TY - JOUR
T1 - A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny
AU - Azani, Nasim
AU - Babineau, Marielle
AU - Bailey, C. Donovan
AU - Banks, Hannah
AU - Barbosa, Ariane R.
AU - Pinto, Rafael Barbosa
AU - Boatwright, James S.
AU - Borges, Leonardo M.
AU - Brown, Gillian K.
AU - Bruneau, Anne
AU - Candido, Elisa
AU - Cardoso, Domingos
AU - Chung, Kuo Fang
AU - Clark, Ruth P.
AU - Conceição, Adilva De S.
AU - Crisp, Michael
AU - Cubas, Paloma
AU - Delgado-Salinas, Alfonso
AU - Dexter, Kyle G.
AU - Doyle, Jeff J.
AU - Duminil, Jérôme
AU - Egan, Ashley N.
AU - De La Estrella, Manuel
AU - Falcão, Marcus J.
AU - Filatov, Dmitry A.
AU - Fortuna-Perez, Ana Paula
AU - Fortunato, Renée H.
AU - Gagnon, Edeline
AU - Gasson, Peter
AU - Rando, Juliana Gastaldello
AU - Tozzi, Ana Maria Goulart de Azevedo
AU - Gunn, Bee
AU - Harris, David
AU - Haston, Elspeth
AU - Hawkins, Julie A.
AU - Herendeen, Patrick S.
AU - Hughes, Colin E.
AU - Iganci, João R.V.
AU - Javadi, Firouzeh
AU - Kanu, Sheku Alfred
AU - Kazempour-Osaloo, Shahrokh
AU - Kite, Geoffrey C.
AU - Klitgaard, Bente B.
AU - Kochanovski, Fábio J.
AU - Koenen, Erik J.M.
AU - Kovar, Lynsey
AU - Lavin, Matt
AU - Roux, Marianne Le
AU - Lewis, Gwilym P.
AU - De Lima, Haroldo C.
AU - The Legume Phylogeny Working Group (LPWG)
N1 - Funding Information:
This project was made possible thanks to ongoing collaboration with researchers worldwide who have collected samples of legumes for DNA studies and who have shared material with members of the legume systematics community for over three decades. In particular, we thank the following people for their help with collection, preparation and curation of specimens, and/or with sequencing of the matK locus: Alexandra Clark, Michelle Hart (Royal Botanic Gardens, Edinburgh); Adilson M. Pintor, Marcelo T. Nascimento, Pablo Prieto (Rio de Janeiro); Aécio A. Santos (Goiás, Tocantins); Antônio S.L. da Silva, Camilo Barbosa, Catarina S. Carvalho, Leandro V. Ferreira, Lisandra A. Teixeira, Nara Mota, Pedro L. Viana, Rafael Salomão (Pará); Caio V. Vivas, José Lima Paixão, Tim Baker (Bahia); Claudio Nicoletti, Geovane S. Siqueira (Espirito Santo); Eric Hattori, Fernanda S. Freitas, Flávia Pezzini, Pedro Taucce (Minas Gerais); Marcella Baroni (Mato Grosso do Sul); Flávia Costa (Manaus); Luzmilla Arroyo, Daniel Villaroel, Alexander Germaine Parada (Bolivia); Aniceto Daza, Jose Luis Marcelo-Peña, Reynaldo Linares Palomino, Carlos Reynel, Isau Huamantupa (Peru); Tanja Schuster, Mansi Trivedi, Gabe Johnson, William Cagle, Ailsa Holland, and Xin-Fen Gao (Smithsonian Institution). We thank the ScienceCloud at the University of Zurich for computational resources. Funding for this project was provided by the Natural Sciences and Engineering Research Council of Canada, the U.K. Natural Environment Research Council (grant NE/I028122/1), the Swiss National Science Foundation (grant 31003A_13552), the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/Program POS CSF # 1951/13-0), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Project Sisbiota 563084/2010-3 and Project Casadinho/Procad # 5525892011-0), Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB PES 0053/2011) and the Fundação de Amparo à Pesquisa do Estado de São Paulo FAPESP; Conselho Nacional de Desenvolvimento Científico e Tecnológico CNPq of Brazil, the Smithsonian Institution, the U.S. National Science Foundation (grant DEB-1352217), and the Environment Research and Technology Development Fund (S9) of the Ministry of the Environment of Japan, and Arizona State University. Anne Bruneau acknowledges the Royal Botanic Gardens, Edinburgh, and the Department of Systematic and Evolutionary Botany, University of Zurich for logistical support during a sabbatical in 2015. Finally, we thank Jonathan Amith, Xander van der Burgt, Emilio Constantino, David Du Puy, Flora do Acre, Felix Forest, Paul Hoekstra, Mike Hopkins, Rosangela Melo, Justin Moat, Projecto Flora Reserva Ducke INPA/DFID, Shijin Li, Alex Popovkin, James Ratter, Wolfgang Stuppy, Liam Trethowan, Timothy Utteridge, and André van Proosdij for contributing excellent legume images to Figs. 3–11. The authors thank Michael Pirie, Lars Chatrou, Jefferson Prado, John McNeill, and two anonymous reviewers for advice on nomenclatural issues and comments on the manuscript.
Publisher Copyright:
© International Association for Plant Taxonomy (IAPT) 2017.
PY - 2017/2
Y1 - 2017/2
N2 - The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.
AB - The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.
KW - Caesalpinioideae
KW - Cercidoideae
KW - Detarioideae
KW - Dialioideae
KW - Duparquetioideae
KW - Mimosoid clade
KW - Papilionoideae
KW - Plastid matK phylogeny
UR - http://www.scopus.com/inward/record.url?scp=85009768127&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85009768127&partnerID=8YFLogxK
U2 - 10.12705/661.3
DO - 10.12705/661.3
M3 - Article
AN - SCOPUS:85009768127
SN - 0040-0262
VL - 66
SP - 44
EP - 77
JO - Taxon
JF - Taxon
IS - 1
ER -