botanic Garden Sydney
Helen Hopkins
Christopher Jackson - Royal Botanic Gardens Victoria
Shelley James - Government of Western Australia
Richard Jobson - Royal Botanic Garden Sydney
Gudrun Kadereit - Ludwig-Maximilians-Universität München
Imalka Kahandawala - Royal Botanic Gardens, Kew
Kent Kainulainen - Göteborgs Stads
Masahiro Kato - National Museum of Nature and Science
Elizabeth Kellogg - Donald Danforth Plant Science Center
Graham King
Beata Klejevskaja - Synergy Farm Health
Bente Klitgaard - Royal Botanic Gardens, Kew
Ronell Klopper - South African National Biodiversity Institute
Sandra Knapp - Natural History Museum
Marcus Koch - Heidelberg University
James Leebens-Mack
Frederic Lens - Naturalis Biodiversity Center
Christine Leon - Royal Botanic Gardens, Kew
Étienne Léveillé-Bourret - Université de Montréal
Gwilym Lewis - Royal Botanic Gardens, Kew
De-Zhu Li
Lan Li - ACT Government
Sigrid Liede-Schumann - University of Bayreuth
Tatyana Livshultz - Drexel University
David Lorence - National Tropical Botanical Garden
Meng Lu - Royal Botanic Gardens, Kew
Patricia Lu-Irving - Royal Botanic Garden Sydney
Jaquelini Luber - Instituto de Pesquisas Jardim Botânico do Rio de Janeiro
Eve Lucas - Royal Botanic Gardens, Kew
Manuel Luján - Royal Botanic Gardens, Kew
Mabel Lum - Bioplatforms Australia
Terry Macfarlane - Government of Western Australia
Carlos Magdalena - Royal Botanic Gardens, Kew
Vidal Mansano
Lizo Masters - Royal Botanic Gardens, Kew
Simon Mayo - Royal Botanic Gardens, Kew
Kristina Mccoll - Royal Botanic Garden Sydney
Angela Mcdonnell - St. Cloud State University
Andrew Mcdougall - University of Adelaide
Todd Mclay
Hannah Mcpherson - Royal Botanic Garden Sydney
Rosa Meneses - Universidad Católica del Norte
Vincent Merckx
Fabián Michelangeli - New York Botanical Garden
John Mitchell - New York Botanical Garden
Alexandre Monro - Royal Botanic Gardens, Kew
Michael Moore - Oberlin College
Taryn Mueller - University of Minnesota
Klaus Mummenhoff - Osnabrück University
Jérôme Munzinger - Université de Montpellier, BotAnique et Modélisation de l'Architecture des Plantes et des végétations - AMAP
Priscilla Muriel - Pontificia Universidad Católica del Ecuador
Daniel Murphy - Royal Botanic Garden Sydney
Katharina Nargar - Centre for Australian National Biodiversity Research
Lars Nauheimer - Australian Institute of Tropical Health and Medicine
Francis Nge - State Herbarium of South Australia
Reto Nyffeler - University of Zurich
Andrés Orejuela - Royal Botanic Garden Edinburgh
Edgardo Ortiz
Luis Palazzesi - Bernardino Rivadavia Natural Sciences Museum
Ariane Luna Peixoto - Instituto de Pesquisas Jardim Botânico do Rio de Janeiro
Susan Pell - Santa Barbara Botanic Garden
Jaume Pellicer - Institut Botànic de Barcelona
Darin Penneys - University of North Carolina Wilmington
Oscar Perez-Escobar - Royal Botanic Gardens, Kew
Claes Persson - University of Gothenburg
Marc Pignal - Institut de Systématique, Évolution, Biodiversité
Yohan Pillon - Université de Montpellier
José Pirani - Instituto de Botânica
Gregory Plunkett - New York Botanical Garden
Robyn Powell - Royal Botanic Gardens, Kew
Ghillean Prance - Royal Botanic Gardens, Kew
Carmen Puglisi - Missouri Botanical Garden
Ming Qin - South China Botanical Garden
Richard Rabeler - University of Michigan–Ann Arbor
Paul Rees
Matthew Renner
Eric Roalson - Washington State University
Michele Rodda - National Parks Board
Zachary Rogers - New Mexico State University
Saba Rokni - Royal Botanic Gardens, Kew
Rolf Rutishauser - University of Zurich
Miguel de Salas - University of Tasmania
Hanno Schaefer
Rowan Schley - University of Exeter
Alexander Schmidt-Lebuhn - Centre for Australian National Biodiversity Research
Alison Shapcott - University of the Sunshine Coast
Ihsan Al-Shehbaz - Missouri Botanical Garden
Kelly Shepherd - Government of Western Australia
Mark Simmons - Colorado State University
André Simões - Universidade Estadual de Campinas (UNICAMP)
Ana Rita G. Simões - Royal Botanic Gardens, Kew
Michelle Siros - University of California, San Francisco
Eric Smidt
James Smith - Boise State University
Neil Snow - Pittsburg State University
Douglas Soltis - University of Florida
Pamela Soltis - Florida Museum of Natural History
Robert Soreng - Smithsonian Institution
Cynthia Sothers - Royal Botanic Gardens, Kew
Julian Starr - University of Ottawa
Peter Stevens - Missouri Botanical Garden
Shannon Straub
Lena Struwe - Rutgers, The State University of New Jersey
Jennifer Taylor - ACT Government
Ian Telford - University of New England
Andrew Thornhill - University of Adelaide
Ifeanna Tooth - Royal Botanic Garden Sydney
Anna Trias-Blasi - Royal Botanic Gardens, Kew
Frank Udovicic - Royal Botanic Garden Sydney
Timothy Utteridge
Jose del Valle - Universidad de Sevilla
G. Anthony Verboom - University of Cape Town
Helen Vonow - State Herbarium of South Australia
Maria Vorontsova - Royal Botanic Gardens, Kew
Jurriaan de Vos - University of Basel
Noor Al-Wattar - Royal Botanic Gardens, Kew
Michelle Waycott - University of Adelaide
Cassiano Welker
Adam White - Australian National Herbarium
Jan Wieringa - Naturalis Biodiversity Center
Luis Williamson - University of Adelaide
Trevor Wilson - Royal Botanic Garden Sydney
Sin Yeng Wong - Universiti Malaysia Sarawak
Lisa Woods - Royal Botanic Garden Sydney
Roseina Woods - Royal Botanic Gardens, Kew
Stuart Worboys - James Cook University
Martin Xanthos - Royal Botanic Gardens, Kew
Ya Yang - Twin Cities Orthopedics
Yu-Xiao Zhang
Meng-Yuan Zhou
Sue Zmarzty - Royal Botanic Gardens, Kew
Fernando Zuloaga - Instituto de Botanica Darwinion
Alexandre Antonelli - University of Gothenburg
Sidonie Bellot - Royal Botanic Gardens, Kew
Darren Crayn - James Cook University
Olwen Grace - Royal Botanic Garden Edinburgh
Paul Kersey - Royal Botanic Gardens, Kew
Ilia Leitch - Royal Botanic Gardens, Kew
Hervé Sauquet - Royal Botanic Garden Sydney
Stephen Smith - University of Michigan–Ann Arbor
Wolf Eiserhardt - Aarhus University
Félix Forest - Royal Botanic Gardens, Kew
William Baker - Aarhus University
Publication Details: Nature, Vol.629, pp.843-850
Identifiers: 9934316609311
Academic Unit: Diversité, Adaptation et Développement des plantes - DIADE; BotAnique et Modélisation de l'Architecture des Plantes et des végétations - AMAP
Language: English
Resource Type: Journal article
Local Fields: hal-04560060