Phylogenomics and the rise of the angiosperms
Authors: Zuntini Alexandre R. , Carruthers Tom , Maurin Olivier , Bailey Paul C. , Leempoel Kevin , Brewer Grace E. , Epitawalage Niroshini , Françoso Elaine , Gallego-Paramo Berta , McGinnie Catherine , Negrão Raquel , Roy Shyamali R. , Simpson Lalita , Toledo Romero Eduardo , Barber Vanessa M. A. , Botigué Laura , Clarkson James J. , Cowan Robyn S. , Dodsworth Steven , Johnson Matthew G. , Kim Jan T. , Pokorny Lisa , Wickett Norman J. , Antar Guilherme M. , DeBolt Lucinda , Gutierrez Karime , Hendriks Kasper P. , Hoewener Alina , Hu Ai-Qun , Joyce Elizabeth M. , Kikuchi Izai A. B. S. , Larridon Isabel , Larson Drew A. , de Lírio Elton John , Liu Jing-Xia , Malakasi Panagiota , Przelomska Natalia A. S. , Shah Toral , Viruel Juan , Allnutt Theodore R. , Ameka Gabriel K. , Andrew Rose L. , Appelhans Marc S. , Arista Montserrat , Ariza María Jesús , Arroyo Juan , Arthan Watchara , Bachelier Julien B. , Bailey C. Donovan , Barnes Helen F. , Barrett Matthew D. , Barrett Russell L. , Bayer Randall J. , Bayly Michael J. , Biffin Ed , Biggs Nicky , Birch Joanne L. , Bogarín Diego , Borosova Renata , Bowles Alexander M. C. , Boyce Peter C. , Bramley Gemma L. C. , Briggs Marie , Broadhurst Linda , Brown Gillian K. , Bruhl Jeremy J. , Bruneau Anne , Buerki Sven , Burns Edie , Byrne Margaret , Cable Stuart , Calladine Ainsley , Callmander Martin W. , Cano Ángela , Cantrill David J. , Cardinal-McTeague Warren M. , Carlsen Mónica M. , Carruthers Abigail J. A. , de Castro Mateo Alejandra , Chase Mark W. , Chatrou Lars W. , Cheek Martin , Chen Shilin , Christenhusz Maarten J. M. , Christin Pascal-Antoine , Clements Mark A. , Coffey Skye C. , Conran John G. , Cornejo Xavier , Couvreur Thomas L. P. , Cowie Ian D. , Csiba Laszlo , Darbyshire Iain , Davidse Gerrit , Davies Nina M. J. , Davis Aaron P. , van Dijk Kor-jent , Downie Stephen R. , Duretto Marco F. , Duvall Melvin R. , Edwards Sara L. , Eggli Urs , Erkens Roy H. J. , Escudero Marcial , de la Estrella Manuel , Fabriani Federico , Fay Michael F. , Ferreira Paola de L. , Ficinski Sarah Z. , Fowler Rachael M. , Frisby Sue , Fu Lin , Fulcher Tim , Galbany-Casals Mercè , Gardner Elliot M. , German Dmitry A. , Giaretta Augusto , Gibernau Marc , Gillespie Lynn J. , González Cynthia C. , Goyder David J. , Graham Sean W. , Grall Aurélie , Green Laura , Gunn Bee F. , Gutiérrez Diego G. , Hackel Jan , Haevermans Thomas , Haigh Anna , Hall Jocelyn C. , Hall Tony , Harrison Melissa J. , Hatt Sebastian A. , Hidalgo Oriane , Hodkinson Trevor R. , Holmes Gareth D. , Hopkins Helen C. F. , Jackson Christopher J. , James Shelley A. , Jobson Richard W. , Kadereit Gudrun , Kahandawala Imalka M. , Kainulainen Kent , Kato Masahiro , Kellogg Elizabeth A. , King Graham J. , Klejevskaja Beata , Klitgaard Bente B. , Klopper Ronell R. , Knapp Sandra , Koch Marcus A. , Leebens-Mack James H. , Lens Frederic , Leon Christine J. , Léveillé-Bourret Étienne , Lewis Gwilym P. , Li De-Zhu , Li Lan , Liede-Schumann Sigrid , Livshultz Tatyana , Lorence David , Lu Meng , Lu-Irving Patricia , Luber Jaquelini , Lucas Eve J. , Luján Manuel , Lum Mabel , Macfarlane Terry D. , Magdalena Carlos , Mansano Vidal F. , Masters Lizo E. , Mayo Simon J. , McColl Kristina , McDonnell Angela J. , McDougall Andrew E. , McLay Todd G. B. , McPherson Hannah , Meneses Rosa I. , Merckx Vincent S. F. T. , Michelangeli Fabián A. , Mitchell John D. , Monro Alexandre K. , Moore Michael J. , Mueller Taryn L. , Mummenhoff Klaus , Munzinger Jérôme , Muriel Priscilla , Murphy Daniel J. , Nargar Katharina , Nauheimer Lars , Nge Francis J. , Nyffeler Reto , Orejuela Andrés , Ortiz Edgardo M. , Palazzesi Luis , Peixoto Ariane Luna , Pell Susan K. , Pellicer Jaume , Penneys Darin S. , Perez-Escobar Oscar A. , Persson Claes , Pignal Marc , Pillon Yohan , Pirani José R. , Plunkett Gregory M. , Powell Robyn F. , Prance Ghillean T. , Puglisi Carmen , Qin Ming , Rabeler Richard K. , Rees Paul E. J. , Renner Matthew , Roalson Eric H. , Rodda Michele , Rogers Zachary S. , Rokni Saba , Rutishauser Rolf , de Salas Miguel F. , Schaefer Hanno , Schley Rowan J. , Schmidt-Lebuhn Alexander , Shapcott Alison , Al-Shehbaz Ihsan , Shepherd Kelly A. , Simmons Mark P. , Simões André O. , Simões Ana Rita G. , Siros Michelle , Smidt Eric C. , Smith James F. , Snow Neil , Soltis Douglas E. , Soltis Pamela S. , Soreng Robert J. , Sothers Cynthia A. , Starr Julian R. , Stevens Peter F. , Straub Shannon C. K. , Struwe Lena , Taylor Jennifer M. , Telford Ian R. H. , Thornhill Andrew H. , Tooth Ifeanna , Trias-Blasi Anna , Udovicic Frank , Utteridge Timothy M. A. , Del Valle Jose C. , Verboom G. Anthony , Vonow Helen P. , Vorontsova Maria S. , de Vos Jurriaan M. , Al-Wattar Noor , Waycott Michelle , Welker Cassiano A. D. , White Adam J. , Wieringa Jan J. , Williamson Luis T. , Wilson Trevor C. , Wong Sin Yeng , Woods Lisa A. , Woods Roseina , Worboys Stuart , Xanthos Martin , Yang Ya , Zhang Yu-Xiao , Zhou Meng-Yuan , Zmarzty Sue , Zuloaga Fernando O. , Antonelli Alexandre , Bellot Sidonie , Crayn Darren M. , Grace Olwen M. , Kersey Paul J. , Leitch Ilia J. , Sauquet Hervé , Smith Stephen A. , Eiserhardt Wolf L. , Forest Félix , Baker William J. 
Published: April 2024

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.