A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

Nasim Azani; Marielle Babineau; C. Donovan Bailey; Hannah Banks; Ariane R. Barbosa; Rafael Barbosa Pinto; James S. Boatwright; Leonardo M. Borges; Gillian K. Brown; Anne Bruneau; Elisa Candido; Domingos Cardoso; Kuo Fang Chung; Ruth P. Clark; Adilva De S. Conceição; Michael Crisp; Paloma Cubas; Alfonso Delgado-Salinas; Kyle G. Dexter; Jeff J. Doyle; Jérôme Duminil; Ashley N. Egan; Manuel De La Estrella; Marcus J. Falcão; Dmitry A. Filatov; Ana Paula Fortuna-Perez; Renée H. Fortunato; Edeline Gagnon; Peter Gasson; Juliana Gastaldello Rando; Ana Maria Goulart de Azevedo Tozzi; Bee Gunn; David Harris; Elspeth Haston; Julie A. Hawkins; Patrick S. Herendeen; Colin E. Hughes; João R.V. Iganci; Firouzeh Javadi; Sheku Alfred Kanu; Shahrokh Kazempour-Osaloo; Geoffrey C. Kite; Bente B. Klitgaard; Fábio J. Kochanovski; Erik J.M. Koenen; Lynsey Kovar; Matt Lavin; Marianne Le Roux; Gwilym P. Lewis; Haroldo C. De Lima; The Legume Phylogeny Working Group (LPWG)

doi:10.12705/661.3

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

Nasim Azani, Marielle Babineau, C. Donovan Bailey, Hannah Banks, Ariane R. Barbosa, Rafael Barbosa Pinto, James S. Boatwright, Leonardo M. Borges, Gillian K. Brown, Anne Bruneau^*, Elisa Candido, Domingos Cardoso, Kuo Fang Chung, Ruth P. Clark, Adilva De S. Conceição, Michael Crisp, Paloma Cubas, Alfonso Delgado-Salinas, Kyle G. Dexter, Jeff J. DoyleJérôme Duminil, Ashley N. Egan, Manuel De La Estrella, Marcus J. Falcão, Dmitry A. Filatov, Ana Paula Fortuna-Perez, Renée H. Fortunato, Edeline Gagnon, Peter Gasson, Juliana Gastaldello Rando, Ana Maria Goulart de Azevedo Tozzi, Bee Gunn, David Harris, Elspeth Haston, Julie A. Hawkins, Patrick S. Herendeen, Colin E. Hughes, João R.V. Iganci, Firouzeh Javadi, Sheku Alfred Kanu, Shahrokh Kazempour-Osaloo, Geoffrey C. Kite, Bente B. Klitgaard, Fábio J. Kochanovski, Erik J.M. Koenen, Lynsey Kovar, Matt Lavin, Marianne Le Roux, Gwilym P. Lewis, Haroldo C. De Lima, The Legume Phylogeny Working Group (LPWG)

^*Corresponding author for this work

Program in Biological Sciences-Chicago Botanic Garden

Research output: Contribution to journal › Article › peer-review

850 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	44-77
Number of pages	34
Journal	Taxon
Volume	66
Issue number	1
DOIs	https://doi.org/10.12705/661.3
State	Published - Feb 2017

Funding

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); A\u00E9cio A. Santos (Goi\u00E1s, Tocantins); Ant\u00F4nio S.L. da Silva, Camilo Barbosa, Catarina S. Carvalho, Leandro V. Ferreira, Lisandra A. Teixeira, Nara Mota, Pedro L. Viana, Rafael Salom\u00E3o (Par\u00E1); Caio V. Vivas, Jos\u00E9 Lima Paix\u00E3o, Tim Baker (Bahia); Claudio Nicoletti, Geovane S. Siqueira (Espirito Santo); Eric Hattori, Fernanda S. Freitas, Fl\u00E1via Pezzini, Pedro Taucce (Minas Gerais); Marcella Baroni (Mato Grosso do Sul); Fl\u00E1via Costa (Manaus); Luzmilla Arroyo, Daniel Villaroel, Alexander Germaine Parada (Bolivia); Aniceto Daza, Jose Luis Marcelo-Pe\u00F1a, 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 Coordena\u00E7\u00E3o de Aperfei\u00E7oamento de Pessoal de N\u00EDvel Superior (CAPES/Program POS CSF # 1951/13-0), Conselho Nacional de Desenvolvimento Cient\u00EDfico e Tecnol\u00F3gico (Project Sisbiota 563084/2010-3 and Project Casadinho/Procad # 5525892011-0), Funda\u00E7\u00E3o de Amparo \u00E0 Pesquisa do Estado da Bahia (FAPESB PES 0053/2011) and the Funda\u00E7\u00E3o de Amparo \u00E0 Pesquisa do Estado de S\u00E3o Paulo FAPESP; Conselho Nacional de Desenvolvimento Cient\u00EDfico e Tecnol\u00F3gico 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 Andr\u00E9 van Proosdij for contributing excellent legume images to Figs. 3\u201311. 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.

Keywords

Caesalpinioideae
Cercidoideae
Detarioideae
Dialioideae
Duparquetioideae
Mimosoid clade
Papilionoideae
Plastid matK phylogeny

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Plant Science

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10.12705/661.3

Cite this

Azani, N., Babineau, M., Bailey, C. D., Banks, H., Barbosa, A. R., Pinto, R. B., Boatwright, J. S., Borges, L. M., Brown, G. K., Bruneau, A., Candido, E., Cardoso, D., Chung, K. F., Clark, R. P., Conceição, A. D. S., Crisp, M., Cubas, P., Delgado-Salinas, A., Dexter, K. G., ... The Legume Phylogeny Working Group (LPWG) (2017). A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny. Taxon, 66(1), 44-77. https://doi.org/10.12705/661.3

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title = "A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny",

abstract = "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.",

keywords = "Caesalpinioideae, Cercidoideae, Detarioideae, Dialioideae, Duparquetioideae, Mimosoid clade, Papilionoideae, Plastid matK phylogeny",

author = "Nasim Azani and Marielle Babineau and Bailey, {C. Donovan} and Hannah Banks and Barbosa, {Ariane R.} and Pinto, {Rafael Barbosa} and Boatwright, {James S.} and Borges, {Leonardo M.} and Brown, {Gillian K.} and Anne Bruneau and Elisa Candido and Domingos Cardoso and Chung, {Kuo Fang} and Clark, {Ruth P.} and Concei{\c c}{\~a}o, {Adilva De S.} and Michael Crisp and Paloma Cubas and Alfonso Delgado-Salinas and Dexter, {Kyle G.} and Doyle, {Jeff J.} and J{\'e}r{\^o}me Duminil and Egan, {Ashley N.} and {De La Estrella}, Manuel and Falc{\~a}o, {Marcus J.} and Filatov, {Dmitry A.} and Fortuna-Perez, {Ana Paula} and Fortunato, {Ren{\'e}e H.} and Edeline Gagnon and Peter Gasson and Rando, {Juliana Gastaldello} and Tozzi, {Ana Maria Goulart de Azevedo} and Bee Gunn and David Harris and Elspeth Haston and Hawkins, {Julie A.} and Herendeen, {Patrick S.} and Hughes, {Colin E.} and Iganci, {Jo{\~a}o R.V.} and Firouzeh Javadi and Kanu, {Sheku Alfred} and Shahrokh Kazempour-Osaloo and Kite, {Geoffrey C.} and Klitgaard, {Bente B.} and Kochanovski, {F{\'a}bio J.} and Koenen, {Erik J.M.} and Lynsey Kovar and Matt Lavin and Roux, {Marianne Le} and Lewis, {Gwilym P.} and {De Lima}, {Haroldo C.} and {The Legume Phylogeny Working Group (LPWG)}",

note = "Publisher Copyright: {\textcopyright} International Association for Plant Taxonomy (IAPT) 2017.",

year = "2017",

month = feb,

doi = "10.12705/661.3",

language = "English (US)",

volume = "66",

pages = "44--77",

journal = "Taxon",

issn = "0040-0262",

publisher = "International Association for Plant Taxonomy",

number = "1",

}

Azani, N, Babineau, M, Bailey, CD, Banks, H, Barbosa, AR, Pinto, RB, Boatwright, JS, Borges, LM, Brown, GK, Bruneau, A, Candido, E, Cardoso, D, Chung, KF, Clark, RP, Conceição, ADS, Crisp, M, Cubas, P, Delgado-Salinas, A, Dexter, KG, Doyle, JJ, Duminil, J, Egan, AN, De La Estrella, M, Falcão, MJ, Filatov, DA, Fortuna-Perez, AP, Fortunato, RH, Gagnon, E, Gasson, P, Rando, JG, Tozzi, AMGDA, Gunn, B, Harris, D, Haston, E, Hawkins, JA, Herendeen, PS, Hughes, CE, Iganci, JRV, Javadi, F, Kanu, SA, Kazempour-Osaloo, S, Kite, GC, Klitgaard, BB, Kochanovski, FJ, Koenen, EJM, Kovar, L, Lavin, M, Roux, ML, Lewis, GP, De Lima, HC & The Legume Phylogeny Working Group (LPWG) 2017, 'A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny', Taxon, vol. 66, no. 1, pp. 44-77. https://doi.org/10.12705/661.3

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)

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

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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 -

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

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