Phylogenomics and the rise of the angiosperms

Authors: Alexandre R. Zuntini, Tom Carruthers, Olivier Maurin, Paul Bailey, Kevin Leempoel, Grace E. Brewer, Niroshini Epitawalage, Elaine Françoso, Berta Gallego, Catherine McGinnie, Raquel Negrão, Shyamali Roy, Lalita Simpson, Eduardo Toledo Romero, Vanessa Barber, Laura R. Botigué, James J. Clarkson, Robyn S. Cowan, Steven Dodsworth, Matthew G. Johnson, Jan T. Kim, Lisa Pokorny, Norman J. Wickett, Guilherme Medeiros Antar, Lucinda DeBolt, Karime Gutierrez, Kasper Hendriks, Alina Hoewener, Ai‐Qun Hu, Elizabeth Joyce, Izai A. B. Sabino 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 Ameka, Rose L. Andrew, Marc S. Appelhans, Montserrat Arista, María Jesús Ariza, Juan Arroyo, Watchara Arthan, Julien Bachelier, C. Donovan Bailey, Helen F. Barnes, Matthew D. Barrett, Russell L. Barrett, Randall J. Bayer, Michael J. Bayly, Ed Biffin, N. L. 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 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, I. D. Cowie, Laszlo Csiba, Iain Darbyshire, Gerrit Davidse, Nina M. Davies, Aaron P. Davis, Kor‐jent van Dijk, Stephen R. Downie, Marco F. Duretto, Melvin R. Duvall, Sara L. Edwards, U. Eggli, Roy H. J. Erkens, Marcial Escudero, Manuel de la Estrella, Federico Fabriani, Michael F. Fay, Paola de Lima 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, D. J. Goyder, Sean W. Graham, Aurélie Grall, Laura Green, Bee F. Gunn, Diego G. Gutiérrez, Jan Hackel, Thomas Haevermans, A. 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 James, Richard W. Jobson, Gudrun Kadereit, Imalka M. Kahandawala, Kent Kainulainen, Masahiro Kato, Elizabeth A. Kellogg, Graham J.W. King, Beata Klejevskaja, Bente Klitgaard, Ronell R. Klopper, Sandra Knapp, Мarcus A. Koch, Jim Leebens‐Mack, Frederic Lens, Christine Léon, Étienne Léveillé‐Bourret, Gwilym P. Lewis, Li D, Lan Li, Sigrid Liede‐Schumann, Tatyana Livshultz, David H. Lorence, Meng Lu, Patricia Lu‐Irving, Jaquelini Luber, Eve Lucas, Manuel Luján, Mabel Lum, Terry Desmond Macfarlane, Carlos Magdalena, Vidal de Freitas Mansano, Lizo E. Masters, Simon Joseph Mayo, Kristina McColl, Angela McDonnell, Andrew E. McDougall, Todd G. B. McLay, Hannah McPherson, Rosa Isela 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. Pérez‐Escobar, Claes Persson, Marc Pignal, Yohan Pillon, José Rubens Pirani, Gregory M. Plunkett, Robyn F. Powell, Ghillean Τ. Prance, Carmen Puglisi, Ming Qin, Richard K. Rabeler, Paul E. J. Rees, Matt A. M. Renner, Eric H. Roalson, Michele Rodda, Zachary S. Rogers, Saba Rokni, Rolf Rutishauser, Miguel F. de Salas, Hanno Schaefer, Rowan Schley, Alexander N. Schmidt‐Lebuhn, Alison Shapcott, Ihsan A. Al‐Shehbaz, Kelly Anne Shepherd, Mark P. Simmons, André Olmos Simões, Ana Rita G. Simões, Michelle Siros, Eric de Camargo 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 Telford, Andrew H. Thornhill, Ifeanna Tooth, Anna Trias‐Blasi, Frank Udovicic, Timothy M. A. Utteridge, José Carlos del Valle, G. Anthony Verboom, Helen P. Vonow, Maria S. Vorontsova, Jurriaan M. de Vos, Noor Al-Wattar, Michelle Waycott, Cassiano Aimberê Dorneles Welker, Adam J. White, Jan J. Wieringa, Luis T. 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 O. Zuloaga, Alexandre Antonelli, Sidonie Bellot, Darren M. Crayn, Olwen M. Grace, Paul Kersey, Ilia J. Leitch, Hervé Sauquet, Stephen A. Smith, Wolf L. Eiserhardt, Félix Forest, William J. Baker - Nature 2024 cited by 388

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.