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1. New national and regional bryophyte records, 65

Author

L. T. Ellis, C. Ah-Peng, G. Aslan, V. A. Bakalin, A. Bergamini, D. A. Callaghan, P. Campisi, F. M. Raimondo, S. S. Choi, J. Csiky, É. Csikyné Radnai, B. Cykowska-Marzencka, I. V. Czernyadjeva, Yu M. Kalinina, O. M. Afonina, G. Domina, P. Drapela, V. E. Fedosov, E. Fuertes, R. Gabriel, M. Kubová, I. Soares Albergaria, G. Gospodinov, R. Natcheva, A. Graulich, T. Hedderson, E. Hernández-Rodríguez, V. Hugonnot, C. W. Hyun, M. Kırmacı, U. Çatak, S. Kubešová, J. Kučera, C. La Farge, J. Larraín, P. Martin, B. Mufeed, C. N. Manju, K. P. Rajesh, Cs. Németh, J. Nagy, N. Norhazrina, N. Syazwana, S. V. O’Leary, S. J. Park, A. P. Peña-Retes, A. Rimac, A. Alegro, V. Šegota, N. Koletić, N. Vuković, S. Rosadziński, J. A. Rosselló, M. S. Sabovljević, A. D. Sabovljević, A. Schäfer-Verwimp, C. Sérgio, A. V. Shkurko, D. Shyriaieva, V. M. Virchenko, M. Smoczyk, D. Spitale, P. Srivastava, I. Omar, A. K. Asthana, M. Staniaszek-Kik, A. Cienkowska, M.-M. Ștefănuţ, S. Ștefănuţ, G. Tamas, C.-C. Bîrsan, G.-R. Nicoară, M. C. Ion, T. Pócs, G. Kunev, E. I. Troeva, J. van Rooy, P. Wietrzyk-Pełka, M. H. Węgrzyn, G. J. Wolski, D. Bożyk, The Natural History Museum [London] (NHM), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Adnan Menderes Üniversitesi, Botanical Garden-Institute, Far-East Branch, Russian Academy of Sciences, Vladivostok, Russia, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Bryophyte Surveys Ltd, Università degli studi di Palermo - University of Palermo, National Institute of Environmental Research [South Korea] (NIER), University of Pecs, Lajos Nagy Grammar School of the Cistercian Order, Polish Academy of Sciences (PAN), Komarov Botanical Institute of Russian Academy of Science, Russian Academy of Sciences [Moscow] (RAS), Lomonosov Moscow State University (MSU), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), University of the Azores, Centre for Ecology, Evolution and Environmental Changes (cE3c) /Azorean Biodiversity Group and Universidade dos Açores - Faculdade de Ciências Agrárias e do Ambiente, Angra do Heroísmo, Açores, Bulgarian Academy of Sciences (BAS), Institute of Biodiversity and Ecosystem Research, University of Cape Town, Department of Biological Sciences, Bolus Herbarium, Université du Québec en Abitibi-Témiscamingue (UQAT), Incheon National University, Biyoloji Bolumu, Moravian Museum, University of South Bohemia, University of Alberta, Pontificia Universidad Católica de Valparaíso (PUCV), The Zamorin's Guruvayurappan College, Szent István University, Universiti Kebangsaan Malaysia, Jeonbuk National University, Univ Nacl Autonoma Mexico, University of Zagreb, Universitat de València (UV), University of Belgrade [Belgrade], Université de Belgrade, Botanical Garden, Centre for Ecology - Evolution and Environmental Changes (cE3c), Universidade de Lisboa (ULISBOA), Natl Acad Sci Ukraine, Museo delle Scienze, Lucknow University, Council of Scientific and Industrial Research [India] (CSIR), University of Lódź, University of Bucharest (UniBuc), Institute of Biology Bucharest of Romanian Academy, Université Eszterházy Károly/Eszterházy Károly Egyetem [Eger, Hungary] (UEK/EKE), Institute of Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences (SB RAS), South African National Biodiversity Institute, University of the Witwatersrand [Johannesburg] (WITS), School of Animal, Plant & Environmental Sciences, Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), The field work in the study was particulary supported by The Rufford Foundation (project ID 27637-1). The work of G. Gospodinov was supported by the Bulgarian Ministry of Education and Science under 249 the National Research Programme ‘Young scientists and postdoctoral students’ approved by 250 DCM no. 577/17.08.2018. Esther Fuertes and Juan Larraín thank Jörn Hentschel for confirming the identity of the Tierra del Fuego specimen of Frullania glomerata. E. Fuertes' research is funded by projects AECI, A-3818-2005, A-6307-2006 y A- 8930-2007 of the Science and Innovation Ministry of Spain. J. Larraín's research is funded by CONICYT postdoctoral grant 3160556. N. Norhazrina and N. Syazwana would like to thank Universiti Kebangsaan Malaysia for supporting this research project through Geran Universiti Penyelidikan (GUP-2018-016 and GGPM-2017-090), and thank L.T. Ellis (BM) for confirming the identity of their collection of Calymperes. The work of S. S. Choi, V. A. Bakalin and S. J. Park was supported by the grant ‘National ecosystem Survey’ from the National Institute of Ecology, while that of S. S. Choi, V. A. Bakalin and C. W. Hyun was supported by the grant ‘Biological Diversity Survey of the Flora of Korean Bryophyta (NIBR201902104)’ from the National Institute of Biological Resources of Ministry of Environment in Korea to C. W. Hyun. Laboratory work of S. S Choi was also supported by the grant ‘National ecosystem Survey’ from the National Institute of Ecology. The study by Yu. M. Kalinina and O. M. Afonina was funded by RFBR, project number 19-34-90033. The work of V. Fedosov was supported by RSF Grant 18-14-00121. T. A. Hedderson is grateful to the National Research Foundation of South Africa for their continued financial support, and to the Himalayan Wildlife Project for their logistical support in Pakistan. The contribution of E. Hernández-Rodríguez and A. P. Peña-Retes is part of the project ‘Effect of forest management on two contrasting groups: mosses and medium and large mammals, Sierra Norte, Oaxaca, Mexico’ supported by Consejo Nacional de Ciencia y Tecnología, Mexico (ID 595991) and The Sigma Xi Grant-in-Aid of Research (ID G201603152071095) through scholarships to E. Hernández-Rodríguez. The work of I. V. Czernyadjeva was supported by Russian Foundation for Basic Research (grants # 18-05-60093) and it was carried out within the framework of the institutional research project (no. АААА-А19-119020690077-4) of the Komarov Botanical Institute of the Russian Academy of Sciences. The work of G. Gospodinov and R. Natcheva was supported by The Bulgarian National Science Fund, project ‘Cryptic species in Bulgarian flora—molecular species delimitation in the Aneura pinguis complex’. Thanks are also due to the Department of Biotechnology, New Delhi for providing financial assistance. S. Ştefănuţ, G. Tamas, C.-C. Bîrsan, G.-R. Nicoară and M. C. Ion acknowledge the support by project no. RO1567-IBB03/2020 through Institute of Biology Bucharest of Romanian Academy. A. V. Shkurko was supported by governmental contract 118021490111-5 of Tsitsin Main Botanical Garden. The contribution by Beata Cykowska-Marzencka has been financially supported by the statutory fund of the W. Szafer Institute of Botany of the Polish Academy of Sciences. The field research in 2017 leading to her results has received funding from the European Union’s Horizon 2020 project INTERACT, under grant agreement No 730938. The laboratory analyses were financed by National Science Centre in Poland (research project No. 2017/27/N/ST10/00862). The work of Paulina Wietrzyk-Pełka was supported by Etiuda project of the National Science Centre in Poland (research project No. 2019/32/T/ST10/00182). M. Kırmacı, G. Aslan and U. Çatak give many thanks to Aydın Adnan Menderes University's scientific research project department (BAP) for supporting their research (FEF 18018) and to Dr Metin Armağan (Adnan Menderes University) for helping during their field trip., European Project: 262693,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,INTERACT(2011), Universiti Kebangsaan Malaysia (UKM), and Universidade de Lisboa = University of Lisbon (ULISBOA)

Subjects
Riccia rhenana, liverworts, bryophytes, Croatia, 0106 biological sciences, Pseudoamblystegium subtile (Hedw.), business.industry, [SDV]Life Sciences [q-bio], Aneura maxima, Bryophytes, Coal mining, Forestry, Plant Science, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Geography, Bryophyte, business, Azores, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 010606 plant biology & botany
Abstract

Pseudoamblystegium subtile (Hedw.) Vanderp. & Hedenäs. CONTRIBUTORS: R. Gabriel, M. Kubová, C. Sérgio and I. Soares Albergaria. PORTUGAL, AZORES: Terceira Island, Angra do Heroísmo, municipal garden ‘Jardim Duque da Terceira’, 38° 39′ 24.0′′N, 27°13′ 05.99′′W, 31 m a.s.l, on the base of a shrub, in acidic conditions, 7 April 2017, leg. Michaela Kubová s.n. (AZU). A new understanding of the pleurocarpous moss species Pseudoamblystegium subtile was proposed by Vanderpoorten and Hedenäs (2009). The new genus is separated from the other Amblystegiaceae primarily due to its phylogenetic consistency and is characterised by the possession of leaves with a very short nerve, and erect capsules (Vanderpoorten and Hedenäs 2009). (excerpt) info:eu-repo/semantics/publishedVersion

Published
2021

2. Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l

Author

Julian R. Starr, Isabel Larridon, Lisa Pokorny, William J. Baker, Izai A. B. Sabino Kikuchi, Étienne Léveillé-Bourret, Félix Forest, Ilias Semmouri, Niroshini Epitawalage, Alexandre R. Zuntini, Isabel Fairlie, Pedro Jiménez-Mejías, Grace E. Brewer, Muthama Muasya, University of Ottawa [Ottawa], Universidad Autonoma de Madrid (UAM), Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Royal Botanic Gardens, Kew, Institut de Recherches en Biologie Végétale [Montréal] (IRBV), Université de Montréal (UdeM), Universiteit Gent = Ghent University [Belgium] (UGENT), Faculty of Bioscience Engineering - Laboratory of Environmental Toxicology and Aquatic Ecology, University of Cape Town, Department of Biological Sciences, Bolus Herbarium, University of Sheffield [Sheffield], Universiteit Leiden [Leiden], Hortus Botanicus Leiden, Hortus botanicus Leiden, This study was supported by the National Science and Engineering Research Council (NSERC) of Canada Discovery Grant to JRS (RGPIN 2018‐04115), enabling a 6‐week research stay at the Royal Botanic Gardens, Kew, covering part of the laboratory work and sequencing costs. The remaining costs were covered by the Calleva Foundation and the Sackler Trust through the Plant and Fungal Trees of Life programme (https://www.kew.org/science/our‐science/projects/plant‐and‐fungal‐trees‐of‐life), and a grant to IL from the Royal Botanic Gardens, Kew to support monographic research using targeted sequencing., and UAM. Departamento de Biología

Subjects
0106 biological sciences, Paraphyly, Evolution, [SDV]Life Sciences [q-bio], Plant Science, Tribe (biology), 010603 evolutionary biology, 01 natural sciences, Monophyly, taxonomy, Behavior and Systematics, Genus, taxon limits, Schoenoplectus, Cyperaceae, targeted sequencing, Clade, Ecology, Evolution, Behavior and Systematics, biology, Ecology, Biology and Life Sciences, Angiosperms353, biology.organism_classification, Biología y Biomedicina / Biología, classification, Fuireneae, Evolutionary biology, Taxonomy (biology), 010606 plant biology & botany
Abstract

International audience; Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing to (i) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae, and Cypereae; (ii) define the limits of Fuireneae s.s., and (iii) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognize as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr. nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub-Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognized tribes and genera are provided.

Published
2021

3. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

Author

Azani, Nasim, Babineau, Marielle, Bailey, C. Donovan, Banks, Hannah, Barbosa, Ariane R., Pinto, Rafael Barbosa, Boatwright, James S., Borges, Leonardo M., Brown, Gillian K., Bruneau, Anne, Candido, Elisa, Cardoso, Domingos, Chung, Kuo-Fang, Clark, Ruth P., Conceicao, Adilva S., Crisp, Michael, Cubas, Paloma, Delgado-Salinas, Alfonso, Dexter, Kyle G., Doyle, Jeff J., Duminil, Jerome, Egan, Ashley N., La Estrella, Manuel, Falcao, Marcus J., Filatov, Dmitry A., Fortuna-Perez, Ana Paula, Fortunato, Renee H., Gagnon, Edeline, Gasson, Peter, Rando, Juliana Gastaldello, Goulart Azevedo Tozzi, Ana Maria, Gunn, Bee, Harris, David, Haston, Elspeth, Hawkins, Julie A., Herendeen, Patrick S., Hughes, Colin E., Iganci, Joao R. V., Javadi, Firouzeh, Kanu, Sheku Alfred, Kazempour-Osaloo, Shahrokh, Kite, Geoffrey C., Klitgaard, Bente B., Kochanovski, Fabio J., Koenen, Erik J. M., Kovar, Lynsey, Lavin, Matt, Le Roux, Marianne, Lewis, Gwilym P., Lima, Haroldo C., Lopez-Roberts, Maria Cristina, Mackinder, Barbara, Maia, Vitor Hugo, Malecot, Valery, Mansano, Vidal F., Marazzi, Brigitte, Mattapha, Sawai, Miller, Joseph T., Mitsuyuki, Chika, Moura, Tania, Murphy, Daniel J., Nageswara-Rao, Madhugiri, Nevado, Bruno, Neves, Danilo, Ojeda, Dario I., Pennington, R. Toby, Prado, Darirn E., Prenner, Gerhard, Queiroz, Luciano Paganucci, Ramos, Gustavo, Ranzato Filardi, Fabiana L., Ribeiro, Petala G., Rico-Arce, Maria Lourdes, Sanderson, Michael J., Santos-Silva, Juliana, Sao-Mateus, Wallace M. B., Silva, Marcos J. S., Simon, Marcelo F., Sinou, Carole, Snak, Cristiane, Souza, Elvia R., Sprent, Janet, Steele, Kelly P., Steier, Julia E., Steeves, Royce, Charles Stirton, Tagane, Shuichiro, Torke, Benjamin M., Toyama, Hironori, Cruz, Daiane Trabuco Da, Vatanparast, Mohammad, Wieringa, Jan J., Wink, Michael, Wojciechowski, Martin F., Yahara, Tetsukazu, Yi, Tingshuang, Zimmerman, Erin, Department of Plant Science, University of Oxford [Oxford], Institut de Recherche en Biologie Végétale, Université de Montréal (UdeM), Département de Sciences Biologiques, University of Montreal, Department of Biology, Northern Arizona University [Flagstaff], Royal Botanic Gardens, Kew, Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Departamento de Biologia Vegetal, Universidad de Barcelona, Department of Biodiversity and Conservation Biology, University of Western Cape, Departamento de Botânica, Universidade Federal da Bahia (UFBA), School of BioSciences, Australia and Queensland Herbarium, University of Melbourne, Instituto de Biologia, Universidade Federal de Pelotas = Federal University of Pelotas (UFPel), School of Forestry and Resource Conservation, National Taiwan University, Departamento de Educação, Campus VIII, Universidade do Estado da Bahia, Research School of Biology, Australian National University (ANU), Departamento de Biología Vegetal II, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Instituto de Biología – Botánica, Universidad Nacional Autónoma de México (UNAM), School of GeoSciences, University of Edinburgh, Plant Biology Department, Cornell University [New York], Service Évolution Biologique et Écologie, Université libre de Bruxelles (ULB), Department of Botany, Smithsonian Institution, National Museum of Natural History, Jardim Botânico do Rio de Janeiro, Instituto de Pesquisas, Department of Plant Sciences, University of California, Instituto de Recursos Biologicos, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Instituto Nacional de Tecnología Agropecuaria (INTA), University of Morón, Ciências Ambientais, Universidade Federal do Oeste da Bahia (UFOB), Royal Botanic Gardens, School of Biological Sciences [Reading], University of Reading (UOR), Chicago Botanic Garden, Department of Systematic and Evolutionary Botany, University of Vienna [Vienna], Institute of Decision Science for a Sustainable Society, Kyushu University, Department of Agriculture and Animal Health, University of South Africa (UNISA), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Department Plant Sciences and Plant Pathology [Bozeman], Montana State University (MSU), South African National Biodiversity Institute, Department of Botany and Plant Biotechnology (DBPB), Department of Botany and Plant Biotechnology-Universite of Johannesburg, Departamento de Biologia, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Museo Cantonale di Storia Naturale, Office of International Science and Engineering, National Science Foundation, Missouri Botanical Garden, Plant Sciences and Biodiversity, Royal Botanic Gardens Victoria, Instituto de Investigaciones en Ciencias Agrarias de Rosario [Zavalla] (IICAR), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Agrarias [Zavalla] (FCAGR), Universidad Nacional de Rosario [Santa Fe]-Universidad Nacional de Rosario [Santa Fe], Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Sistemática e Evolução, Universidade Federal do Rio Grande do Norte [Natal] (UFRN), Departamento de Botânica, Instituto de Ciências Biológicas, Federal University of Goiás (UFG), Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Department of Biological Sciences, Bolus Herbarium, University of Cape Town, Institute of Systematic Botany, New York Botanical Garden (NYBG), Naturalis Biodiversity Center, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Natural Sciences and Engineering Research Council of Canada, U.K. Natural Environment Research Council [NE/I028122/1], Swiss National Science Foundation [31003A_13552], Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES/Program POS CSF) [1951/13-0], Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Project Sisbiota) [563084/2010-3], Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Project Casadinho/Procad) [5525892011-0], Fundacao de Amparo a Pesquisa do Estado da Bahia (FAPESB PES) [0053/2011], Fundacao de Amparo a Pesquisa do Estado de Sao Paulo FAPESP, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico CNPq of Brazil, Smithsonian Institution, U.S. National Science Foundation [DEB-1352217], Environment Research and Technology Development Fund (S9) of the Ministry of the Environment of Japan, Arizona State University, Université de Montréal [Montréal], Royal Botanic Gardens Kew, Universidad Complutense de Madrid [Madrid] (UCM), Cornell University, Université Libre de Bruxelles [Bruxelles] (ULB), Universidade Federal do Oeste da Bahia, The Royal Veterinary and Agricultural University, Pontificia Universidade Católica do Rio de Janeiro, Missouri Botanical Garden (USA), Kunming Institute of Botany, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), and Naturalis Biodiversity Center [Leiden]

Subjects
plastid matK phylogeny, Caesalpinioideae, [SDV]Life Sciences [q-bio], Cercidoideae, mimosoid clade, Papilionoideae, Detarioideae, Duparquetioideae, Dialioideae
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 clade-based 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.

Published
2017

4. Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.

Author

Vuruputoor VS, Starovoitov A, Cai Y, Liu Y, Rahmatpour N, Hedderson TA, Wilding N, Wegrzyn JL, and Goffinet B

Subjects
Genomics methods, Molecular Sequence Annotation, Gene Transfer, Horizontal, Bryopsida genetics, Genome, Plant, Phylogeny
Abstract

The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Published
2024
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5. Tinnea gombea (Lamiaceae), a new species from the Sudanian savanna region, Nigeria based on integrative evidence.

Author

Zhigila DA, Aigbokhan EI, and Muasya AM

Subjects
Phylogeny, DNA, Plant, Nigeria, Grassland, Lamiaceae
Abstract

Tinnea gombea, endemic to the Sudan savanna grasslands in northern Nigeria, is described and illustrated. We used integrative evidence from morphological characters, ecology and molecular phylogenetic data. The new species is morphologically and ecologically similar to T. barteri and T. aethiopica, but can be readily delimited from these taxa by unique characters including a subshrub growth habit, leaves alternate to subopposite, blades lanceolate, apically acuminate, inflorescences raceme, bearing solitary flowers in upper leaf and bract axils, lilac to purplish dusky flowers and the inflated fruits dehiscent. The distribution and habitat of T. gombea are also distinctive, being restricted to the Sudan savanna, while the two most similar species are widespread in tropical Africa. Additionally, molecular phylogenetic assessments using nrITS and chloroplast trnL-F, matK and rbcL support the placement of T. gombea as a distinct species. Tinnea gombea is here assessed as Critically Endangered due to its small population size and restriction to a small area lacking conservation prioritization., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Zhigila et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Published
2023
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6. An integrative monograph of Carex section Schoenoxiphium (Cyperaceae).

Author

Luceño M, Villaverde T, Márquez-Corro JI, Sánchez-Villegas R, Maguilla E, Escudero M, Jiménez-Mejías P, Sánchez-Villegas M, Miguez M, Benítez-Benítez C, Muasya AM, and Martín-Bravo S

Abstract

Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described ( C. gordon-grayae ). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium . We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium , an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum ., Competing Interests: Marcial Escudero and Santiago Martín-Bravo are Academic Editors for PeerJ. The authors declare that they have no competing interests., (© 2021 Luceño et al.)

Published
2021
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7. Delimiting the genera of the Ficinia Clade (Cypereae, Cyperaceae) based on molecular phylogenetic data.

Author

Muasya AM and Larridon I

Abstract

Generic delimitations in the Ficinia Clade of tribe Cypereae are revisited. In particular, we aim to establish the placement of annual species currently included in Isolepis of which the phylogenetic position is uncertain. Phylogenetic inference is based on two nuclear markers (ETS, ITS) and five plastid markers (the genes matK , ndhF , rbcL and rps16 , the trnL intron and trnL-F spacer) data, analyzed using model based methods. Topologies based on nuclear and plastid data show incongruence at the backbone. Therefore, the results are presented separately. The monophyly of the smaller genera ( Afroscirpoides , Dracoscirpoides , Erioscirpus , Hellmuthia , Scirpoides ) is confirmed. However, Isolepis is paraphyletic as Ficinia is retrieved as one of its clades. Furthermore, Ficinia is paraphyletic if I. marginata and allies are excluded. We take a pragmatic approach based on the nuclear topology, driven by a desire to minimize taxonomic changes, to recircumscribe Ficinia to include the annual Isolepis species characterized by cartilaginous glumes and formally include all the Isolepis species inferred outside the core Isolepis clade. Consequently, the circumscription of Isolepis is narrowed to encompass only those species retrieved as part of the core Isolepis clade. Five new combinations are made ( Ficinia neocapensis, Ficinia hemiuncialis, Ficinia incomtula, Ficinia leucoloma, Ficinia minuta ). We present nomenclatural summary at genus level, identification keys and diagnostic features., Competing Interests: Isabel Larridon is an Academic Editor for PeerJ., (© 2021 Muasya and Larridon.)

Published
2021
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8. Revision of the Afro-Madagascan genus Costularia (Schoeneae, Cyperaceae): infrageneric relationships and species delimitation.

Author

Larridon I, Rabarivola L, Xanthos M, and Muasya AM

Abstract

A recent molecular phylogenetic study revealed four distinct evolutionary lineages in the genus Costularia s.l. (Schoeneae, Cyperaceae, Poales). Two lineages are part of the Oreobolus clade of tribe Schoeneae: the first being a much-reduced genus Costularia s.s. , and the second a lineage endemic to New Caledonia for which a new genus Chamaedendron was erected. The other two lineages were shown to be part of the Tricostularia clade of tribe Schoeneae. Based on morphological and molecular data, the genus Costularia is here redelimited to represent a monophyletic entity including 15 species, which is restricted in distribution to southeastern Africa (Malawi, Mozambique, South Africa, Swaziland, Zimbabwe), Madagascar, the Mascarenes (La Réunion, Mauritius), and the Seychelles (Mahé). Molecular phylogenetic data based on two nuclear markers (ETS, ITS) and a chloroplast marker ( trnL-F ) resolve the studied taxa as monophyletic where multiple accessions could be included (except for Costularia laxa and Costularia purpurea , which are now considered conspecific), and indicate that the genus dispersed once to Africa, twice to the Mascarenes, and once to the Seychelles. Two endemic species from Madagascar are here described and illustrated as new to science, as is one additional species endemic to La Réunion. Two taxa previously accepted as varieties of Costularia pantopoda are here recognised at species level ( Costularia baronii and Costularia robusta ). We provide a taxonomic revision including an identification key, species descriptions and illustrations, distribution maps and assessments of conservation status for all species., Competing Interests: The authors declare that they have no competing interests.

Published
2019
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9. Molecular phylogenetics of the genus Costularia (Schoeneae, Cyperaceae) reveals multiple distinct evolutionary lineages.

Author

Larridon I, Bauters K, Semmouri I, Viljoen JA, Prychid CJ, Muasya AM, Bruhl JJ, Wilson KL, Senterre B, and Goetghebeur P

Subjects
Africa, Bayes Theorem, Biodiversity, Cyperaceae anatomy & histology, Likelihood Functions, Madagascar, New Caledonia, Sequence Analysis, DNA, Seychelles, Time Factors, Cyperaceae classification, Cyperaceae genetics, Phylogeny
Abstract

We investigated the monophyly of Costularia (25 species), a genus of tribe Schoeneae (Cyperaceae) that illustrates a remarkable distribution pattern from southeastern Africa, over Madagascar, the Mascarenes and Seychelles, to Malesia and New Caledonia. A further species, Tetraria borneensis, has been suggested to belong to Costularia. Relationships and divergence times were inferred using an existing four marker phylogeny of Cyperaceae tribe Schoeneae expanded with newly generated sequence data mainly for Costularia s.l. species. Phylogenetic reconstruction was executed using Bayesian inference and maximum likelihood approaches. Divergence times were estimated using a relaxed molecular clock model, calibrated with fossil data. Based on our results, Tetraria borneensis is not related to the species of Costularia. Costularia s.l. is composed of four distinct evolutionary lineages. Two lineages, one including the type species, are part of the Oreobolus clade, i.e. a much reduced genus Costularia restricted to southeastern Africa, Madagascar, the Mascarenes and Seychelles, and a small endemic genus from New Caledonia for which a new genus Chamaedendron is erected based on Costularia subgenus Chamaedendron. The other two lineages are part of the Tricostularia clade, i.e. a separate single-species lineage from the Seychelles for which a new genus (Xyroschoenus) is described, and Costularia subgenus Lophoschoenus. For the latter, more research is needed to test whether they are congeneric with the species placed in the reticulate-sheathed Tetraria clade., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Published
2018
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