Phylogenomics and the rise of the angiosperms - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement
Journal Articles Nature Year : 2024

Phylogenomics and the rise of the angiosperms

Alexandre Zuntini (1) , Tom Carruthers (1) , Olivier Maurin (1) , Paul Bailey (1) , Kevin Leempoel (1) , Grace Brewer (1) , Niroshini Epitawalage (1) , 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 (2) , 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 (3) , 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 (2) , Yohan Pillon (4, 5) , 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 (1)
Alexandre Zuntini
Olivier Maurin
Paul Bailey
Kevin Leempoel
Elaine Françoso
Berta Gallego-Paramo
Catherine Mcginnie
  • Function : Author
Raquel Negrão
Shyamali Roy
  • Function : Author
Lalita Simpson
  • Function : Author
Eduardo Toledo Romero
  • Function : Author
Vanessa Barber
  • Function : Author
Laura Botigué
James Clarkson
  • Function : Author
Robyn Cowan
  • Function : Author
Steven Dodsworth
Matthew Johnson
Jan Kim
  • Function : Author
Lisa Pokorny
Norman Wickett
Guilherme Antar
Lucinda Debolt
  • Function : Author
Karime Gutierrez
  • Function : Author
Kasper Hendriks
Alina Hoewener
Ai-Qun Hu
Elizabeth Joyce
Izai Kikuchi
Isabel Larridon
Drew Larson
Elton John de Lírio
Jing-Xia Liu
  • Function : Author
Panagiota Malakasi
  • Function : Author
Natalia Przelomska
Toral Shah
  • Function : Author
Juan Viruel
Theodore Allnutt
Gabriel Ameka
Rose Andrew
Marc Appelhans
  • Function : Author
Montserrat Arista
María Jesús Ariza
  • Function : Author
Juan Arroyo
  • Function : Author
Watchara Arthan
Julien Bachelier
  • Function : Author
C. Donovan Bailey
  • Function : Author
Helen Barnes
  • Function : Author
Matthew Barrett
Russell Barrett
Randall Bayer
Michael Bayly
Ed Biffin
Nicky Biggs
  • Function : Author
Joanne Birch
Diego Bogarín
Renata Borosova
Alexander Bowles
Peter Boyce
  • Function : Author
Gemma Bramley
  • Function : Author
Marie Briggs
Linda Broadhurst
Gillian Brown
  • Function : Author
Jeremy Bruhl
  • Function : Author
Anne Bruneau
Sven Buerki
Edie Burns
  • Function : Author
Margaret Byrne
Stuart Cable
  • Function : Author
Ainsley Calladine
Martin Callmander
Ángela Cano
David Cantrill
Warren Cardinal-Mcteague
Mónica Carlsen
Abigail Carruthers
Alejandra de Castro Mateo
  • Function : Author
Mark Chase
Lars Chatrou
Martin Cheek
  • Function : Author
Shilin Chen
Maarten Christenhusz
Pascal-Antoine Christin
Mark Clements
  • Function : Author
Skye Coffey
John Conran
Xavier Cornejo
  • Function : Author
Thomas Couvreur
Ian Cowie
  • Function : Author
Laszlo Csiba
  • Function : Author
Iain Darbyshire
Gerrit Davidse
  • Function : Author
Nina Davies
Aaron Davis
Kor-Jent van Dijk
Stephen Downie
Marco Duretto
Melvin Duvall
  • Function : Author
Sara Edwards
  • Function : Author
Urs Eggli
Roy Erkens
Marcial Escudero
Manuel de la Estrella
Federico Fabriani
Michael Fay
Paola de L. Ferreira
  • Function : Author
Sarah Ficinski
  • Function : Author
Rachael Fowler
Sue Frisby
  • Function : Author
Lin Fu
Tim Fulcher
  • Function : Author
Mercè Galbany-Casals
Elliot Gardner
Dmitry German
Augusto Giaretta
  • Function : Author
Marc Gibernau
  • Function : Author
Lynn Gillespie
Cynthia González
David Goyder
Sean Graham
Aurélie Grall
  • Function : Author
Laura Green
Bee Gunn
Diego Gutiérrez
  • Function : Author
Jan Hackel
Anna Haigh
Jocelyn Hall
Tony Hall
  • Function : Author
Melissa Harrison
  • Function : Author
Sebastian Hatt
  • Function : Author
Oriane Hidalgo
Trevor Hodkinson
Gareth Holmes
Helen Hopkins
Christopher Jackson
  • Function : Author
Shelley James
Richard Jobson
Gudrun Kadereit
  • Function : Author
Imalka Kahandawala
  • Function : Author
Kent Kainulainen
Masahiro Kato
Elizabeth Kellogg
Graham King
Beata Klejevskaja
  • Function : Author
Bente Klitgaard
  • Function : Author
Ronell Klopper
Sandra Knapp
Marcus Koch
James Leebens-Mack
Frederic Lens
Christine Leon
  • Function : Author
Étienne Léveillé-Bourret
Gwilym Lewis
De-Zhu Li
Lan Li
  • Function : Author
Sigrid Liede-Schumann
Tatyana Livshultz
David Lorence
  • Function : Author
Meng Lu
Patricia Lu-Irving
Jaquelini Luber
  • Function : Author
Eve Lucas
Manuel Luján
  • Function : Author
Mabel Lum
Terry Macfarlane
Carlos Magdalena
  • Function : Author
Vidal Mansano
  • Function : Author
Lizo Masters
Simon Mayo
  • Function : Author
Kristina Mccoll
  • Function : Author
Angela Mcdonnell
Andrew Mcdougall
Todd Mclay
Hannah Mcpherson
Rosa Meneses
Vincent Merckx
Fabián Michelangeli
John Mitchell
  • Function : Author
Alexandre Monro
Michael Moore
Taryn Mueller
Klaus Mummenhoff
Priscilla Muriel
Daniel Murphy
Katharina Nargar
Lars Nauheimer
Francis Nge
Reto Nyffeler
Andrés Orejuela
Edgardo Ortiz
Luis Palazzesi
Ariane Luna Peixoto
  • Function : Author
Susan Pell
Jaume Pellicer
Darin Penneys
Oscar Perez-Escobar
  • Function : Author
Claes Persson
  • Function : Author
José Pirani
Gregory Plunkett
Robyn Powell
  • Function : Author
Ghillean Prance
  • Function : Author
Carmen Puglisi
Ming Qin
  • Function : Author
Richard Rabeler
Paul Rees
  • Function : Author
Matthew Renner
Eric Roalson
Michele Rodda
Zachary Rogers
Saba Rokni
  • Function : Author
Rolf Rutishauser
  • Function : Author
Miguel de Salas
Hanno Schaefer
Rowan Schley
Alexander Schmidt-Lebuhn
Alison Shapcott
Ihsan Al-Shehbaz
  • Function : Author
Kelly Shepherd
Mark Simmons
  • Function : Author
André Simões
  • Function : Author
Ana Rita G. Simões
Michelle Siros
Eric Smidt
James Smith
  • Function : Author
Neil Snow
  • Function : Author
Douglas Soltis
Pamela Soltis
Robert Soreng
Cynthia Sothers
Julian Starr
  • Function : Author
Peter Stevens
  • Function : Author
Shannon Straub
Lena Struwe
  • Function : Author
Jennifer Taylor
  • Function : Author
Ian Telford
  • Function : Author
Andrew Thornhill
Ifeanna Tooth
  • Function : Author
Anna Trias-Blasi
  • Function : Author
Frank Udovicic
Timothy Utteridge
Jose del Valle
G. Anthony Verboom
  • Function : Author
Helen Vonow
Maria Vorontsova
Jurriaan de Vos
Noor Al-Wattar
  • Function : Author
Michelle Waycott
Cassiano Welker
Adam White
  • Function : Author
Jan Wieringa
Luis Williamson
Trevor Wilson
Sin Yeng Wong
Lisa Woods
  • Function : Author
Roseina Woods
  • Function : Author
Stuart Worboys
Martin Xanthos
  • Function : Author
Ya Yang
Yu-Xiao Zhang
  • Function : Author
Meng-Yuan Zhou
Sue Zmarzty
  • Function : Author
Fernando Zuloaga
  • Function : Author
Alexandre Antonelli
Sidonie Bellot
Darren Crayn
Olwen Grace
Paul Kersey
Ilia Leitch
Hervé Sauquet
Stephen Smith
Wolf Eiserhardt
Félix Forest
William Baker

Abstract

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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Dates and versions

hal-04560060 , version 1 (26-04-2024)

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Alexandre Zuntini, Tom Carruthers, Olivier Maurin, Paul Bailey, Kevin Leempoel, et al.. Phylogenomics and the rise of the angiosperms. Nature, 2024, 629, pp.843-850. ⟨10.1038/s41586-024-07324-0⟩. ⟨hal-04560060⟩
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