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Phylogenomics and the rise of the angiosperms

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2024年4月24日

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

摘要

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.