@article{4230d9dd77f846d4bfc0e0ff6f70b153,
title = "A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence",
abstract = "Grasses (Poaceae) comprise c. 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. We inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a newly inferred 910-tip plastome tree. We recovered most of the tribes and subfamilies previously established, despite pervasive incongruence among nuclear gene trees. The early diversification of the PACMAD clade could represent a hard polytomy. Gene tree–species tree reconciliation suggests that reticulation events occurred repeatedly. Nuclear–plastome incongruence is rare, with very few cases of supported conflict. We provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture.",
keywords = "Angiosperms353, genome, incongruence, phylogenomics, plastome, Poaceae, target capture, transcriptomics",
author = "{Grass Phylogeny Working Group III} and Watchara Arthan and Baker, {William J.} and Barrett, {Matthew D.} and Barrett, {Russell L.} and Bennetzen, {Jeffrey L.} and Guillaume Besnard and Bianconi, {Matheus E.} and Birch, {Joanne L.} and Pilar Catal{\'a}n and Wenli Chen and Maarten Christenhusz and Christin, {Pascal Antoine} and Clark, {Lynn G.} and Columbus, {J. Travis} and Couch, {Charlotte A.} and Crayn, {Darren M.} and Gerrit Davidse and Soejatmi Dransfield and Dunning, {Luke T.} and Duvall, {Melvin R.} and Ficinski, {Sarah Z.} and Fisher, {Amanda E.} and Siri Fjellheim and F{\'e}lix Forest and Gillespie, {Lynn J.} and Jan Hackel and Thomas Haevermans and Hodkinson, {Trevor R.} and Huang, {Chien Hsun} and Weichen Huang and Humphreys, {Aelys M.} and Jobson, {Richard W.} and Kayombo, {Canisius J.} and Kellogg, {Elizabeth A.} and Kimeu, {John M.} and Isabel Larridon and Rokiman Letsara and Li, {De Zhu} and Liu, {Jing Xia} and Ximena Londo{\~n}o and Luke, {Quentin W.R.} and Hong Ma and Macfarlane, {Terry D.} and Olivier Maurin and McKain, {Michael R.} and McLay, {Todd G.B.} and Moreno-Aguilar, {Maria Fernanda} and Murphy, {Daniel J.} and Nanjarisoa, {Olinirina P.} and Onjalalaina, {Guy E.} and Peterson, {Paul M.} and Rakotonasolo, {Rivontsoa A.} and Jacqueline Razanatsoa and Saarela, {Jeffery M.} and Lalita Simpson and Snow, {Neil W.} and Soreng, {Robert J.} and Sosef, {Marc S.M.} and Thompson, {E. John} and Paweena Traiperm and Verboom, {G. Anthony} and Vorontsova, {Maria S.} and Walsh, {Neville G.} and Washburn, {Jacob D.} and Teera Watcharamongkol and Michelle Waycott and Welker, {Cassiano A.D.} and Xanthos, {Martin D.} and Nianhe Xia and Lin Zhang and Alexander Zizka and Zuloaga, {Fernando O.} and Zuntini, {Alexandre R.}",
note = "Publisher Copyright: {\textcopyright} 2024 The Author(s). New Phytologist {\textcopyright} 2024 New Phytologist Foundation.",
year = "2025",
month = jan,
doi = "10.1111/nph.20263",
language = "English",
volume = "245",
pages = "818--834",
journal = "New Phytologist",
issn = "0028-646X",
number = "2",
}