Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)

Jens J. Ringelberg; Erik J. M. Koenen; João R. Iganci; Luciano P. de Queiroz; Daniel J. Murphy; Myriam Gaudeul; Anne Bruneau; Melissa Luckow; Gwilym P. Lewis; Colin E. Hughes

doi:10.3897/phytokeys.205.85866

Eduardo Estrada Castillón, José Ángel Villarreal Quintanilla, Juan Antonio Encina Domínguez, Arturo Mora Olivo, Jaime Sánchez Salas, Gisela Muro Pérez, Eduardo Alanís Rodríguez, Renata Aidé Valdés Alameda, Nelly Sandoval Mata, Gilberto Ocampo (2025)
The Fabaceae in Northeastern Mexico (Subfamily Papilionoideae, Tribes Amorpheae, Brongniartieae, and Dalbergieae). Plants 14: 789.

DOI: 10.3390/plants14050789

Erik J. M. Koenen (2022)
Osodendron gen. nov. (Leguminosae, Caesalpinioideae), a new genus of mimosoid legumes of tropical Africa. PhytoKeys 205: 453.

DOI: 10.3897/phytokeys.205.82821

Roberto Contreras-Díaz, Felipe S. Carevic, Liesbeth van den Brink, Wilson Huanca-Mamani, Patrick Jung (2024)
Structure, gene composition, divergence time and phylogeny analysis of the woody desert species Neltuma alba, Neltuma chilensis and Strombocarpa strombulifera. Scientific Reports 14: .

DOI: 10.1038/s41598-024-64287-y

Leonardo M. Borges, Peter W. Inglis, Marcelo F. Simon, Pétala Gomes Ribeiro, Luciano P. de Queiroz (2022)
Misleading fruits: The non-monophyly of Pseudopiptadenia and Pityrocarpa supports generic re-circumscriptions and a new genus within mimosoid legumes. PhytoKeys 205: 239.

DOI: 10.3897/phytokeys.205.82275

Guojin Zhang, Hong Ma (2024)
Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. Journal of Integrative Plant Biology 66: 546.

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Gabriela Aviles Peraza, Erik J. M. Koenen, Ricarda Riina, Colin E. Hughes, Jens J. Ringelberg, German Carnevali Fernández-Concha, Ivón Mercedes Ramírez Morillo, Lilia Lorena Can Itza, Ivan Tamayo-Cen, Jorge Humberto Ramírez Prado, Xavier Cornejo, Sawai Mattapha, Rodrigo Duno de Stefano (2022)
Re-establishment of the genus Pseudalbizzia (Leguminosae, Caesalpinioideae, mimosoid clade): the New World species formerly placed in Albizia. PhytoKeys 205: 371.

DOI: 10.3897/phytokeys.205.76821

Érica Mangaravite, Thamyres Cardoso da Silveira, Christina Cleo Vinson, Marcelo Leandro Bueno, Roberta dos Santos Silva, Maria Antonia Carniello, Joseph W Veldman, Magali Gonçalves Garcia, Luiz Orlando de Oliveira (2024)
Unlocking the secret diversity of Anadenanthera: insights from molecular genetics of four evolving species. Botanical Journal of the Linnean Society 204: 47.

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Eduardo Estrada-Castillón, José Ángel Villarreal-Quintanilla, Gerardo Cuéllar-Rodríguez, Leticia Torres-Colín, Juan Antonio Encina-Domínguez, Jaime Sánchez-Salas, Gisela Muro-Pérez, Diego Axayácatl González-Cuéllar, Oralia Magaly Galván-García, Luis Gerardo Rubio-Pequeño, Arturo Mora-Olivo (2024)
The Fabaceae in Northeastern Mexico (Subfamilies Caesalpinioideae (Excluding Tribe Mimoseae), Cercidoideae, and Detarioideae). Plants 13: 2477.

DOI: 10.3390/plants13172477

Yi-Shan Zhao, Teng-Xiang Wang, Shu-Mei Xiao, Shu-Feng Li, Jian Huang (2025)
Fossil pods of tropical tree Peltophorum (Caesalpinioideae, Fabaceae) from southwestern China. Review of Palaeobotany and Palynology 334: 105282.

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G.D. Pedersoli, V.F. Mansano, T.C. De Barros, J.V. Paulino, S.P. Teixeira (2023)
Sympetaly in the mimosoid clade (Leguminosae, Caesalpinioideae): An unusual trait in the rosid group. Perspectives in Plant Ecology, Evolution and Systematics 60: 125747.

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Vanessa Terra, Jens J. Ringelberg, Bruce Maslin, Erik J. M. Koenen, John Ebinger, David Seigler, Colin E. Hughes (2022)
Dilemmas in generic delimitation of Senegalia and allies (Caesalpinioideae, mimosoid clade): how to reconcile phylogenomic evidence with morphology and taxonomy?. PhytoKeys 205: 261.

DOI: 10.3897/phytokeys.205.79378

Julia Ferm, Catarina Rydin (2024)
Taxonomic adjustments in Mimoseae (Fabaceae): new genera described to accommodate Zygia/Inga inundata and Zygia sabatieri, and a recombination of Marmaroxylon ocumarense . Botanical Journal of the Linnean Society : .

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Martín Juárez (2024)
Neltuma humilis (Fabaceae, Mimoseae): nuevo registro para la flora de la provincia de Santa Fe, Argentina. Lilloa : 39.

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Leonardo Martin Gatica‐Soria, M. Emilia Roulet, Walter D. Tulle, Hector A. Sato, M. Eugenia Barrandeguy, M. Virginia Sanchez‐Puerta (2025)
Highly variable mitochondrial chromosome content in a holoparasitic plant due to recurrent gains of foreign circular DNA. Physiologia Plantarum 177: .

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Gillian K. Brown, Javier Aju, Michael J. Bayly, Daniel J. Murphy, Todd G. B. McLay (2022)
Phylogeny and classification of the Australasian and Indomalayan mimosoid legumes Archidendron and Archidendropsis (Leguminosae, subfamily Caesalpinioideae, mimosoid clade). PhytoKeys 205: 299.

DOI: 10.3897/phytokeys.205.79381

Iván Tamayo-Cen, Benjamin M. Torke, José Enrique López Contreras, German Carnevali Fernández-Concha, Ivón Ramírez Morillo, Lilia Lorena Can Itza, Rodrigo Duno de Stefano (2022)
Revisiting the phylogeny and taxonomy of the Pithecellobium clade (Leguminosae, Caesalpinioideae) with new generic circumscriptions. PhytoKeys 205: 279.

DOI: 10.3897/phytokeys.205.82728

Colin E. Hughes, Jens J. Ringelberg, Melissa Luckow, José Luis Contreras Jiménez (2022)
Mezcala – a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the Balsas Depression in Mexico. PhytoKeys 205: 191.

DOI: 10.3897/phytokeys.205.78297

Colin E. Hughes, Jens J. Ringelberg, Gwilym P. Lewis, Santiago A. Catalano (2022)
Disintegration of the genus Prosopis L. (Leguminosae, Caesalpinioideae, mimosoid clade). PhytoKeys 205: 147.

DOI: 10.3897/phytokeys.205.75379

Gregory W. Stull, Kasey K. Pham, Pamela S. Soltis, Douglas E. Soltis (2023)
Deep reticulation: the long legacy of hybridization in vascular plant evolution. The Plant Journal 114: 743.

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Jing Cai, Chuang Yang, Leyang Wang, Jiaqing He, Qiang Wang (2025)
Phylogeny of Cassieae based on seed morphological and ITS evidence. PeerJ 13: e18947.

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Quentin Cronk, Leonardo M. Borges (2024)
Sexual system variation in legumes (Leguminosae): underpinning genomic study with new tools to describe inflorescence morphology. Brazilian Journal of Botany 47: 1101.

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Lucas Sá Barreto Jordão, Marli Pires Morim, Marcelo Fragomeni Simon, José Fernando A Baumgratz (2025)
Advances in systematics of Mimosa (Fabaceae): phylogeny and biogeography of the Petiolovariabilis clade. Botanical Journal of the Linnean Society : .

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Élvia Rodrigues de Souza, Priscilla Gomes C. de Almeida, Lamarck Rocha, Erik J.M. Koenen, Margoth Atahuachi Burgos, Gwilym P. Lewis, Colin E. Hughes (2022)
Boliviadendron, a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the interior Andean valleys of Bolivia. PhytoKeys 205: 439.

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Francis J. Nge, Tanawat Chaowasku, Anissara Damthongdee, Chattida Wiya, Vincent R.C. Soulé, Carlos Rodrigues‐Vaz, David Bruy, Cédric Mariac, Lars W. Chatrou, Junhao Chen, Le Min Choo, Léo‐Paul M.J. Dagallier, Roy H.J. Erkens, David M. Johnson, Charan Leeratiwong, Adriana Q. Lobão, Jenifer C. Lopes, Maria Fernanda Martínez‐Velarde, Jérôme Munzinger, Nancy A. Murray, Wei Ling Neo, Mijoro Rakotoarinivo, Andres E. Ortiz‐Rodriguez, Bonaventure Sonké, Daniel C. Thomas, Jan J. Wieringa, Thomas L.P. Couvreur (2024)
Complete genus‐level phylogenomics and new subtribal classification of the pantropical plant family Annonaceae. TAXON 73: 1341.

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Erik J. M. Koenen (2022)
On the taxonomic affinity of Albizia carbonaria Britton (Leguminosae, Caesalpinioideae-mimosoid clade). PhytoKeys 205: 363.

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Anne Bruneau, Luciano Paganucci de Queiroz, Jens J. Ringelberg, Leonardo M. Borges, Roseli Lopes da Costa Bortoluzzi, Gillian K. Brown, Domingos B. O. S. Cardoso, Ruth P. Clark, Adilva de Souza Conceição, Matheus Martins Teixeira Cota, Else Demeulenaere, Rodrigo Duno de Stefano, John E. Ebinger, Julia Ferm, Andrés Fonseca-Cortés, Edeline Gagnon, Rosaura Grether, Ethiéne Guerra, Elspeth Haston, Patrick S. Herendeen, Héctor M. Hernández, Helen C. F. Hopkins, Isau Huamantupa-Chuquimaco, Colin E. Hughes, Stefanie M. Ickert-Bond, João Iganci, Erik J. M. Koenen, Gwilym P. Lewis, Haroldo Cavalcante de Lima, Alexandre Gibau de Lima, Melissa Luckow, Brigitte Marazzi, Bruce R. Maslin, Matías Morales, Marli Pires Morim, Daniel J. Murphy, Shawn A. O’Donnell, Filipe Gomes Oliveira, Ana Carla da Silva Oliveira, Juliana Gastaldello Rando, Pétala Gomes Ribeiro, Carolina Lima Ribeiro, Felipe da Silva Santos, David S. Seigler, Guilherme Sousa da Silva, Marcelo F. Simon, Marcos Vinícius Batista Soares, Vanessa Terra (2024)
Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification. PhytoKeys 240: 1.

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Charlotte Hagelstam-Renshaw, Jens J. Ringelberg, Carole Sinou, Warren Cardinal-McTeague, Anne Bruneau (2024)
Biome evolution in subfamily Cercidoideae (Leguminosae): a tropical arborescent clade with a relictual depauperate temperate lineage. Brazilian Journal of Botany 48: .

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Jens J. Ringelberg, Erik J. M. Koenen, Benjamin Sauter, Anahita Aebli, Juliana G. Rando, João R. Iganci, Luciano P. de Queiroz, Daniel J. Murphy, Myriam Gaudeul, Anne Bruneau, Melissa Luckow, Gwilym P. Lewis, Joseph T. Miller, Marcelo F. Simon, Lucas S. B. Jordão, Matías Morales, C. Donovan Bailey, Madhugiri Nageswara-Rao, James A. Nicholls, Oriane Loiseau, R. Toby Pennington, Kyle G. Dexter, Niklaus E. Zimmermann, Colin E. Hughes (2023)
Precipitation is the main axis of tropical plant phylogenetic turnover across space and time. Science Advances 9: .

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Thainara Policarpo Mendes, Marcelo Fragomeni Simon, Marcos José da Silva (2024)
Molecular phylogeny supports a new circumscription of Mimosa subser. Polycephalae, a species-rich lineage centered in the Brazilian Cerrado. Brazilian Journal of Botany 48: .

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Matheus Martins Teixeira Cota, Juliana Gastaldello Rando, Domingos Cardoso, Adilva de Souza Conceição, Cristiane Snak, Luciano Paganucci de Queiroz (2025)
Circumscribing Chamaecrista section Baseophyllum (Caesalpinioideae, Leguminosae) based on molecular data and morphology. Botanical Journal of the Linnean Society : .

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Alexandre G. de Lima, Juliana de Paula-Souza, Jens J. Ringelberg, Marcelo F. Simon, Luciano P. de Queiroz, Leonardo M. Borges, Vidal de F. Mansano, Vinicius C. Souza, Viviane R. Scalon (2022)
New segregates from the Neotropical genus Stryphnodendron (Leguminosae, Caesalpinioideae, mimosoid clade). PhytoKeys 205: 203.

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José Martins Fernandes, Célia Regina Araújo Soares, Ana Kelly Koch, Temilze Gomes Duarte, Anderson Alex Sandro Domingos de Almeida (2025)
New records of the mimosoide clade (Caesalpinioideae, Leguminosae) for the state of Mato Grosso, Brazil. Rodriguésia 76: .

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Jong-Soo Park, Youngsung Kim, Iseon Kim, Ho-Rim Hwang, Changkyun Kim (2024)
Complete chloroplast genome of Albizia kalkora (Fabaceae) in Korea and its taxonomic position. Journal of Asia-Pacific Biodiversity 17: 235.

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Anderson Javier Alvarado-Reyes, Juliana Villela Paulino, Vanessa Terra, Vidal de Freitas Mansano (2024)
Floral ontogeny reveals potential synapomorphies for Senegalia sect. Monacanthea p.p. (Leguminosae). Journal of Plant Research 137: 907.

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Shawn A. O’Donnell, Jens J. Ringelberg, Gwilym P. Lewis (2022)
Re-circumscription of the mimosoid genus Entada including new combinations for all species of the phylogenetically nested Elephantorrhiza (Leguminosae, Caesalpinioideae, mimosoid clade). PhytoKeys 205: 99.

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Mats Thulin (2024)
Studies of Asian ‘Calliandra' lead to expansion ofSanjappa(Fabaceae‐Caesalpinioideae). Nordic Journal of Botany 2024: .

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Yue Zhao, Ya-Ping Chen, Jing-Chen Yuan, Alan J. Paton, Maxim S. Nuraliev, Fei Zhao, Bryan T. Drew, Yasaman Salmaki, Orzimat T. Turginov, Miao Sun, Alexander N. Sennikov, Xiang-Qin Yu, Bo Li, Chun-Lei Xiang (2023)
Museomics in Lamiaceae: Resolving the taxonomic mystery of Pseudomarrubium. Current Plant Biology 35-36: 100300.

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Tatiana Arias, Juan David Saldarriaga, Henry Arenas-Castro, Álvaro Idárraga-Piedrahita, Norberto López-Alvarez, Eduardo Tovar Luque, Germán Torres-Morales, Mailyn A. Gonzalez, Iván Darío Soto-Calderón (2024)
Reconstructing the Phylogeny of Calliandra sect. Androcallis (Fabaceae): Inclusion of Colombian Species, with a Focus on the Enigmatic Taxon Calliandra medellinensis. Systematic Botany 49: 364.

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Else Demeulenaere, Tom Schils, J. Gordon Burleigh, Jens J. Ringelberg, Erik J. M. Koenen, Stefanie M. Ickert-Bond (2022)
Phylogenomic assessment prompts recognition of the Serianthes clade and confirms the monophyly of Serianthes and its relationship with Falcataria and Wallaceodendron in the wider ingoid clade (Leguminosae, Caesalpinioideae). PhytoKeys 205: 335.

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Moabe Ferreira Fernandes, Gwilym P. Lewis, Mohammad Vatanparast, Flávia Fonseca Pezzini, Matilda J. M. Brown, Luciano P. de Queiroz, Domingos Cardoso, R. Toby Pennington (2024)
Knowledge gaps in legume diversity and distribution and prospects for future research. Brazilian Journal of Botany 48: .

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Vinicius Delgado da Rocha, Thaís Carolina da Silva Dal’Sasso, Christina Cleo Vinson Williams, Marcelo Fragomeni Simon, Marcelo Leandro Bueno, Luiz Orlando de Oliveira (2024)
From forest to savanna and back to forest: Evolutionary history of the genus Dimorphandra (Fabaceae). Journal of Plant Research 137: 377.

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Euan K. James (2022)
The seeds of nodulation. Journal of Plant Physiology 278: 153812.

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Marcos Vinicius Batista Soares, Erik Jozef Mathieu Koenen, João Ricardo Vieira Iganci, Marli Pires Morim (2022)
A new generic circumscription of Hydrochorea (Leguminosae, Caesalpinioideae, mimosoid clade) with an amphi-Atlantic distribution. PhytoKeys 205: 401.

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Daniel J. Murphy, Bruce Maslin (2023)
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Johannes J. Le Roux, María L. Castillo (2024)
The Ecology and Management of Invasive Prosopis Trees in Eastern Africa. : 31.

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