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Phylogenomics and the rise of the angiosperms

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Resource type
Journal article
Creator (person)
Zuntini, Alexandre R.
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Carruthers, Tom
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Maurin, Olivier
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Bailey, Paul C.
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Leempoel, Kevin
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Brewer, Grace E.
Epitawalage, Niroshini
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Françoso, Elaine
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Gallego-Paramo, Berta
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McGinnie, Catherine
Negrão, Raquel
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Roy, Shyamali R.
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Simpson, Lalita
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Toledo Romero, Eduardo
Barber, Vanessa M. A.
Botigué, Laura
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Clarkson, James J.
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Cowan, Robyn S.
Dodsworth, Steven
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Johnson, Matthew G.
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Kim, Jan T.
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Pokorny, Lisa
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Wickett, Norman J.
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Antar, Guilherme M.
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DeBolt, Lucinda
Gutierrez, Karime
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Hendriks, Kasper P.
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Hoewener, Alina
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Hu, Ai-Qun
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Joyce, Elizabeth M.
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Kikuchi, Izai A. B. S.
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Larridon, Isabel
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Larson, Drew A.
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de Lírio, Elton John
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Liu, Jing-Xia
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Malakasi, Panagiota
Przelomska, Natalia A. S.
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Shah, Toral
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Viruel, Juan
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Allnutt, Theodore R.
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Ameka, Gabriel K.
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Andrew, Rose L.
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Appelhans, Marc S.
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Arista, Montserrat
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Ariza, María Jesús
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Arroyo, Juan
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Arthan, Watchara
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Bachelier, Julien B.
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Bailey, C. Donovan
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Barnes, Helen F.
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Barrett, Matthew D.
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Barrett, Russell L.
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Bayer, Randall J.
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Bayly, Michael J.
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Biffin, Ed
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Biggs, Nicky
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Birch, Joanne L.
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Bogarín, Diego
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Borosova, Renata
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Bowles, Alexander M. C.
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Boyce, Peter C.
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Bramley, Gemma L. C.
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Briggs, Marie
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Broadhurst, Linda
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Brown, Gillian K.
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Bruhl, Jeremy J.
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Bruneau, Anne
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Buerki, Sven
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Burns, Edie
Byrne, Margaret
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Cable, Stuart
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Calladine, Ainsley
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Callmander, Martin W.
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Cano, Ángela
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Cantrill, David J.
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Cardinal-McTeague, Warren M.
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Carlsen, Mónica M.
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Carruthers, Abigail J. A.
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de Castro Mateo, Alejandra
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Chase, Mark W.
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Chatrou, Lars W.
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Cheek, Martin
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Chen, Shilin
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Christenhusz, Maarten J. M.
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Christin, Pascal-Antoine
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Clements, Mark A.
Coffey, Skye C.
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Conran, John G.
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Cornejo, Xavier
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Couvreur, Thomas L. P.
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Cowie, Ian D.
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Csiba, Laszlo
Darbyshire, Iain
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Davidse, Gerrit
Davies, Nina M. J.
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Davis, Aaron P.
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van Dijk, Kor-jent
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Downie, Stephen R.
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Duretto, Marco F.
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Duvall, Melvin R.
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Edwards, Sara L.
Eggli, Urs
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Erkens, Roy H. J.
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Escudero, Marcial
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de la Estrella, Manuel
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Fabriani, Federico
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Fay, Michael F.
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Ferreira, Paola de L.
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Ficinski, Sarah Z.
Fowler, Rachael M.
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Frisby, Sue
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Fu, Lin
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Fulcher, Tim
Galbany-Casals, Mercè
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Gardner, Elliot M.
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German, Dmitry A.
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Giaretta, Augusto
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Gibernau, Marc
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Gillespie, Lynn J.
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González, Cynthia C.
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Goyder, David J.
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Graham, Sean W.
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Grall, Aurélie
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Green, Laura
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Gunn, Bee F.
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Gutiérrez, Diego G.
Hackel, Jan
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Haevermans, Thomas
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Haigh, Anna
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Hall, Jocelyn C.
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Hall, Tony
Harrison, Melissa J.
Hatt, Sebastian A.
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Hidalgo, Oriane
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Hodkinson, Trevor R.
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Holmes, Gareth D.
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Hopkins, Helen C. F.
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Jackson, Christopher J.
James, Shelley A.
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Jobson, Richard W.
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Kadereit, Gudrun
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Kahandawala, Imalka M.
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Kainulainen, Kent
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Kato, Masahiro
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Kellogg, Elizabeth A.
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King, Graham J.
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Klejevskaja, Beata
Klitgaard, Bente B.
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Klopper, Ronell R.
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Knapp, Sandra
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Koch, Marcus A.
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Leebens-Mack, James H.
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Lens, Frederic
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Leon, Christine J.
Léveillé-Bourret, Étienne
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Lewis, Gwilym P.
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Li, De-Zhu
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Li, Lan
Liede-Schumann, Sigrid
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Livshultz, Tatyana
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Lorence, David
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Lu, Meng
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Lu-Irving, Patricia
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Luber, Jaquelini
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Lucas, Eve J.
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Luján, Manuel
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Lum, Mabel
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Macfarlane, Terry D.
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Magdalena, Carlos
Mansano, Vidal F.
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Masters, Lizo E.
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Mayo, Simon J.
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McColl, Kristina
McDonnell, Angela J.
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McDougall, Andrew E.
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McLay, Todd G. B.
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McPherson, Hannah
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Meneses, Rosa I.
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Merckx, Vincent S. F. T.
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Michelangeli, Fabián A.
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Mitchell, John D.
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Monro, Alexandre K.
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Moore, Michael J.
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Mueller, Taryn L.
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Mummenhoff, Klaus
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Munzinger, Jérôme
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Muriel, Priscilla
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Murphy, Daniel J.
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Nargar, Katharina
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Nauheimer, Lars
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Nge, Francis J.
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Nyffeler, Reto
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Orejuela, Andrés
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Ortiz, Edgardo M.
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Palazzesi, Luis
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Peixoto, Ariane Luna
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Pell, Susan K.
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Pellicer, Jaume
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Penneys, Darin S.
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Perez-Escobar, Oscar A.
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Date published
April 24, 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.
Contributor (person)
Persson, Claes
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Pignal, Marc
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Pillon, Yohan
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Pirani, José R.
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Plunkett, Gregory M.
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Powell, Robyn F.
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Prance, Ghillean T.
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Puglisi, Carmen
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Qin, Ming
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Rabeler, Richard K.
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Rees, Paul E. J.
Renner, Matthew
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Roalson, Eric H.
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Rodda, Michele
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Rogers, Zachary S.
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Rokni, Saba
Rutishauser, Rolf
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de Salas, Miguel F.
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Schaefer, Hanno
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Schley, Rowan J.
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Schmidt-Lebuhn, Alexander
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Shapcott, Alison
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Al-Shehbaz, Ihsan
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Shepherd, Kelly A.
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Simmons, Mark P.
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Simões, André O.
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Simões, Ana Rita G.
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Siros, Michelle
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Smidt, Eric C.
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Smith, James F.
Snow, Neil
Soltis, Douglas E.
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Soltis, Pamela S.
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Soreng, Robert J.
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Sothers, Cynthia A.
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Starr, Julian R.
Stevens, Peter F.
Straub, Shannon C. K.
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Struwe, Lena
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Taylor, Jennifer M.
Telford, Ian R. H.
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Thornhill, Andrew H.
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Tooth, Ifeanna
Trias-Blasi, Anna
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Udovicic, Frank
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Utteridge, Timothy M. A.
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Del Valle, Jose C.
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Verboom, G. Anthony
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Vonow, Helen P.
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Vorontsova, Maria S.
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de Vos, Jurriaan M.
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Al-Wattar, Noor
Waycott, Michelle
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Welker, Cassiano A. D.
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White, Adam J.
Wieringa, Jan J.
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Williamson, Luis T.
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Wilson, Trevor C.
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Wong, Sin Yeng
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Woods, Lisa A.
Woods, Roseina
Worboys, Stuart
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Xanthos, Martin
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Yang, Ya
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Zhang, Yu-Xiao
Zhou, Meng-Yuan
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Zmarzty, Sue
Zuloaga, Fernando O.
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Antonelli, Alexandre
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Bellot, Sidonie
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Crayn, Darren M.
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Grace, Olwen M.
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Kersey, Paul J.
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Leitch, Ilia J.
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Sauquet, Hervé
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Smith, Stephen A.
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Eiserhardt, Wolf L.
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Forest, Félix
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Baker, William J.
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Project(s)
Priority 4: Accelerated Taxonomy
Plant and Fungal Tree of Life Project
Funder
Funder nameAwards
Calleva Foundation, United Kingdom
Plant and Fungal Tree of Life Project
Bioplatforms Australia
Villum Fonden, Denmark
Grant no. 00025354
Aarhus University Research Foundation, Denmark
Grant no. AUFF-E-2017-7-19
National Science Foundation, United States
DBI 1930030 - DEB 1917146
Biotechnology and Biological Sciences Research Council, United Kingdom
‘UK’s Crop Diversity Bioinformatics HPC’ (BBSRC grant no. BB/S019669/1)
Journal title
Nature
Publisher
Springer Science and Business Media LLC
Place of publication
Berlin/Heidelberg, Germany
ISSN
0028-0836
eISSN
1476-4687
Date accepted
March 15, 2024
Official URL
http://dx.doi.org/10.1038/s41586-024-07324-0
Licence
https://creativecommons.org/licenses/by/4.0/
DOI
10.1038/s41586-024-07324-0
Keywords
Plant evolution
Phylogenomics
Angiosperms
Speciation
Phylogenetics
Additional information
IF = 64.8 (2023-2024)
Collection
Plant and Fungal Trees of Life project
Managed by the British Library and supported by the AHRC

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