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1. Identifying and classifying banana cultivars

Author: Australia Fisheries, Steven B. Janssens, Belgium Botanic Garden Meise, and Jeff Daniells
Subjects: Horticulture, Cultivar
Published: 2020

2. Modelling the monthly abundance of Culicoides biting midges in nine European countries using Random Forests machine learning

Author: Ståle Sviland, Franz Josef Conraths, Magdalena Larska, Miguel Ángel Miranda Chueca, Alexander Mathis, Rene Bødker, Henrik Skovgård, Claire Garros, Thomas Balenghien, Renke Lühken, David Chavernac, Ignace Rakotoarivony, Delphine Delecolle, Bethsabée Scheid, Xavier Allene, Jan Chirico, Sonja Steinke, Petter Hopp, Marie-Laure Setier-Rio, Javier Lucientes, Ellen Kiel, Franz Rubel, Mats Gunnar Andersson, Bruno Mathieu, Anders Lindström, Anders Stockmarr, Anna Orłowska, Inger Sofie Hamnes, R. Estrada, Jörn Gethmann, Roger Venail, Wesley Tack, Katharina Brugger, Carlos Barceló, Ana Carolina Cuellar, Jonathan Lhoir, Søren Nielsen, Lene Jung Kjær, Andreas Baum, Marcin Smreczak, Jean-Claude Delécolle, Technical University of Denmark [Lyngby] (DTU), Aarhus University [Aarhus], Roskilde Universitet [Roskilde], National Veterinary Institute, University of Hamburg, Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), University of Oldenburg, Friedrich-Loeffler-Institut (FLI), National Veterinary Research Institute [Pulawy, Pologne] (NVRI), Norwegian Veterinary Institute [Oslo], University of Veterinary Medicine, Vienna, Austria, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University Hassan II [Casablanca], Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de Parasitologie et de Pathologie Tropicale (IPPTS), Université de Strasbourg (UNISTRA), Entente interdépartementale pour la démoustication du littoral méditerranéen [Montpellier] (EID Méditerranée), EID-Méditerranée, University of the Balearic Islands (UIB), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Universität Zürich [Zürich] = University of Zurich (UZH), Entente Interdépartementale pour la Démoustication du Littoral Méditerranéen, Avia-GIS [Zoersel], Botanic Garden Meise, and This study was funded by the EMIDA ERA-NET-supported project VICE (Vector-borne Infections: Risk-based and Cost-Effective Surveillance Systems). Culicoides data from Germany were partly collected within the German part of the VICE project funded by EMIDA ERA-NET through the Federal Office for Agriculture and Food (grant no. 314-06.01-2811ERA248).
Subjects: 0301 basic medicine, Culicoides imicola, Entomology, Climate, [SDV]Life Sciences [q-bio], Population Dynamics, Distribution (economics), Ceratopogonidae, computer.software_genre, L73 - Maladies des animaux, law.invention, Machine Learning, 0302 clinical medicine, Abundance (ecology), law, apprentissage machine, 2. Zero hunger, biology, U10 - Informatique, mathématiques et statistiques, Culicoides, Random Forest machine learning, technique de prévision, Europe, Infectious Diseases, Transmission (mechanics), African horse sickness, Seasons, système d'aide à la décision, Culicoides seasonality, L72 - Organismes nuisibles des animaux, Modèle mathématique, Farms, 030231 tropical medicine, Distribution des populations, Machine learning, Spatial predictions, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Virus bluetongue, Journal Article, Animals, Culicoides abundance, lcsh:RC109-216, Ecosystem, Transmission des maladies, business.industry, Research, Models, Theoretical, 15. Life on land, biology.organism_classification, Environmental variables, Insect Vectors, 030104 developmental biology, Virus peste équine africaine, Vector (epidemiology), Parasitology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Artificial intelligence, business, computer
Abstract: Background Culicoides biting midges transmit viruses resulting in disease in ruminants and equids such as bluetongue, Schmallenberg disease and African horse sickness. In the past decades, these diseases have led to important economic losses for farmers in Europe. Vector abundance is a key factor in determining the risk of vector-borne disease spread and it is, therefore, important to predict the abundance of Culicoides species involved in the transmission of these pathogens. The objectives of this study were to model and map the monthly abundances of Culicoides in Europe. Methods We obtained entomological data from 904 farms in nine European countries (Spain, France, Germany, Switzerland, Austria, Poland, Denmark, Sweden and Norway) from 2007 to 2013. Using environmental and climatic predictors from satellite imagery and the machine learning technique Random Forests, we predicted the monthly average abundance at a 1 km2 resolution. We used independent test sets for validation and to assess model performance. Results The predictive power of the resulting models varied according to month and the Culicoides species/ensembles predicted. Model performance was lower for winter months. Performance was higher for the Obsoletus ensemble, followed by the Pulicaris ensemble, while the model for Culicoides imicola showed a poor performance. Distribution and abundance patterns corresponded well with the known distributions in Europe. The Random Forests model approach was able to distinguish differences in abundance between countries but was not able to predict vector abundance at individual farm level. Conclusions The models and maps presented here represent an initial attempt to capture large scale geographical and temporal variations in Culicoides abundance. The models are a first step towards producing abundance inputs for R0 modelling of Culicoides-borne infections at a continental scale.
Published: 2020

3. Outline of Fungi and fungus-like taxa

Author: David L. Hawksworth, R. G. U. Jayalal, L. F. Zhang, G. A. da Silva, Samantha C. Karunarathna, Saowaluck Tibpromma, Kazuaki Tanaka, Saranyaphat Boonmee, I. V. Issi, Sajeewa S. N. Maharachchikumbura, Rajesh Jeewon, Oleg N. Shchepin, J. Ma, Fritz Oehl, P. B. Gannibal, Cristina Maria de Souza-Motta, Dhanushka N. Wanasinghe, Kunhiraman C. Rajeshkumar, A. A. Lateef, Ting-Chi Wen, L. K. T. Al-Ani, Kevin D. Hyde, Armin Mešić, Hans-Peter Grossart, Gabriela Heredia, Roshni Khare, Einar Timdal, Shubhi Avasthi, F. A. de Souza, Mounes Bakhshi, Richard A. Humber, Subhash Gaikwad, Dmitry V. Leontyev, Noha H. Youssef, Alexandre G. S. Silva-Filho, Sudhir Navathe, María Prieto, Marco Thines, Paul M. Kirk, Yuri Tokarev, Marc Stadler, P. O. Fiuza, André Aptroot, Damien Ertz, Monika C. Dayarathne, Julia Pawłowska, P. Liu, H. T. Lumbsch, Peter E. Mortimer, Elaine Malosso, Nalin N. Wijayawardene, Belle Damodara Shenoy, Huzefa A. Raja, Mikhail P. Zhurbenko, Somayeh Dolatabadi, Jos Houbraken, S. Mohammad, Zdenko Tkalčec, Andrei Tsurykau, Rampai Kodsueb, Mubashar Raza, Darbhe J. Bhat, Dsa Wijesundara, Jadson D. P. Bezerra, Javier Etayo, Walter P. Pfliegler, Leho Tedersoo, Jurga Motiejunaite, James D. Lawrey, Felipe Wartchow, Anusha H. Ekanayaka, Laura Selbmann, Sinang Hongsanan, Gothamie Weerakoon, Rafael F. Castañeda-Ruiz, Francis Q. Brearley, Enikő Horváth, R. L Zhao, B. O. Sharma, Y. Wang, Iván Sánchez-Castro, Martin Schnittler, Steven L. Stephenson, Y. Kang, Renate Radek, Eleni Gentekaki, Dagmar Triebel, F. R. Barbosa, Martina Réblová, Q. R. Li, Sayanh Somrithipol, Y. M. Li, D. K. A. Silva, L. Z. Tang, Hugo Madrid, Asha J. Dissanayake, Satinee Suetrong, Eric H. C. McKenzie, Mingkwan Doilom, E. S. Nassonova, J. C. Cavender, Neven Matočec, A. L. Firmino, R. K. Saxena, Olinto Liparini Pereira, J. Xu, V. Vázquez, M. Q. He, Xinlei Fan, Khadija Jobim, Martin Kukwa, Andrey Yurkov, R. F. Xu, K. Kolaríková, Lakmali S. Dissanayake, P. Alvarado, Rungtiwa Phookamsak, Dong-Qin Dai, Qing Tian, Ulrike Damm, D. W. Li, Pradeep K. Divakar, Jian-Kui Liu, Ajay Kumar Gautam, Viktor Papp, Peter M. Letcher, Pamela Rodriguez-Flakus, E. Kuhnert, F. Tian, I. Kusan, Makbule Erdoğdu, Alejandra Gabriela Becerra, B. T. Goto, Eric W.A. Boehm, K. Bensch, Sally C. Fryar, Yuri K. Novozhilov, Han Zhang, V. P. Hustad, André Luiz Cabral Monteiro de Azevedo Santiago, Danny Haelewaters, Gregorio Delgado, V. Dima, C. Y. Deng, Y. Z. Lu, Moslem Papizadeh, Ave Suija, Janusz Błaszkowski, Paul G. Mungai, Bryce Kendrick, Leonor Costa Maia, Gerhard Rambold, Adam Flakus, Alan J. L. Phillips, Josiane Santana Monteiro, Susumu Takamatsu, Ziraat Fakültesi, Makbule Erdoğdu / 0000-0001-8255-2041, Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Netherlands Institute for Neuroscience (NIN), Qujing Normal University, Abhilashi University, Jiwaji University, National Science and Technology Development Agency -NSTDA, University of Oslo, Universidade Federal da Paraíba, FRANCISCO ADRIANO DE SOUZA, CNPMS, Agroscope, Competence Div Plants & Plant Prod., Universidade Federal de Pernambuco, West Pomeranian University of Technology, Universidade Federal do Rio Grande do Norte, Universidade Federal de Mato Grosso, University of Ilorin, Kunming Institute of Botany, Mae Fah Luang University, ALVALAB, Shenzhen University, Hirosaki University, University of Electronic Science and Technology of China, Museu Paraense Emílio Goeldi, Leibnitz Institute of Freshwater Ecology and Inland Fisheries - IGB, University of Tartu, Helmholtz-Zentrum für Infektionsforschung GmbH, Institute of Microbiology Chinese Academy of Sciences, University of Mauritius, Russian Academy of Sciences, Universidad Rey Juan Carlos, University of Sri Lanka, K?r?ehir Ahi Evran University, Leibniz Institute, Ernst Moritz Arndt University Greifswald, Goethe University., USDA-ARS Emerging Pests and Pathogens Research, University of South Bohemia, National Fungal Culture Collection of India -NFCCI, State Key Laboratory of Mycology, Universidade Federal de Mato Grosso do Sul, Skovoroda Kharkiv National Pedagogical University, University Road, All-Russian Institute of Plant Protection, Universidade de Lisboa, University of Tuscia, University of Debrecen, Royal Botanic Gardens, Czech Academy of Sciences, University of North Carolina at Greensboro, Freie Universität Berlin, Szent István University, Eötvös Loránd University, Jiangxi Agricultural University, Flinders University, EMLab P&K Houston, Academy of Sciences, Chiang Mai University, Sabzevar University of New Technology, University of Warsaw, Pibulsongkram Rajabhat University, Universidad de Granada, Universidad Complutense de Madrid, CSIR-National Institute of Oceanography Regional Centre, Instituto de Investigaciones Fundamentales en AgriculturaTropical, BIOTEC, National Science and Technology Development Agency - NSTDA, Guizhou University, Valley Laboratory, Ru?er Boškovi? Institute, Pasteur Institute of Iran, Instituto de Ecolog? 'a A. C., Iranian Research Institute of Plant Protection, Oklahoma State University, Northwest Missouri State University, George Mason University, Universidade Federal de Uberlândia, The Natural History Museum, IES Zizur, Skorina Gomel State University, University of Málaga, Kenya Wildlife Service, Senckenberg Museum of Natural History Görlitz, Guizhou Medical University, Kunming University of Science and Technology, Universidad Nacional de Córdoba, Manchester Metropolitan University, Nature Research Centre, Agharkar Research Institute, National Institute of Fundamental Studies, Szafer Institute of Botany, Manaaki Whenua-Landcare Research, Jilin Agricultural University, Ohio University, Iranian Research Organization for Science and Technology -IROST, Guizhou Academy of Science, Universidade Federal de Viçosa, Beijing Forestry University, Leibniz University, Leibnitz Institute of Freshwater Ecology and Inland Fisheries -IGB, University of Baghdad, The University of Alabama, University of Arkansas, Botanic Garden Meise, The Field Museum, University of Gda?sk, Universidad Mayor, Mie University, Universität of Bayreuth, and Staatliche Naturwissenschaftliche Sammlungen Bayerns
Subjects: Plant Science, Blastocladiomycota, 030308 mycology & parasitology, purl.org/becyt/ford/1 [https], Glomeromycota, Genus, Neopereziida, Amblyosporida ord. nov, 0303 health sciences, Ascomycota, biology, ord. nov, Basal clades, Classification, FOUR NEW TAXA, GEN. NOV, CELLULAR SLIME-MOLDS, POLAR TUBE, SP.-NOV, Leotiomycetes, four new taxa, ascomycota, basal clades, basidiomycota, classification, emendation, microsporidia, Neopereziida ord. nov, Ovavesiculida ord. nov, Protosporangiaceae fam. nov, Redonographaceae stat nov, MOLECULAR PHYLOGENY, Four new taxa, BASAL CLADES, GENERIC NAMES, CLASSIFICATION, 03 medical and health sciences, Botany, MICROSPORIDIAN, NATURAL CLASSIFICATION, purl.org/becyt/ford/1.6 [https], Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Fungo, Entomophthoromycota, Phylum, Basidiomycota, Biology and Life Sciences, Emendation, 15. Life on land, biology.organism_classification, SUB-ANTARCTIC ISLANDS, Microsporidia, Polar tube, SP-NOV, Amblyosporidae, LEVEL PHYLOGENETIC CLASSIFICATION
Abstract: This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi., Nalin N. Wijayawardene thanks Mushroom Research Foundation and National Science Foundation of China (No. NSFC 31950410558) for financially supporting this project. Kevin D. Hyde acknowledges the Foreign Experts Bureau of Yunnan Province, Foreign Talents Program (2018; grant no. YNZ2018002), Thailand Research grants entitled Biodiversity, phylogeny and role of fungal endophytes on above parts of Rhizophora apiculata and Nypa fruticans (grant no: RSA5980068), the future of specialist fungi in a changing climate: baseline data for generalist and specialist fungi associated with ants, Rhododendron species and Dracaena species (grant no: DBG6080013), Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion (grant no: RDG6130001). H.T. Lumbsch thanks support by the Grainger Bioinformatics Center. E. Malosso is grateful to CAPES for financial support (grant no. 88881.062172/2014-01). B.T. Goto, G.A. Silva and K. Jobim, L.C. Maia acknowledges CNPq (Brazilian Scientific Council, grants no. 465.420/2014-1, 307.129/2015-2 and 408011/2016-5) and CAPES for support. The study was partially supported by the National Science Centre, Poland, under Grants No. 2015/17/D/NZ8/00778 and 2017/25/B/NZ8/00473 to Julia Pawłowska. The research of Martin Kukwa received support from the National Science Centre (NCN) in Poland (project no 2015/17/B/NZ8/02441). Alan J.L. Phillips acknowledges the support from UID/MULTI/04046/2019 Research Unit grant from FCT, Portugal to BioISI. H. Zhang is financially supported by the National Natural Science Foundation of China (Project ID: NSF 31500017). S. Boonmee would like to thank the Thailand Research Fund (Project No. TRG6180001). Dong-Qin Dai and Li-Zhou Tang would like to thank the National Natural Science Foundation of China (No. NSFC 31760013, NSFC 31260087, NSFC 31460561), the Scientific Research Foundation of Yunnan Provincial Department of Education (2017ZZX186) and the Thousand Talents Plan, Youth Project of Yunnan Provinces for support. R. Phookamsak, M. Doilom, D. N. Wanasinghe, S.C. Karunarathna and J.C. Xu express sincere appreciations to Key Research Program of Frontier Sciences of the Chinese Academy of Sciences (grant no. QYZDY-SSW-SMC014) for research financial support. R. Phookamsak thanks the Yunnan Provincial Department of Human Resources and Social Security (grant no. Y836181261), Chiang Mai University and National Science Foundation of China (NSFC) project code 31850410489 for research financial support. S.C. Kaunarathna thanks CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (No. 2018PC0006) and the National Science Foundation of China (NSFC) for funding this work under the project code 31851110759. S. Tibpromma would like to thank the International Postdoctoral Exchange Fellowship Program (number Y9180822S1), CAS President’s International Fellowship Initiative (PIFI) (number 2020PC0009), China Postdoctoral Science Foundation and the Yunnan Human Resources, and Social Security Department Foundation for funding her postdoctoral research. Yuri S. Tokarev, Elena S. Nassonova and Irma V. Issi are indebtful to Yuliya Y. Sokolova (Institute of Cytology RAS, St. Petersbug, Russia) and Anastasia V. Simakova (Tomsk State University, Tomsk, Russia) for kind permission of reproduction of electron microscopy images of Metchnikovella incurvata and Crepidulospora beklemishevi, respectively. Yuri S. Tokarev and Irma V. Issi thank Russian Foundation of Basic Research, grant number 17-04-00871 (taxonomy of Rozellomycota). Elena S. Nassonova thank Russian Foundation of Basic Research, grant number 18-04-01359 (early evolution of Microsporidia, phylogeny of Metchnikovellida). Adam Flakus and Pamela Rodriguez-Flakus are greatly indebted to all staff of the Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz and the SERNAP (http://sernap.gob.bo), for their generous cooperation providing permits, assistance and facilities support for scientific studies. The research of AF and PRF were financially supported by the National Science Centre (NCN) in Poland (DEC-2013/11/D/NZ8/03274). Adam Flakus and Pamela Rodriguez-Flakus received additional support under statutory funds from the W. Szafer Institute of Botany, Polish Academy of Sciences, Krakow, Poland. The authors would like to thank Yunnan Innovation Platform for Development and Utilization of Symbiotic Fungi Resources for finance support. Li-Fang Zhang would like to thank grant-in-aid from Science and Technology Department of Yunnan Province (2018FD080) for finance support. Chun-Ying Deng thanks the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (2019HJ2096001006). Yingqian Kang would like to thank Guizhou Scientific Plan Project [(2019) 2873]; Excellent Youth Talent Training Project of Guizhou Province [(2017) 5639]; Guiyang Science and Technology Project [(2017) No. 5-19]; Talent Base Project of Guizhou Province, China [FCJD2018-22]; Research Fund of Education Bureau of Guizhou Province, China [(2018) 481]. D. N. Wanasinghe would like to thank the CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (number 2019PC0008), the National Science Foundation of China and the Chinese Academy of Sciences for financial support under the following grants: 41761144055, 41771063 and Y4ZK111B01. Yuri K. Novozhilov and Oleg N. Shchepin acknowledge support from the Russian Foundation of Basic Research, project 18-04-01232 А. Ivana Kušan, Neven Matočec, Armin Mešić and Zdenko Tkalčec are grateful to Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). K. Tanaka would like to thank the Japan Society for the Promotion of Science (JSPS 19K06802)
Published: 2020

4. Outline of Fungi and fungus-like taxa – 2021

Author: Wijayawardene, NN, Hyde, KD, Dai, DQ, Sánchez-García, M, Goto, BT, Saxena, RK, Erdoğdu, M, Selçuk, F, Rajeshkumar, KC, Aptroot, A, Błaszkowski, J, Boonyuen, N, da Silva, GA, de Souza, FA, Dong, W, Ertz, D, Haelewaters, Danny, Jones, EBG, Karunarathna, SC, Kirk, PM, Kukwa, M, Kumla, J, Leontyev, DV, Lumbsch, HT, Maharachchikumbura, SSN, Marguno, F, Martínez-Rodríguez, P, Mešić, A, Monteiro, JS, Oehl, F, Pawłowska, J, Pem, D, Pfliegler, WP, Phillips, AJL, Pošta, A, He, MQ, Li, JX, Raza, M, Sruthi, OP, Suetrong, S, Suwannarach, N, Tedersoo, L, Thiyagaraja, V, Tibpromma, S, Tkalčec, Z, Tokarev, YS, Wanasinghe, DN, Wijesundara, DSA, Wimalaseana, SDMK, Madrid, H, Zhang, GQ, Gao, Y, Sánchez-Castro, I, Tang, LZ, Stadler, M, Yurkov, A, Thines, M, Qujing Normal University, University of Warsaw, Mae Fah Luang Universit, University of Debrecen, Universidade de Lisboa, Ruder Boskovic Institute, Institute of Microbiology, Chinese Academy of Sciences, National Fungal Culture Collection of India -NFCCI, National Science and Technology Development Agency -NSTDA, Chiang Mai University, University of Tartu, Mae Fah Luang University, Kunming Institute of Botany, All-Russian Institute of Plant Protection, National Institute of Fundamental Studies, University of Ruhuna, Estación Experimental del Zaidín, Jiangxi normal University, Technische Universitat Braunschweig, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Goethe University., Swedish University of Agricultural Sciences, Universidade Federal do Rio Grande do Norte, University Road, Kirsehir Ahi Evran University, Universidade Federal de Mato Grosso do Sul, West Pomeranian University of Technology, Universidade Federal de Pernambuco, FRANCISCO ADRIANO DE SOUZA, CNPMS, Zhongkai University of Agriculture and Engineering, Botanic Garden Meise, University of South Bohemia, King Saud University, Royal Botanic Gardens, University of Gdansk, Skovoroda Kharkiv National Pedagogical University, The Field Museum, University of Electronic Science and Technology of China, University of Silesia in Katowice, Universidad de Granada, Museu Paraense Emílio Goeldi, Agroscope, Plant Protection Products - Impact and Assessment, Team Applied Ecotoxicology, National Natural Science Foundation of China, Guizhou University, and Croatian Science Foundation
Subjects: Fossil fungi, Evolution, MOLECULAR PHYLOGENY, Plant Science, Behavior and Systematics, Ascomycota, Basal fungi, PHYLOGENETIC ANALYSIS, INCORPORATING ANAMORPHIC FUNGI, NATURAL CLASSIFICATION, Biology, Ecology, Evolution, Behavior and Systematics, Fungo, basal fungi, Ecology, LICHENIZED FUNGI, Basidiomycota, Classification, Rozellomycota, Biology and Life Sciences, Forestry, MULTIGENE PHYLOGENY, Interdisciplinary Natural Sciences, FRESH-WATER ASCOMYCETE, Microsporidia, GEN. NOV, Amblyosporidae, SP.-NOV, TAXONOMIC REVISION
Abstract: This paper provides an updated classification of the Kingdom Fungi (including fossil fungi) and fungus-like taxa. Five-hundred and twenty-three (535) notes are provided for newly introduced taxa and for changes that have been made since the previous outline. In the discussion, the latest taxonomic changes in Basidiomycota are provided and the classification of Mycosphaerellales are broadly discussed. Genera listed in Mycosphaerellaceae have been confirmed by DNA sequence analyses, while doubtful genera (DNA sequences being unavailable but traditionally accommodated in Mycosphaerellaceae) are listed in the discussion. Problematic genera in Glomeromycota are also discussed based on phylogenetic results., National Natural Science Foundation of China (NSFC) NSFC 31950410558 NSFC 31760013 32100011, Department of Science and Technology of Yunnan Province 2018FB050, State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University FAMP201906K, Science and Technology Department of Guizhou Province QKHRCPT[2017] 5101, High-Level Talent Recruitment Plan of Yunnan Province ("Young Talents" Program), Chiang Mai University, Croatian Science Foundation HRZZ-IP-2018-01-1736 HRZZ-2018-09-7081, LOEWE initiative of the government of Hessen, Distinguished Scientist Fellowship (DSFP), King Saud University, Kingdom of Saudi Arabia, CAS President's International Fellowship Initiative (PIFI) 2020PB0115 2020PC0009 2018PC0006, National Science Centre, Poland 2017/25/B/NZ8/00473, International Postdoctoral Exchange Fellowship Program Y9180822S1, China Postdoctoral Science Foundation, Yunnan Human Resources, and Social Security Department Foundation, National Natural Science Foundation of China (NSFC) 31750110478, China Postdoctoral Science Foundation 2021M693361, Portuguese Foundation for Science and Technology, European Commission UIDB/04046/2020 UIDP/04046/2020, High-Level Talent Recruitment Plan of Yunnan Province ("High-End Foreign Experts" Program)
Published: 2022

5. Taxonomic description and pollination ecology of Cyrtorchis okuensis (Orchidaceae, Angraecinae), a new species endemic to the Cameroon Volcanic Line

Author: Laura N. Azandi, Bonaventure Sonké, Murielle Simo-Droissart, Tania D'haijère, Vincent Droissart, Tariq Stévart, University of Yaoundé [Cameroun], Université libre de Bruxelles (ULB), Herbarium et Bibliothèque de Botanique africaine (BRLU), Meise Botanic Garden [Belgium] (Plantentuin), Missouri Botanical Garden, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Botanic Garden Meise
Subjects: Orchidaceae, geography, geography.geographical_feature_category, biology, Ecology, Hawkmoth, Cyrtorchis, Plant Science, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Volcano, Angraecinae, Systematics, IUCN Red List Categories and Criteria, Epiphyte, Line (text file), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Angraecoid orchids, Pollination, Pollination ecology
Abstract: Background and aims – A recent taxonomic and molecular study of the genus Cyrtorchis revealed three new species. Here, we describe one of these new species, endemic to the Cameroon Volcanic Line (CVL), and compare it to its closest relatives. Its conservation status is provided along with detailed information on its ecology and reproductive biology.Material and methods – A detailed examination of 21 herbarium specimens was performed using standard practices of herbarium taxonomy. The conservation status of the new species was assessed using the IUCN Red List Categories and Criteria. Furthermore, we investigated the reproductive biology of the new species in an easily accessible subpopulation in Cameroon and tested the hypothesis of hawkmoth pollination in the genus Cyrtorchis. Key results – The newly discovered species, here named C. okuensis, is restricted to the montane forest (1600 to 2500 m elevation) of the CVL and is currently assessed as Near Threatened (NT). Among angraecoid orchids in which hawkmoth pollination is recorded (~16 species), C. okuensis has the shortest nectar spur (19–40 mm). In situ observations revealed hawkmoths with short proboscis of the genus Hippotion (H. celerio, H. eson, and H. osiris) as the main pollinators. The rate of pollination and fruiting under natural conditions was low and among the 448 surveyed flowers only 38.8% (174/448 flowers) had their pollinia removed, 19% produced fruits (87/448 flowers), and 16% (70/448 flowers) set mature fruits. Conclusion – Cyrtorchis okuensis is clearly differentiated from C. submontana by its longer and wider floral bracts, longer anther caps, and wider triangular dorsal sepal.
Published: 2021

6. Congruent population genetic structures and divergence histories in anther-smut fungi and their host plants Silene italica and the S. nutans species complex

Author: Fabienne Van Rossum, Cécile Godé, Tatiana Giraud, Alodie Snirc, Fanny E. Hartmann, Stéphanie Le Prieur, Amandine Cornille, Jacqui A. Shykoff, Elisabeth Fournier, Pascal Touzet, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Botanic Garden Meise, Fédération Wallonie-Bruxelles, Partenaires INRAE, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Meise Botanic Garden [Belgium] (Plantentuin), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Ecologie Systématique et Evolution [ESE], Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], and Biologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
Subjects: 0106 biological sciences, Sympatry, cryptic speciation, Species complex, Population, host-pathogen interaction, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, approximate Bayesian computation, population genetic structure, education, 030304 developmental biology, genetic divergence, 0303 health sciences, education.field_of_study, biology, coevolution, Host (biology), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Silene nutans, food and beverages, 15. Life on land, biology.organism_classification, Evolutionary biology, Genetic structure, Microbotryum
Abstract: The study of population genetic structure congruence between hosts and pathogens gives important insights into their shared phylogeographic and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (Microbotryumgenus) and of their host plants, theSilene nutansspecies complex, and the morphologically and genetically closeS. italica,which can be found in sympatry. Phylogeographic population genetic structure related to persistence in separate glacial refugia has been recently revealed in theS. nutansplant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic SNPs. We found clear differentiation between fungal populations parasitizingS. nutansandS. italicaplants. The population genetic structure of fungal strains parasitizing theS. nutansplant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages onS. nutanswas congruent with the one previously inferred for the host plant and likely occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of host-pathogen individual pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies are still scarce.
Published: 2021

7. New insights into the diversity, taxonomy and history of the fern genus Trichomanes (Hymenophyllaceae, Polypodiidae), with a focus on Africa and the western Indian Ocean

Author: Vincent Droissart, Samuli Lehtonen, Alexandre Salino, Hanna Tuomisto, Timothée Le Péchon, Jean-Yves Dubuisson, Atsushi Ebihara, Sabine Hennequin, Germinal Rouhan, Vincent Deblauwe, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Botanic Garden Meise, Université libre de Bruxelles (ULB), International Institute of Tropical Agriculture (IITA-Cameroon), International Institute of Tropical Agriculture [Nigeria] (IITA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of California [Los Angeles] (UCLA), University of California, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and University of Turku
Subjects: 0106 biological sciences, 0303 health sciences, biology, Ecology, media_common.quotation_subject, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Plant Science, biology.organism_classification, Hymenophyllaceae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Indian ocean, Genus, Trichomanes, Taxonomy (biology), 14. Life underwater, Fern, Ecology, Evolution, Behavior and Systematics, Polypodiidae, 030304 developmental biology, Diversity (politics), media_common
Abstract: The filmy fern genus Trichomanes mainly comprises Neotropical species and a few taxa in Africa and the western Indian Ocean. The aim of this study is to infer the phylogenetic placement of all five Afro-Malagasy taxa in the genus and to investigate their history via an expanded and dated phylogenetic analysis including 39 species representing over half the diversity of the genus. The results support the monophyly of Trichomanes including all the sampled species attributed to the genus, but also suggest the inclusion of the species Abrodictyum cellulosum, revealing a morphological diversity of the genus greater than what was traditionally recognized, and highlighting the importance of the campanulate sorus as a generic diagnostic character. To accommodate those new phylogenetic results and morphological investigations, we describe a new subgenus Afrotrichomanes grouping the Afro-Malagasy taxa (except T. crenatum). The dated history of the genus among the trichomanoids suggests at least two origins for the Palaeotropical species. A recent Cainozoic colonization from the Neotropics towards Africa gave rise to the West African taxon T. crenatum, and a possible Mesozoic vicariance event gave rise to subgenus Afrotrichomanes. The low species diversity of the genus in the Afro-Malagasy region is discussed.
Published: 2021

8. An efficient method for defining plant species under High Conservation Value (HCV) criterion 1 based on the IUCN Red List criteria: A case study using species endemic to Gabon

Author: Gilles Dauby, Porter P. Lowry, Nicolas Texier, Tariq Stévart, Ehoarn Bidault, Davy U. Ikabanga, Université libre de Bruxelles (ULB), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Missouri Botanical Garden, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), and Botanic Garden Meise
Subjects: 0106 biological sciences, Ecology, Agroforestry, 010604 marine biology & hydrobiology, Sustainable forest management, Logging, Rare species, Endangered species, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Geography, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Habitat, Threatened species, IUCN Red List, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Endemism, Nature and Landscape Conservation
Abstract: International audience; The High Conservation Value (HCV) concept, developed by the Forest Stewardship Council to promote sustainable forest management, is widely employed for certification of forestry and agriculture concessions, and has been adopted by many logging and palm oil companies. HCV criterion 1, which deals with “endemic, and rare, threatened or endangered species”, is rarely used in certification, mainly because lists of these species are incomplete, especially for plants, and performing threat assessments is time-consuming. The IUCN Red List Categories are often suggested as a suitable basis to define threatened taxa for the application of HCV1, but this requires the rapid and efficient assessment of large numbers of species. Using the plants endemic to Gabon as a case study, we propose a rapid, two-step procedure to identify HCV1 species. First, based on 3,298 verified and geo-referenced herbarium records, we used GIS layers and an automated computational workflow in the R environment to identify potentially threatened species using an approach aligned with IUCN Red List criteria A, B, and D. Ninety percent of the automated assessments correctly indicated the risk of extinction; errors involved incorrect assessments of species whose habitat is in reality not threatened, or occurred during the calculation of the number of locations (sensu IUCN) when a single threat impacts large areas. In a second step designed to correct these issues and comply with the Red List guidelines, we performed species-by-species verification of the automated assessments, taking into account the ecology and habitat of each species and the nature of the threats it faces. Of the 389 endemic taxa analyzed, 86 % were identified as threatened (83 CR, 171 EN, and 80 VU); of these, only 35 % are recorded from at least one National Park, but most are found in logging/oil palm (72 %) or mining (55 %) concessions, underscoring the need to improve the application of the HCV concept. To strengthen the use of HVC subcriterion 1.2 (rare, threatened or endangered species), we propose an explicit method for identifying rare species based on a quantitative threshold of the Extent of Occurrence (20,000 km²), and we examine the concept of endemicity with respect to the application of HVC subcriterion 1.3 (endemic species). The proposed methodology addresses an urgent need to develop a national interpretation of the HCV concept in Gabon, adopted as a national standard for logging concessions, and offers an efficient, reliable approach for the application of HVC1 elsewhere in Central Africa.
Published: 2021

9. A near comprehensive phylogenetic framework gives new insights toward a natural classification of the African genus Cyrtorchis (Angraecinae, Orchidaceae)

Author: Tania D'haijère, Simon Verlynde, Esra Kaymak, Tariq Stévart, João N.M. Farminhão, Bonaventure Sonké, Murielle Simo-Droissart, Laura N. Azandi, Vincent Droissart, Université de Yaoundé I, Université libre de Bruxelles (ULB), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), New York Botanical Garden (NYBG), Missouri Botanical Garden, and Botanic Garden Meise
Subjects: 0106 biological sciences, integrative systematics, Cyrtorchis, Homocolleticon, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Natural (archaeology), Vandeae, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Genus, Angraecinae, molecular analyses, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Orchidaceae, biology, Phylogenetic tree, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, character-state evolution, Evolutionary biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, morphometry
Abstract: International audience; The genus Cyrtorchis is renowned for its conspicuous white, long-spurred flowers, but also for its challenging problems of species delimitation due to the great morphological resemblance of their flowers. Based on a preliminary visual inspection of 1752 specimens, 27 morphogroups were defined including 6 unpublished taxa. Then, we used a representative sampling of 171 dried and alcohol-preserved specimens representing 20 morphogroups to perform linear morphometrics through multivariate analyses on 43 morphological characters in order to confirm morphogroups delineation and identify their discriminant characters. Moreover, the monophyly of the two sections and of 21 morphological entities was tested through molecular analyses in order to produce a natural classification of the genus. DNA sequences from 69 Cyrtorchis specimens belonging to 15 published taxa (seven from C. sect. Homocolleticon, eight from C. sect. Cyrtorchis), six putative new Cyrtorchis taxa, as well as four taxa used as outgroups, were produced using one nuclear (nrITS-1) and five plastid regions (matK, rps16, trnC-petN intergenic spacer, trnL-trnF intergenic spacer, ycf1), and were analyzed using maximum likelihood and Bayesian approaches. We used this phylogenetic framework to infer the morphological character-state evolution of six floral traits and assess their taxonomic value. Morphological analysis revealed two groups corresponding to the published sections. However, while molecular results recovered the monophyly of C. sect. Cyrtorchis, C. sect. Homocolleticon appears paraphyletic. Of the 21 morphologically defined taxa that were included in the molecular analyses, eight, namely C. aschersonii, C. henriquesiana, C. monteiroae, C. praetermissa, C. ringens, and three new taxa were proven monophyletic. The delimitation of the 19 remaining morphologically identified taxa was assessed using morphological approach only. The ancestral state reconstruction provided new insights into character-state evolution in the genus by inferring the insertion point of the stipites at the rear third of the length of the viscidium as one of the main synapomorphic characters supporting the monophyly of the genus. Furthermore, viscidium structure, stipites shape, and the lateral lobes of the rostellum were found to be important to infer phylogenetic relationships within the genus.
Published: 2021

10. Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability

Author: Florent Martos, João N.M. Farminhão, Simon Verlynde, Esra Kaymak, Murielle Simo-Droissart, Vincent Droissart, Tariq Stévart, Géromine Collobert, Université libre de Bruxelles (ULB), New York Botanical Garden (NYBG), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Yaoundé [Cameroun], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Botanic Garden Meise, and Missouri Botanical Garden
Subjects: 0106 biological sciences, 0301 basic medicine, Asia, Genetic Speciation, Karyotype, Pantropical, Late Miocene, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, African rainforest, Phylogenetic nomenclature, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Angraecinae, Genetics, Madagascar, Epiphyte, Plastids, Clade, Orchidaceae, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, Likelihood Functions, Phylogenetic tree, biology, Pseudotriploid, Bayes Theorem, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Biological Evolution, Phylogeography, 030104 developmental biology, Cladogenesis, Evolutionary biology, Africa, Diversification analysis, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Angraecoid orchids present a remarkable diversity of chromosome numbers, which makes them a highly suitable system for exploring the impact of karyotypic changes on cladogenesis, diversification and morphological differentiation. We compiled an annotated cytotaxonomic checklist for 126 species of Angraecinae, which was utilised to reconstruct chromosomal evolution using a newly-produced, near-comprehensive phylogenetic tree that includes 245 angraecoid taxa. In tandem with this improved phylogenetic framework, using combined Bayesian, maximum likelihood and parsimony approaches on ITS-1 and five plastid markers, we propose a new cladistic nomenclature for the angraecoids, and we estimate a new timeframe for angraecoid radiation based on a secondary calibration, and calculate diversification rates using a Bayesian approach. Coincident divergence dates between clades with identical geographical distributions in the angraecoids and the pantropical orchid genus Bulbophyllum suggest that the same events may have intervened in the dispersal of these two epiphytic groups between Asia, continental Africa, Madagascar and the Neotropics. The major angraecoid lineages probably began to differentiate in the Middle Miocene, and most genera and species emerged respectively around the Late Miocene-Pliocene boundary and the Pleistocene. Ancestral state reconstruction using maximum likelihood estimation revealed an eventful karyotypic history dominated by descending dysploidy. Karyotypic shifts seem to have paralleled cladogenesis in continental tropical Africa, where approximately 90% of the species have descended from at least one inferred transition from n = 17–18 to n = 25 during the Middle Miocene Climatic Transition, followed by some clade-specific descending and ascending dysploidy from the Late Miocene to the Pleistocene. Conversely, detected polyploidy is restricted to a few species lineages mostly originating during the Pleistocene. No increases in net diversification could be related to chromosome number changes, and the apparent net diversification was found to be highest in Madagascar, where karyotypic stasis predominates. Finally, shifts in chromosome number appear to have paralleled the evolution of rostellum structure, leaflessness, and conspicuous changes in floral colour.
Published: 2021

11. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

Author: Tasnim Patel, Marc Kochzius, Ann Vanreusel, Henri Robert, Anton Van de Putte, Frederik Leliaert, Camille Moreau, Marie Verheye, Francesca Pasotti, Filip Volckaert, Isa Schön, Bruno Danis, Franz Maximilian Heindler, Henrik Christiansen, Quentin Jossart, Bart Hellemans, Biology, Ecology and Systematics, Laboratory of Biodiversity and Evolutionary Genomics, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Marine Biology Group, Vrije Universiteit Brussel [Bruxelles] (VUB), Marine Biology Research Group, Universiteit Gent = Ghent University [Belgium] (UGENT), Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences (RBINS), Laboratoire de Biologie Marine (LBM), Université libre de Bruxelles (ULB), Botanic Garden Meise, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), and Funded by the Belgian Science Policy Office (BELSPO, Contract no. BR/132/A1/vERSO) and contribution no. 8 of the RECTO project (BELSPO, Contract no. BR/154/A1/ RECTO), BELSPO, by the Scientific Research Network 'Eco-evolutionary dynamics in natural and anthropogenic communities' (grant W0.037.10 N), and the European Marine Biological Resource Center (EMBRC) Belgium, both funded by the Research Foundation – Flanders (FWO), by an individual grant from the former Flemish Agency for Innovation by Science and Technology, now managed through Flanders Innovation & Entrepreneurship (VLAIO, grant no. 141328).
Subjects: 0106 biological sciences, MESH: Sequence Analysis, DNA, ECOLOGICAL GENOMICS, Genome Scan, QH426-470, 01 natural sciences, Genome, Population genomics, MARKERS, MESH: Animals, SOUTHERN-OCEAN, biodiversity, Genetics & Heredity, 0303 health sciences, education.field_of_study, CLIMATE-CHANGE, MESH: Genomics, MESH: Research Design, In silico digestion, Biodiversity, Genomics, CAPTURE, Research Design, Genotyping by sequencing, MESH: Metagenomics, DNA microarray, Biologie, Life Sciences & Biomedicine, Biotechnology, CONSERVATION, Population, Biotechnologie, SNP, Locus (genetics), Computational biology, Biology, 010603 evolutionary biology, Molecular ecology, 03 medical and health sciences, Genetics, Animals, Humans, MESH: Genome, DNA CONTENT, Southern Ocean, education, Genome size, Selection (genetic algorithm), 030304 developmental biology, MESH: Humans, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Science & Technology, Research, RAD, Sequence Analysis, DNA, RADseq, Restriction enzyme, SIZE, Biotechnology & Applied Microbiology, Metagenomics, Genome scan, TP248.13-248.65
Abstract: Background: Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results: In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions: Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2021

12. Four new species of Agaricus subgenus Spissicaules from China

Author: Mao-Qiang He, Zhi-Lin Ling, Philippe Callac, Rui-Lin Zhao, Jun-Liang Zhou, André De Kesel, Bin Cao, Luis A. Parra, Chinese Academy of Sciences [Beijing] (CAS), Kunming University of Science and Technology (KMUST), Botanic Garden Meise, Unité de recherche Mycologie et Sécurité des Aliments (MycSA), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Paraphyly, Asia, Physiology, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, 030308 mycology & parasitology, 03 medical and health sciences, Agaricus, Genetics, Agaricaceae, Agaricales, China, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 4 new taxa, 0303 health sciences, biology, Phylogenetic tree, Cell Biology, General Medicine, multigene phylogeny, biology.organism_classification, Evolutionary biology, [SDE]Environmental Sciences, Subgenus
Abstract: International audience; Agaricus subgenus Spissicaules is widely distributed in the world. In this study, 114 specimens were included in multigene phylogenetic analyses that allowed a better circumscription of the four sections in A. subg. Spissicaules. Three new species from China, A. brunneovariabilis, A. beijingensis, and A. planiceps, are described and placed in different sections. The invalidly described A. catenariocystidiosus is validated here as an additional new species. Comparisons between the sequences of the three closely related species A. thiersii, A. parasubrutilescens, and A. linzhiensis support the distinction between these three species despite the paraphyly of A. linzhiensis, which results from its high intraspecific variability with numerous heteromorphisms.
Published: 2021

13. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Author: Couvreur, Thomas, Dauby, Gilles, Blach-Overgaard, Anne, Deblauwe, Vincent, Dessein, Steven, Droissart, Vincent, Hardy, Oliver, Harris, David, Janssens, Steven, Ley, Alexandra, Mackinder, Barbara, Sonké, Bonaventure, Sosef, Marc, Stévart, Tariq, Svenning, Jens-Christian, Wieringa, Jan, Faye, Adama, Missoup, Alain, Tolley, Krystal, Nicolas, Violaine, Ntie, Stéphan, Fluteau, Frédéric, Robin, Cécile, Guillocheau, Francois, Barboni, Doris, Sepulchre, Pierre, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aarhus University [Aarhus], University of California [Los Angeles] (UCLA), University of California (UC), Meise Botanic Garden [Belgium] (Plantentuin), Université libre de Bruxelles (ULB), Université de Yaoundé I, Missouri Botanical Garden, Royal Botanic Garden [Edinburgh], Martin-Luther-University Halle-Wittenberg, Naturalis Biodiversity Center [Leiden], LNRPV Laboratoire National de Recherches et de Productions Végétales, Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), LPF, University of Douala, South African National Biodiversity Institute, University of the Witwatersrand [Johannesburg] (WITS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université des Sciences et Techniques de Masuku (USTM), Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation du climat (CLIM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-15- CE02-0002-01, Agence Nationale de la Recherche, RAINBIO, Fondation pour la Recherche sur la Biodiversite, ANR-15-CE02-0002,AFRODYN,Forêts tropicales humides d'Afrique Centrale : dynamiques passées et résiliences futures(2015), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of California, Botanic Garden Meise, Royal Botanic Garden Edinburgh, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)
Subjects: [SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics, tropical Africa, Cenozoic, dated molecular phylogenies, palaeoclimate models, African geology, speciation models, Original Articles, Biodiversity, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Plants, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Animals, Original Article, fossils, Biologie, Ecosystem, Phylogeny, ComputingMilieux_MISCELLANEOUS
Abstract: Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2021

14. Filling the gaps in gene banks: Collecting, characterizing, and phenotyping wild banana relatives of Papua New Guinea

Author: Catherine Breton, Julie Sardos, Janet Paofa, Simon Kallow, Claude Welcker, Bart Panis, David Eyland, Steven Janssens, François Tardieu, Sebastien Carpentier, Rony Swennen, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Royal Botanic Gardens [Kew], Bioversity International [Belgique], International Institute of Tropical Agriculture (IITA-Tanzania), International Institute of Tropical Agriculture [Nigeria] (IITA), PNG National Agricultural Research Institute (NARI), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Meise Botanic Garden [Belgium] (Plantentuin), 'Adapting Agriculture to Climate Change: Collecting, Pro-tecting and Preparing Crop Wild Relatives,' which is supported by the Government of Norway., Global Crop Diversity Trust in part-nership with national and international gene banks and plant breeding institutes around the world (http://www.cwrdiversity.org/)., The Deutsche Gesellschaft für Interna-tionale Zusammenarbiet GIZ, scholarship funded by the Global TRUST foundation project 'Crop wild Relatives Evaluation of drought tolerance in wild bananas from Papua New Guinea', CGIAR Fund (https://www.cgiar.org/funders/), CGIAR Research Program Roots, Tubers and Bananas (RTB-CRP), Belgian Development Cooperation project ‘‘More fruit for food security: Developing climate-smart bananas for the African Great Lakes region.', European Project: 731013 ,EPPN2020(2017), Royal Botanic Gardens, Kew, Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Botanic Garden Meise
Subjects: 2. Zero hunger, 0106 biological sciences, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Vapour Pressure Deficit, business.industry, Drought tolerance, Plant genetics, 15. Life on land, Biology, biology.organism_classification, 01 natural sciences, Musa peekelii, Crop, 03 medical and health sciences, Horticulture, Gene bank, Agriculture, Shoot, business, Agronomy and Crop Science, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Since natural habitats are disappearing fast, there is an urgent need to collect, characterize, and phenotype banana (Musa spp.) crop wild relatives to identify unique genotypes with specific traits that fill the gaps in our gene banks. We report on a collection mission in Papua New Guinea carried out in 2019. Seed containing bunches were collected from Musa peekelii ssp. angustigemma (N.W.Simmonds) Argent (3), M. schizocarpa N. W. Simmonds (4), M. balbisiana Colla (3), M. acuminata ssp. banksii (F. Muell.) Simmonds (14), M. boman Argent (3), M. ingens Simmonds (2), M. maclayi ssp. maclayi F.Muell. ex Mikl.-Maclay (1), and M. lolodensis Cheesman (1). This material, together with the seeds collected during a previous mission in 2017, form the basis for the development of a wild banana seed bank. For characterization and phenotyping, we focused on the most ubiquitous indigenous species of Papua New Guinea: M. acuminata ssp. banksii, the ancestor of most edible bananas. We calculated that the median genomic dissimilarity of the M. acuminata ssp. banksii accessions was 4% and that they differed at least 5% from accessions present in the International Transit Centre, the world's largest banana gene bank. High-throughput phenotyping revealed drought avoidance strategies with significant differences in root/shoot ratio, soil water content sensitivity, and response towards vapor pressure deficit (VPD). We deliver a proof of principle that the wild diversity is not yet fully covered in the gene banks and that wild M. acuminata ssp. banksii populations contain individuals with unique traits, useful for drought tolerance breeding programs.
Published: 2021

15. Thelopsis challenges the generic circumscription in the Gyalectaceae and brings new insights to the taxonomy of Ramonia

Author: Neil Sanderson, Damien Ertz, Marc Lebouvier, Meise Botanic Garden [Belgium] (Plantentuin), Chercheur indépendant, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut Polaire Français Paul Emile Victor, IPEV, Botanic Garden Meise, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 0106 biological sciences, 0301 basic medicine, Ramonia, biology, Arthoniales, multispory, 030108 mycology & parasitology, biology.organism_classification, lichen, phylogeny, 010603 evolutionary biology, 01 natural sciences, Stictidaceae, 03 medical and health sciences, Monophyly, Evolutionary biology, Genus, Polyphyly, Gyalectales, Molecular phylogenetics, Taxonomy (biology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract: The genus Thelopsis was classified in the family Stictidaceae but its systematic position has never been investigated by molecular methods. In order to determine its family placement and to test its monophyly, fungal DNA of recent collections of Thelopsis specimens was sequenced. Phylogenetic analyses using nuLSU, RPB2 and mtSSU sequences reveal that members of Thelopsis form a monophyletic group within the genus Gyalecta as currently accepted. The placement of Thelopsis, including the generic type T. rubella, within the genus Gyalecta challenges the generic circumscription of this group because Thelopsis is well recognized by the combination of morphological characters: perithecioid ascomata, well-developed periphysoids, polysporous asci and small, few-septate ellipsoid-oblong ascospores. The sterile sorediate Opegrapha corticola is also placed in the Gyalectaceae as sister species to Thelopsis byssoidea + T. rubella. Ascomata of O. corticola are illustrated for the first time and support its placement in the genus Thelopsis. The hypothesis that O. corticola might represent the sorediate fertile morph of T. rubella is not confirmed because the species is phylogenetically and morphologically distinct. Thelopsis is recovered as polyphyletic, with T. melathelia being placed as sister species to Ramonia. The new combinations Thelopsis corticola (Coppins & P. James) Sanderson & Ertz comb. nov. and Ramonia melathelia (Nyl.) Ertz comb. nov. are introduced and a new species of Gyalecta, G. amsterdamensis Ertz, is described from Amsterdam and Saint-Paul Islands, characterized by a sterile thallus with discrete soralia. Petractis luetkemuelleri and P. nodispora are accommodated in the new genus Neopetractis, differing from the generic type (P. clausa) by having a different phylogenetic position and a different photobiont. Francisrosea bicolor Ertz & Sanderson gen. & sp. nov. is described for a sterile sorediate lichen somewhat similar to Opegrapha corticola but having an isolated phylogenetic position as sister to a clade including Gyalidea praetermissa and the genera Neopetractis and Ramonia. Gyalecta farlowii, G. nidarosiensis and G. carneola are placed in a molecular phylogeny for the first time. The taxonomic significance of morphological characters in Gyalectaceae is discussed.
Published: 2021

16. Moss-inhabiting diatom communities from Ile Amsterdam (TAAF, southern Indian Ocean)

Author: Marc Lebouvier, Bart Van de Vijver, Barbora Chattová, Vít Syrovátka, Masaryk University [Brno] (MUNI), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), University of Antwerp (UA), Meise Botanic Garden [Belgium] (Plantentuin), French Polar Institute [IPEV 136], ERASMUS scholarship, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Botanic Garden Meise
Subjects: 0106 biological sciences, biology, 010604 marine biology & hydrobiology, sub-Antarctic region, Plant Science, 15. Life on land, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Moss, diatoms, mosses, Indian ocean, Oceanography, Geography, Diatom, Ile Amsterdam, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bacillariophyta, ecology, southern Indian Ocean, Biology
Abstract: International audience; Background and aims - Despite the ongoing taxonomical revision of the entire (sub)-Antarctic diatom flora, our knowledge on the ecology and community associations of moss-inhabiting diatoms is still rather limited. In the present study, our research aim was to survey the diversity together with the environmental factors structuring the epiphytic moss diatom communities on Ile Amsterdam (TAAF), a small volcanic island in the southern Indian Ocean. Material and methods - A morphology-based dataset and (physico)chemical measurements were used for the ecological and biogeographical analysis of moss-inhabiting diatom flora from Ile Amsterdam. In total, 148 moss samples were examined using light microscopy. Key results - The analysis revealed the presence of 125 diatom taxa belonging to 38 genera. The uniqueness of the Ile Amsterdam diatom flora is mainly reflected by the species composition of the dominant genera Pinnularia, Nitzschia, Humidophila, and Luticola, with a large number of unknown and often new species. This highly specific diatom flora, together with differences in the habitats sampled and the isolated position of the island, resulted in very low similarity values between Ile Amsterdam and the other islands of the Southern Ocean. From a biogeographical point of view, 40% of the taxa have a typical cosmopolitan distribution, whereas 22% of all observed species can be considered endemic to Ile Amsterdam, with another 17% species showing a restricted sub-Antarctic distribution. The NMDS analysis, based on a cluster dendrogram, divides the samples into six main groups. For each group, indicator species were determined. Both environmental data and diatom distributions indicate that apart from elevation, specific conductance, pH, and moisture are the major factors determining the structure of moss-inhabiting diatom communities on Ile Amsterdam. Conclusion - The isolated geographic position and unique climatological and geological features of the island shaped the presence of a unique diatom flora, characterised by many endemic species. The results of the study are of prime importance for further (palaeo-)ecological and biogeographical research.
Published: 2021

17. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

Author: Magali Schweizer, Frederik Leliaert, Jan Pawlowski, Rodolphe Rougerie, Frédéric Rimet, Torbjørn Ekrem, Alexis Canino, Teofana Chonova, David G. Mann, Agnès Bouchez, Régis Lionel Vivien, Christian Chauvin, Chloé Goulon, Valentin Vasselon, Romain Gastineau, Rosa Trobajo, Christophe Laplace-Treyture, Jonas Zimmermann, Eva Aylagas, Wolf-Henning Kusber, Andrzej Witkowski, Vona Méléder, Frédéric Marchand, Sinziana F. Rivera, Maria Kahlert, Muriel Gugger, Filipe O. Costa, Maria Holzmann, Benoît J.D. Ferrari, Serena Rasconi, Alexander M. Weigand, Regine Jahn, Fedor Čiampor, Florian Leese, Ángel Borja, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdullah University of Science and Technology (KAUST), Basque Research and Technology Alliance (BRTA), King Abdulaziz University, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Slovak Academy of Science [Bratislava] (SAS), Universidade do Minho, Swiss Centre for Applied Ecotoxicology (Ecotox Center), Ecole Polytechnique Fédérale de Lausanne (EPFL), Technical university of Szczecin, Collection des Cyanobactéries, Institut Pasteur [Paris], University of Geneva [Switzerland], Freie Universität Berlin, Swedish University of Agricultural Sciences (SLU), Universitat Duisberg-Essen, Botanic Garden Meise, Institute of Agrifood Research and Technology [Sant Carles de la Ràpita] (IRTA), Institute of Agrifood Research and Technology (IRTA), Royal Botanic Garden Edinburgh, Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique - U3E (Rennes, France) (U3E ), Université de Nantes (UN), Polish Academy of Sciences (PAN), ID-Gene ecodiagnostics [Geneva], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire de Planétologie et Géodynamique [UMR 6112] (LPG), Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), SCIMABIO Interface SAS, Musée National d'Histoire Naturelle de Luxembourg (MNHN), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), This paper was written under COST Action DNAqua-Net. The European COST Action DNAqua-Net (CA 15219 collaborative network which gathers several hundreds of scientists and water managers, with the objective of developing new genetic tools for bioassessment and monitoring of aquatic ecosystems (Leese et al. 2016)., European Project, West Pomeranian University of Technology in Szczecin (ZUT), Universidade do Minho = University of Minho [Braga], Université de Genève = University of Geneva (UNIGE), Institut Pasteur [Paris] (IP), Meise Botanic Garden [Belgium] (Plantentuin), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Royal Botanic Garden [Edinburgh], Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Producció Animal, and Aigües Marines i Continentals
Subjects: 0106 biological sciences, 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Ciências Biológicas [Ciências Naturais], computer.software_genre, Barcode, 01 natural sciences, DNA barcoding, law.invention, law, QH540-549.5, aquatic organisms, media_common, Database, Ecology, Quality, Voucher, Identification (information), Aquatic organisms, quality, Biologie, Traceability, media_common.quotation_subject, reference library, Engenharia e Tecnologia::Engenharia do Ambiente, 010603 evolutionary biology, 03 medical and health sciences, Genetics (medical genetics to be 30107 and agricultural genetics to be 40402), Genetics, Quality (business), Relevance (information retrieval), 14. Life underwater, Molecular Biology, Nature and Landscape Conservation, Engenharia do Ambiente [Engenharia e Tecnologia], Metadata, Ciências Naturais::Ciências Biológicas, metadata, barcode, Reference library, DNA, 030104 developmental biology, traceability, Animal Science and Zoology, computer
Abstract: DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data, (undefined)
Published: 2021

18. Phylogenetic relationships amongst the African genera of subtribe Orchidinae s.l. (Orchidaceae; Orchideae): Implications for subtribal and generic delimitations

Author: Dirk U. Bellstedt, Thierry Pailler, Benny Bytebier, Florent Martos, Grace Ngugi, Timothée Le Péchon, University of KwaZulu-Natal (UKZN), National Museums of Kenya, Botanic Garden Meise, Fédération Wallonie-Bruxelles, Partenaires INRAE, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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), Stellenbosch University, The authors would like to thank Ezemvelo KwaZulu-Natal Wildlife Scientific Services and the Mpumalanga Tourism and Parks Agency (Wildlife Protection Services Division) for granting us permits (HO/4009/13, MPB 1252 and MPB 1252/2) to collect plant material within their parks, the South African National Research Foundation (KFD20100804000014875 Grant 74467), and Bibliotheque Du Vivant (France) and University of KwaZulu-Natal for their financial support. G. Ngugi was funded by the National Research Foundation, F. Martos and T. Le Pechon were funded by the Claude Leon Foundation as part of a postdoctoral fellowship.
Subjects: 0106 biological sciences, 0301 basic medicine, DNA, Plant, 010603 evolutionary biology, 01 natural sciences, Habenaria, 03 medical and health sciences, Sensu, Polyphyly, Habenariinae, Genetics, Plastids, Orchidaceae, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, Taxonomy, Phylogenetic tree, biology, Orchideae, Bayes Theorem, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Orchids, Holothrix, Orchidinae, 030104 developmental biology, Taxon, Evolutionary biology, Africa, Bartholininae, Cynorkis
Abstract: International audience; Phylogenetic relationships within the Orchideae sensu Pridgeon et al, remain one of the biggest unresolved issues in our understanding of the taxonomy of the orchids. Members of the Orchideae are numerous and widespread in Africa but remain poorly represented in phylogenetic research. In this study we included a broad sampling of African taxa for which we sequenced three plastid (rbcl, matK and trnL + trnL-F) and two nuclear regions (ITS and 18S). We used 368 sequences representing 278 species and 49 genera to infer relationships using the Bayesian Inference and Maximum Likelihood method. Our results show strong support for three clades, two of which almost entirely match the historical circumscription of Orchidinae and Habenariinae, and the third, Bartholininae, sister to the former two, includes the genera Holothrix and Bartholina. Stenoglottis should be assigned to Orchidinae and not to Habenariinae. Several genera such as Habenaria, Cynorkis and Benthamia are shown to be para- or polyphyletic: Bonatea, Centrostigma, Platycoryne and Roeperocharis are all embedded in Habenaria; Physoceras, Arnottia and part of Benthamia are embedded in Cynorkis. We propose a subdivision of Orchideae sensu lato into nine subtribes, but refrain from making generic re-arrangements until more extensive or more in-depth studies have been done.
Published: 2020

19. Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing

Author: Nathan Wales, Krista McGrath, Aurélien Carlier, Juan Viruel, Steven Janssens, Bram Danneels, Paul Wilkin, Universiteit Gent = Ghent University (UGENT), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), University of York [York, UK], Meise Botanic Garden [Belgium] (Plantentuin), Royal Botanic Gardens [Kew], Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Flemish Fonds Wetenschappelijk Onderzoekunder grant G017717N, ANR-19-TERC-0004,PHYLLOSYM,Recrutement des bactéries symbiotiques dans la phyllosphère: mécanismes de reconnaissance, fonctions et réaffectation de symbiotes foliaires héréditaires(2019), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Universiteit Gent = Ghent University [Belgium] (UGENT), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Botanic Garden Meise, and Royal Botanic Garden , Kew
Subjects: 0301 basic medicine, Genome evolution, bacterial genomics, Gene Transfer, Horizontal, Pseudogene, Population, plant-microbe interactions, Biology, phylogeography, Genome, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Dioscorea sansibarensis, evolution, yam, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, Symbiosis, Genome size, herbarium, Phylogeny, education.field_of_study, Phylogenetic tree, Dioscorea, fungi, food and beverages, 15. Life on land, biology.organism_classification, Plant Leaves, 030104 developmental biology, Evolutionary biology, Horizontal gene transfer, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery, Genome, Bacterial
Abstract: International audience; Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or “drip” tips filled with extracellular bacteria of the species Orrella dioscoreae.1 This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae.2,3 Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes).4, 5, 6 We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated.3
Published: 2020

20. Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee)

Author: Dominique Crouzillat, Jean-Jacques Rakotomalala, Coralie Fournier, Serigne Ndiawar Ly, Piet Stoffelen, Eva N. Raharimalala, Steven Janssens, Andrea Garavito, Christophe Guyeux, Romain Guyot, Patrick Descombes, Perla Hamon, Jean-Claude Charr, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad de Caldas [Manizales, Colombia], Nestle Centre R & D [Tours], Nestlé Centre R & D [Lausanne, Suisse], Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Botanic Garden Meise, Universidad Autónoma de Manizales (UAM), Meise Botanic Garden, Institut de Recherche pour le Developpement (IRD), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Meise Botanic Garden [Belgium] (Plantentuin)
Subjects: 0106 biological sciences, 0301 basic medicine, Canephora, Genome, Plastid, Coffea, Coffea canephora, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, Coalescent theory, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Evolution, Molecular, 03 medical and health sciences, Evolutionary history, Species Specificity, Genus, Genetics, Cluster Analysis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Clade, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, Cell Nucleus, Nuclear SNPs, Phylogenetic tree, biology, Coffee species - Coffea canephora, Full plastid genome sequencing, 15. Life on land, biology.organism_classification, 030104 developmental biology, Taxon, Evolutionary biology
Abstract: International audience; For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017-based on 28,800 nuclear SNPs-indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid fullgenome sequences highlighted an incongruous placement of Coffea canephora (Robusta coffee) between maternal and nuclear trees. In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed. In agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates Psilanthus from Coffea (with exception to C. rhamnifolia, closer to Psilanthus than to Coffea). In contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both Psilanthus and Coffea species, and two with either Psilanthus or Coffea species. Interestingly, Coffea and Psilanthus taxa sampled in West and Central Africa are members of the same group. Several mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for C. arabica) are involved in the evolutionary history of the coffee species. While sharing similar morphological characteristics, the genetic relationships within C. canephora have shown that some populations are well differentiated and genetically isolated. Given the position of its closely-related species, we may also consider C. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.
Published: 2020

21. Cradles and museums of generic plant diversity across tropical Africa

Author: Dagallier, Léo-Paul, Janssens, Steven, Dauby, Gilles, Blach-Overgaard, Anne, MacKinder, Barbara, Droissart, Vincent, Svenning, Jens-Christian, Sosef, Marc, Stévart, Tariq, Harris, David, Sonké, Bonaventure, Wieringa, Jan, Hardy, Olivier, Couvreur, Thomas, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Botanic Garden Meise, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aarhus University [Aarhus], Royal Botanic Garden Edinburgh, Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), ANR-15-CE02-0002,AFRODYN,Forêts tropicales humides d’Afrique Centrale : dynamiques passées et résiliences futures(2015), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université libre de Bruxelles (ULB), Missouri Botanical Garden, Université de Yaoundé I, ANR-15-CE02-0002,AFRODYN,Forêts tropicales humides d'Afrique Centrale : dynamiques passées et résiliences futures(2015), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Meise Botanic Garden [Belgium] (Plantentuin), and Royal Botanic Garden [Edinburgh]
Subjects: Full Paper, Research, Museums, Biodiversity, mountains, Full Papers, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, CANAPE, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, East Africa, humanities, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, endemism, Africa, phylogenetic diversity, protected areas, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, angiosperms, Biologie, Phylogeny
Abstract: International audience; Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioriti-zation. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth. Regions containing nonrandom concentrations of young (neo-) and old (paleo-) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time-calibrated mega-phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs). At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo-and paleo-endemism. By contrast, the Guineo-Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%). We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large-scale taxonomically verified distribution datasets and mega-phylogenies lead to an improved understanding of tropical plant biodiversity evolution.
Published: 2020

22. Congruent population genetic structures and divergence histories in anther

Author: Hartmann, Fanny E., Snirc, Alodie, Cornille, Amandine, Godé, Cécile, Touzet, Pascal, van Rossum, Fabienne, Fournier, Elisabeth, Le Prieur, Stéphanie, Shykoff, Jacqui, Giraud, Tatiana, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Botanic Garden Meise, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Union (EU) : PRESTIGE-2016-4-0013, European Fund for Regional Economic Development : Region Hauts-de-France, Ministere de l'Enseignement Superieur et de la Recherche, Louis D. Foundation, ANR-12-ADAP-0009,GANDALF,Génomique et adaptation des traits de vie des champignons impliqués dans les interactions plante-pathogène(2012), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Meise Botanic Garden [Belgium] (Plantentuin), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and 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)
Subjects: [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, food and beverages
Abstract: BGPI : Equipe 5 : Biologie Evolutive des Champignons Phytopathogènes (BECphy); International audience; Study of the congruence of population genetic structure between hosts and pathogens gives important insights into their shared phylogeographical and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (genus Microbotryum) and of their host plants, the Silene nutans species complex, and the morphologically and genetically closely related Silene italica, which can be found in sympatry. Phylogeographical population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic single nucleotide polymorphisms. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with that previously inferred for the host plant and probably occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of individual host-pathogen pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies remain scarce.
Published: 2020

23. A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses

Author: Olivier J. Hardy, Brecht Verstraete, Hans Beeckman, Maxime Réjou-Méchain, C.A.M. Marshall, Marc S.M. Sosef, Vincent Droissart, Vincent S. F. T. Merckx, Olivier Maurin, Steven B. Janssens, William D. Hawthorne, Fidèle Baya, Denis Beina, Michelle van der Bank, Thomas L. P. Couvreur, Gilles Dauby, Samuel Vanden Abeele, Arne Mertens, Maurizio Mascarello, Léo-Paul M.J. Dagallier, Filip Vandelook, Botanic Garden Meise, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Engineering and Science, Jacobs University [Bremen], Ministère Centrafricain des Eaux, Forêts, Chasses et Pêches (MEFCP), Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Evolution Biologique et Ecologie, Université de Bruxelles, Université libre de Bruxelles (ULB), HERBAXYLAREDD project (BR/143/A3/HERBAXYLAREDD), BELSPO research program AFRIFORD, Couvreur, Thomas LP [0000-0002-8509-6587], Mertens, Arne [0000-0003-3272-9464], Dagallier, Leo-Paul MJ [0000-0002-3270-1544], Vanden Abeele, Samuel [0000-0001-9100-3642], Mascarello, Maurizio [0000-0003-0325-2345], Droissart, Vincent [0000-0001-9798-5616], Marshall, Cicely [0000-0002-7397-6472], Apollo - University of Cambridge Repository, Evolutionary and Population Biology (IBED, FNWI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Libre de Bruxelles [Bruxelles] (ULB), Meise Botanic Garden [Belgium] (Plantentuin), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Couvreur, Thomas L P [0000-0002-8509-6587], and Dagallier, Leo-Paul M J [0000-0002-3270-1544]
Subjects: 0106 biological sciences, FOSSIL EVIDENCE, Angiosperms, Evolution, Biodiversity & Conservation, Biology, phylogeny, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, WESTERN INTERIOR, 03 medical and health sciences, GENUS, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Species level, Phylogenetics, evolution, R PACKAGE, lcsh:QH301-705.5, FRUITS, Phylogeny, 030304 developmental biology, NEW-JERSEY, 0303 health sciences, Science & Technology, Phylogenetic tree, Ecology, EARLY EOCENE, NORTH-AMERICA, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, lcsh:Biology (General), Large-scale dating analyses, FOS: Biological sciences, GenBank, large-scale dating analyse, large-scale dating analyses, Biodiversity Conservation, SP-NOV, Research questions, DIVERSIFICATION, ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Scale (map), angiosperms, Biologie, Life Sciences & Biomedicine, Research Article
Abstract: Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology., info:eu-repo/semantics/published
Published: 2020

24. Elemental distribution and chemical speciation of copper and cobalt in three metallophytes from the copper-cobalt belt in Northern Zambia

Author: A. D. Barnabas, François Malaisse, Peter D. Erskine, Jolanta Mesjasz-Przybyłowicz, Wojciech J. Przybyłowicz, Antony van der Ent, Royd Vinya, Hugh H. Harris, Laboratoire Sols et Environnement (LSE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The University of Queensland, University of Queensland [Brisbane], Copperbelt University, Botanic Garden Meise, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, AGH University of Science and Technology [Krakow, PL] (AGH UST), Stellenbosch University, iThemba LABS-National Research Foundation (NRF), PO Box 722, Somerset West 7129, South Africa, and University of Adelaide
Subjects: 0106 biological sciences, 0301 basic medicine, media_common.quotation_subject, Biophysics, chemistry.chemical_element, Zambia, Persicaria, Asteraceae, 01 natural sciences, Biochemistry, Polygonaceae, Biomaterials, 03 medical and health sciences, Metallophyte, Botany, Soil Pollutants, Life Science, Hyperaccumulator, media_common, biology, Chemistry, Metals and Alloys, Cobalt, 15. Life on land, biology.organism_classification, Persicaria capitata, Speciation, 030104 developmental biology, Chemistry (miscellaneous), Phloem, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Copper, 010606 plant biology & botany
Abstract: Three metallophyte species, Persicaria capitata, P. puncata (Polygonaceae), Conyza cordata (Asteraceae) from mineral wastes in the Zambian copper–cobalt belt were studied. This study focused on the elemental distribution in the roots, stems and leaves, using a range of techniques: micro-PIXE, SEM-EDS synchrotron XFM and XAS. The species differed in their responses to growing on Co–Cu-enriched soils: Persicaria puncata is a Co hyperaccumulator (up to 1060 μg g−1 in leaves), while Persicaria capitata and Conyza cordata are Co-excluders. All three species are Cu-accumulators. The highest concentrations of Cu–Co are in the epidermal cells, whereas in Persicaria puncata Co was also enriched in the phloem. The Co coordination chemistry shows that an aqueous Co(ii)–tartrate complex was the predominant component identified in all plants and tissues, along with a minor component of a Co(iii) compound with oxygen donor ligands. For Cu, there was considerable variation in the Cu speciation in the various tissues and across the three species. In contrast to hyperaccumulator plants, excluder and accumulator type plants have received far less attention. This study highlights the different biopathways of transition elements (Cu, Co) in hyper-tolerant plant species showing different responses to metalliferous environments.
Published: 2020

25. Euro+Med-Checklist Notulae, 11

Author: von Raab-Straube, Eckhard, Raus, Thomas, Bazos, Ioannis, Cornec, Jean-Pierre, De Bélair, Gérard, Dimitrakopoulos, Panayiotis G., El Mokni, Ridha, Fateryga, Alexander V., Fateryga, Valentina V., Fridlender, Alain, González, Jaime Gil, V. N., Grigorenko, Hand, Ralf, A., Kovalchuk, A., Mastrogianni, R., Otto, Rätzel, Stefan, Ristow, Michael, Salas-Pascual, Marcos, Strid, Arne, S.A., Svirin, Tsiripidis, Ioannis, Uhlich, Holger, Véla, Errol, Verloove, Filip, K., Vidakis, Yena, Andriy Vasylyovych, P.E., Yevseyenkov, Zeddam, A., Freie Universität Berlin, National and Kapodistrian University of Athens (NKUA), Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Badji Mokhtar - Annaba [Annaba] (UBMA), University of the Aegean, Aix Marseille Université (AMU), University of Potsdam, Universidad de las Palmas de Gran Canaria (ULPGC), Aristotle University of Thessaloniki, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Botanic Garden Meise, International Hellenic University, V.I. Vernadsky Crimean Federal University, Université Badji Mokhtar Annaba (UBMA), University of Potsdam = Universität Potsdam, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Meise Botanic Garden [Belgium] (Plantentuin)
Subjects: 0106 biological sciences, Drimia, Schinus, Erigeron, new combination, [SDV]Life Sciences [q-bio], Med-Checklist, Plant Science, Mediterranean, Euro plus Med PlantBase, 010603 evolutionary biology, 01 natural sciences, Staphyleaceae, taxonomy, Asparagaceae, Bidens, Botany, distribution, new record, vascular plants, Lithraea, Ecology, Evolution, Behavior and Systematics, biology, 15. Life on land, biology.organism_classification, Europe, Centaurea, 010606 plant biology & botany
Abstract: International audience; This is the eleventh of a series of miscellaneous contributions, by various authors, where hitherto unpublished data relevant to both the Med-Checklist and the Euro+Med (or Sisyphus) projects are presented. This instalment deals with the families Anacardiaceae, Asparagaceae (incl. Hyacinthaceae), Bignoniaceae, Cactaceae, Compositae, Cruciferae, Cyperaceae, Ericaceae, Gramineae, Labiatae, Leguminosae, Orobanchaceae, Polygonaceae, Rosaceae, Solanaceae and Staphyleaceae. It includes new country and area records and taxonomic and distributional considerations for taxa in Bidens, Campsis, Centaurea, Cyperus, Drymocallis, Engem, Hoffmannseggia, Hypopitys, Lavandula, Lithraea, Melilotus, Nicotiana, Olimarabidopsis, Opuntia, Orobanche, Phelipanche, Phragmites, Rumex, Salvia, Schinus, Staphylea, and a new combination in Drimia.
Published: 2019

26. Beyond trees: Biogeographical regionalization of tropical Africa

Author: Tariq Stévart, Anne Blach-Overgaard, Jens-Christian Svenning, Olivier J. Hardy, Thomas L. P. Couvreur, Steven Janssens, Bonaventure Sonké, Barbara A. Mackinder, Vincent Droissart, David Harris, Vincent Deblauwe, Gilles Dauby, Marc S.M. Sosef, Jan J. Wieringa, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Evolutionary Biology and Ecology, Department of Organism Biology, Université libre de Bruxelles (ULB), Department of Ecology and Evolutionary Biology, Center for Tropical Research, Institute of the Environment and Sustainability, University of California [Los Angeles] (UCLA), University of California-University of California, Royal Botanical Garden Edinburgh, Royal Botanical Garden, Botanic Garden Meise, Royal Botanic Garden Edinburgh, Aarhus University [Aarhus], University of Yaoundé [Cameroun], Herbarieum et Bibliothèque de Botanique africaine, Section for Ecoinformatics & Biodiversity, Department of Bioscience, Naturalis Biodiversity Center [Leiden], Fondation pour la Recherche sur la Biodiversite Fonds de la Recherche Scientifique - FNRS Villum Fonden 16549 French Foundation for Research on Biodiversity (FRB) Region Provence-Alpes-Cote d'Azur Belgian Fund for Scientific Research, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Libre de Bruxelles [Bruxelles] (ULB), Aarhus University, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, 0301 basic medicine, RAINBIO database, nestedness, CONSERVATION, African bioregions, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Phytogeography, 010603 evolutionary biology, 01 natural sciences, diversity, 03 medical and health sciences, network clustering, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, growth forms, SPECIES COMPOSITION, Growth form, SUB-SAHARAN AFRICA, Endemism, Ecology, Evolution, Behavior and Systematics, PLANT DIVERSITY, 2. Zero hunger, Diversity, FLORA, Ecology, phytogeography, Species diversity, RAIN-FOREST, ENDEMISM, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 15. Life on land, REGIONS, 030104 developmental biology, Geography, Liana, Network clustering, PATTERNS, Nestedness, BIODIVERSITY, Ordination, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Woody plant
Abstract: Aim: To delineate bioregions in tropical Africa and determine whether different plant growth forms (trees, terrestrial herbs, lianas and shrubs) display the same pattern of regionalization, diversity and endemism as the whole flora.Location: Tropical Africa (excl. Madagascar), from 20 degrees N to 25 degrees S.Taxon: Vascular plants.Methods: Analyses were based on occurrences of 24,719 vascular plant species distributed across tropical Africa extracted from the RAINBIO database. The majority of species (93%) were classified into four growth forms: terrestrial herbs, trees, shrubs and lianas. Biogeographical regions (bioregions) were delimited using a bipartite network clustering approach on the whole dataset and then separately for each growth form. Relationships among bioregions were investigated using non-metric multidimensional scaling ordination, flora nestedness and endemism patterns.Results: Analyses of the whole dataset identified 16 bioregions and 11 transition zones. These were congruent with most of the currently recognized phytogeographical classifications, and also highlighted previously under-recognized bioregions. Bioregion endemism rates were lower and species richness higher when compared to estimates from the White/Association pour l'Etude Taxonomique de la Flore d'Afrique Tropicale (AETFAT) classification. Analysed separately, plant growth forms showed contrasting geographical patterns. Bioregionalization was better resolved for closed forest types using trees and lianas and for open vegetation types using terrestrial herbs, while shrubs showed good discriminative power in all vegetation types.Main conclusions: We show that distribution patterns based on solely trees are not sufficient to define floristic bioregions in tropical Africa. Analyses of spatial patterns using different growth forms are complementary, likely reflecting different evolutionary processes and ecological relationships. The contribution of growth forms to delimit geographical floristic patterns across tropical Africa is of critical importance for land use planning and management, and for selecting priority conservation areas.
Published: 2018

27. Craterispermum capitatum and C. gabonicum (Rubiaceae): two new species from the Lower Guinean and Congolian Domains

Author: Hermann Taedoumg, Petra De Block, Bonaventure Sonké, Perla Hamon, University of Yaoundé [Cameroun], Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Botanic Garden Meise, and Meise Botanic Garden [Belgium] (Plantentuin)
Subjects: ORDO, 0106 biological sciences, Identification key, Rubiaceae, Plant Science, dimorphic inflorescences and flowers, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Craterispernum Capitaturn, lcsh:Botany, Cameroon, Plantae, C. capitatum, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, capitatum, Dimorphic influorescences and flowers, lcsh:QK1-989, Congo, Taxonomy (biology), heterostyly, Research Article, Dioecy, 010607 zoology, Zoology, Nigeria, Biology, 010603 evolutionary biology, Magnoliopsida, C, FAMILIA, Botany, Heterostyly, Gabon, Ecology, Evolution, Behavior and Systematics, Craterispernum Gabonicum, dimorphic, gabonicum, 15. Life on land, biology.organism_classification, Affinities, dioecy, Craterispermum, C. gabonicum, inflorescences and flowers, Tracheophyta, Plant morphology, Conservation status, DR Congo, Gentianales
Abstract: International audience; Craterispermum capitatum and C. gabonicum, two new species of Rubiaceae, are described from the Lower Guinea and Congolian Domains. Detailed descriptions and distribution maps are provided for each species, their conservation status is assessed and their taxonomic affinities are discussed. Craterispermum gabonicum is unique within the genus because of the strong dimorphism in brevistylous and longistylous flowers and inflorescences. We hypothesize that this species shows some form of dioecy. The distribution of C. capitatum shows a wide disjunction: the species is present in the Lower Guinean and Congolian Domains but absent from Gabon and South Cameroon. An identification key for the Craterispermum species present in the Lower Guinean and Congolian Domains is given.; Craterispermum capitatum et C. gabonicum, deux nouvelles espèces de la famille des Rubiaceae, des Domaines Bas Guinéen et Congolais sont décrites. Des descriptions détaillées et des cartes de distribution sont données pour chacune des espèces, leur statut de conservation est évalué et leurs affinités taxonomiques discutée. Craterispermum gabonicum est unique dans le genre en raison d’un dimorphisme avéré entre les fleurs, mais aussi les inflorescences brévistyles et longistyles. L’hypothèse de l’existence d’une tendance vers la dioécie chez cette espèce est émise. La distribution C. capitatum présente une importante disjonction: l’espèce est présente dans les Domaines Bas Guinéen et Congolais, mais absente au Gabon et au sud du Cameroun. Une clé d’identification pour les espèces de Craterispermum présentes dans les Domaines Bas Guinéen et Congolais est donnée.
Published: 2017

28. Historical biogeography of the highly diverse brown seaweed Lobophora (Dictyotales, Phaeophyceae)

Author: Zhongmin Sun, Frederik Leliaert, Christophe Vieira, Olivier De Clerck, Suzanne Fredericq, Claude Payri, Olga Camacho, Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Universiteit Gent = Ghent University (UGENT), Université Pierre et Marie Curie - Paris 6 (UPMC), University of Louisiana, CAS Institute of Oceanology (IOCAS), Chinese Academy of Sciences [Beijing] (CAS), Meise Botanic Garden [Belgium] (Plantentuin), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Universiteit Gent = Ghent University [Belgium] (UGENT), and Botanic Garden Meise
Subjects: Ancestral area reconstruction, 0106 biological sciences, Sympatry, Time Factors, Lobophora, Biogeography, Species distribution, Biodiversity, Phaeophyta, 010603 evolutionary biology, 01 natural sciences, Historical biogeography, Species Specificity, Genetics, Vicariance, Animals, 14. Life underwater, Molecular Biology, Phylogeny, Ecology, Evolution, Behavior and Systematics, biology, Ecology, 010604 marine biology & hydrobiology, Species diversity, 15. Life on land, Seaweed, biology.organism_classification, Phylogeography, Algorithmic species estimation, Biological dispersal, Molecular dating, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98–121 species. This diversity by far exceeds traditional diversity estimates based on morphological data. A multi-locus time-calibrated species phylogeny using a relaxed molecular clock, along with DNA-confirmed species distribution data was used to analyse ancestral area distributions, dispersal-vicariance-founder events, and temporal patterns of diversification under different biogeographical models. The origin of Lobophora was estimated in the Upper Cretaceous (−75 to −60 MY), followed by gradual diversification until present. While most speciation events were inferred within marine realms, founder events also played a non-negligible role in Lobophora diversification. The Central Indo-Pacific showed the highest species diversity as a result of higher speciation events in this region. Most Lobophora species have small ranges limited to marine realms. Lobophora probably originated in the Tethys Sea and dispersed repeatedly in the Atlantic (including the Gulf of Mexico) and Pacific Oceans. The formation of the major historical marine barriers (Terminal Tethyan event, Isthmus of Panama, Benguela upwelling) did not act as important vicariance events. Long-distance dispersal presumably represented an important mode of speciation over evolutionary time-scales. The limited geographical ranges of most Lobophora species, however, vouch for the rarity of such events.
Published: 2017

29. Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species

Author: Corrinne E. Grover, Dominique Crouzillat, Jean-Jacques Rakotomalala, Aaron P. Davis, Nathalie Raharimalala, Perla Hamon, Sharon E. Mitchell, Piet Stoffelen, Alexandre de Kochko, Emmanuel Couturon, Serge Hamon, Victor A. Albert, Hosahalli L. Sreenath, Michel Rigoreau, Sélastique Akaffou, Ucu Sumirat, Romain Guyot, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Iowa [Iowa City], Royal Botanic Gardens, Kew, Centre National de Recherche Appliquée au Développement Rural (FOFIFA), University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY), Botanic Garden Meise, Université Jean Lorougnon Guédé (UJloG ), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, 0301 basic medicine, Lineage (evolution), Biogeography, Molecular phylogenetics, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Phylogenetics, Convergent evolution, Genetics, Evolution of caffeine content, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Phylogenetic tree, biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Coffea, biology.organism_classification, Phylogeography, 030104 developmental biology, Evolutionary biology, Genotyping-by-Sequencing, Coffee Agroforests
Abstract: International audience; A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus(Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been lim-ited by low levels of sequence divergence, leading to insufficient topological resolution and statisticalsupport in phylogenetic trees, particularly for the major lineages and for the numerous species occurringin Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesisfor coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed,lab-based workflow to integrate short read next-generation sequencing for low numbers of additionalsamples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) asthe most likely ancestral locality for the origin of the coffee genus, with independent radiations acrossAfrica, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolutionof caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. Highand consistent caffeine content is found only in species from the equatorial, fully humid environmentsof West and Central Africa, possibly as an adaptive response to increased levels of pest predation.Moderate caffeine production, however, evolved at least one additional time recently (between 2 and4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already inplace during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subjectto convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate
Published: 2017

30. Congruent population genetic structures and divergence histories in anther-smut fungi and their host plants Silene italica and the Silene nutans species complex

Author: Stéphanie Le Prieur, Cécile Godé, Tatiana Giraud, Pascal Touzet, Alodie Snirc, Fabienne Van Rossum, Elisabeth Fournier, Amandine Cornille, Jacqui A. Shykoff, Fanny E. Hartmann, Ecologie Systématique et Evolution (ESE), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Botanic Garden Meise, Fédération Wallonie, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Union (EU) : PRESTIGE-2016-4-0013, European Fund for Regional Economic Development : Region Hauts-de-France, Ministere de l'Enseignement Superieur et de la Recherche, Louis D. Foundation, ANR-12-ADAP-0009,GANDALF,Génomique et adaptation des traits de vie des champignons impliqués dans les interactions plante-pathogène(2012), European Project: 309403,EC:FP7:ERC,ERC-2012-StG_20111109,GENOMEFUN(2013), Ecologie Systématique et Evolution [ESE], Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) [GQE-Le Moulon], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Meise Botanic Garden [Belgium] [Plantentuin], and Biologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
Subjects: 0106 biological sciences, 0301 basic medicine, cryptic speciation, [SDV]Life Sciences [q-bio], co-evolution, host-pathogen interaction, 01 natural sciences, Gene flow, Biological Coevolution, population genetic structure, Silene, education.field_of_study, biology, Silene nutans, DNA, Chloroplast, food and beverages, Europe, Phylogeography, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, approximate Bayesian computation, genetic divergence, Genetic structure, Genome, Fungal, Genome, Plant, Gene Flow, Genetic Markers, Species complex, Genotype, Population, Flowers, 010603 evolutionary biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetics, education, Ecology, Evolution, Behavior and Systematics, Plant Diseases, Cell Nucleus, Host (biology), Basidiomycota, fungi, 15. Life on land, biology.organism_classification, Genetic divergence, 030104 developmental biology, Genetics, Population, Evolutionary biology, Microbotryum, Microsatellite Repeats
Abstract: Study of the congruence of population genetic structure between hosts and pathogens gives important insights into their shared phylogeographical and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (genus Microbotryum) and of their host plants, the Silene nutans species complex, and the morphologically and genetically closely related Silene italica, which can be found in sympatry. Phylogeographical population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic single nucleotide polymorphisms. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with that previously inferred for the host plant and probably occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of individual host-pathogen pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies remain scarce.
Published: 2019

31. Molecular phylogeny and taxonomic synopsis of the angraecoid genus Ypsilopus (Orchidaceae, Vandeae)

Author: Gregory M. Plunkett, Murielle Simo-Droissart, Patrick Mardulyn, Tariq Stévart, Ling Dong, Vincent Droissart, Tania D'haijère, Université libre de Bruxelles (ULB), Herbarium et Bibliothèque de Botanique africaine (BRLU), University of Yaoundé [Cameroun], Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Botanic Garden Meise, and Missouri Botanical Garden
Subjects: Morphology, 0106 biological sciences, Ypsilopus, Epidendroideae, Morphology (biology), Molecular phylogeny, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Vandeae, Generic recombination, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, generic recombination, Genus, Botanique systématique, morphology, East africa, Orchidaceae, molecular phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, East Africa, Evolutionary biology, Molecular phylogenetics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Previous phylogenetic analyses focused on angraecoid orchids suggested that the genus Ypsilopus was paraphyletic and that some species of Tridactyle and Rangaeris belong to a clade that included Ypsilopus. These studies, based on three to four genes, sampled few taxa in each genus, and did not include the type of Rangaeris, nor did they take morphological variation into account. To delineate Ypsilopus more precisely, we reconstructed phylogenetic relationships of the genus and seven other closely related genera by analysing sequence variation at the nuclear ribosomal internal transcribed spacer (ITS‐1) and at five plastid markers (matK, rps16, trnC‐petN intergenic spacer, trnL‐trnF intergenic spacer, ycf1), from 42 specimens representing 36 taxa. Trees based on maximum likelihood and Bayesian inference confirm that two species of Tridactyle are nested with three Ypsilopus species, including the type of the latter, and two species of Rangaeris are grouped with this clade. Moreover, we examined morphological variation among all species belonging to these three genera, highlighting morphological features that characterize Ypsilopus, and we used these data to assign the two species of Tridactyle included in the molecular analyses, three other species of Tridactyle not included in the molecular analyses and two species of Rangaeris to Ypsilopus. New combinations for Tridactyle citrina, T. furcistipes, T. sarcodantha, T. tanneri, T. tricuspis, Rangaeris amaniensis and R. schliebenii in Ypsilopus are thus proposed, and one new section (i.e., Ypsilopus sect. Barombiella) is described. Keys to the species of Ypsilopus and closely related genera are provided, along with a table of characters that can be used to differentiate these species.
Published: 2019

32. Development and evaluation of a genome‐wide Coffee 8.5K SNP array and its application for high‐density genetic mapping and for investigating the origin of Coffea arabica L

Author: Christine Tranchant-Dubreuil, Patrick Descombes, Steven Janssens, C. Kiwuka, Pascal Musoli, Valérie Poncet, Piet Stoffelen, Sylviane Metairon, Clara Revel, Coralie Fournier, Alexandre de Kochko, Marie Pégard, Maud Lepelley, Hyacinthe Legnaté, Manon Coulée, Rémi Tournebize, Laurence Bellanger, Ucu Sumirat, João Ferreira da Costa Neto, Vimel Rattina, O. Darracq, Dominique Crouzillat, Jean Léon Kambale, Virginie Mérot-L’Anthoëne, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Nestlé Institute of Health Sciences SA [Lausanne, Switzerland], Botanic Garden Meise, Wageningen University and Research [Wageningen] (WUR), Centre National de la Recherche Agronomique - CNRA (IVORY COAST), Université de Kisangani, This project was partially supported by the Agropolis Foundationunder References ID 1002-009 and ID 1402-003 through the «Investissements d’avenir » program (Labex Agro:ANR-10-LABX0001-01), in the framework of I-SITE MUSE (ANR-16-IDEX-0006)., ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), ANR-16-IDEX-0006,MUSE,MUSE(2016), and Meise Botanic Garden [Belgium] (Plantentuin)
Subjects: 0106 biological sciences, 0301 basic medicine, Genetic Markers, C. eugenioides, Canephora, single‐nucleotide polymorphism, Single-nucleotide polymorphism, Coffea, Plant Science, Coffea canephora, 01 natural sciences, Polymorphism, Single Nucleotide, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Genetic map, Gene mapping, SNP, genetic map, Uganda, Genetic variability, Research Articles, C. canephora, 2. Zero hunger, Genetics, biology, Coffea arabica origin, Coffea arabica, Chromosome Mapping, single-nucleotide polymorphism, biology.organism_classification, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, Centre for Crop Systems Analysis, Crop and Weed Ecology, SNP array, Agronomy and Crop Science, Genome, Plant, 010606 plant biology & botany, Biotechnology, Research Article
Abstract: International audience; Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.
Published: 2019

33. The impact of chromosome number changes on the diversification of angraecoids in tropical Africa (Epidendroideae: Vandeae: Angraecinae)

Author: Farminhão, João N.M., Meerts, Pierre, Verlynde, Simon, Droissart, Vincent, SIMO-DROISSART, MURIELLE, Stévart, Tariq, Herbarium et Bibliothèque de Botanique africaine (BRLU), Université libre de Bruxelles (ULB), Laboratoire d'Ecologie Végétale et Biogéochimie, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Yaoundé [Cameroun], Herbarieum et Bibliothèque de Botanique africaine, Missouri Botanical Garden, Botanic Garden Meise, Herbarium et Bibliothèque de Botanique africaine, Université Libre de Bruxelles [Bruxelles] (ULB), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Missouri Botanical Garden (USA)
Subjects: Systematic, Phylogenetic, Vandeae, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Angraecinae, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Orchidaceae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The impact of the widespread occurrence of polyploidisation anddescending dysploidy on lineage diversification has never been explicitly tested, to our knowledge, in Orchidaceae. Angraecoids (Vandeae: Angraecinae) present a diverse rangeof chromosome numbers which makes them a good study system to understand karyotype evolution and its role in cladogenesis. Within Angraecinae, two major clades are recognised: one mostly confined to Madagascar, where only x= 19 is reported; and the Afroneotropical clade, which apparently presents a rare example of ascending dysploidy in the orchid family, with c. 90% of its species inferred to have x = 25. In this study, we aimed to trace the evolution of the chromosome number in the Afroneotropical cladeand to test, for the first time, the likely impact of chromosome changes on diversification in Orchidaceae. By using a near-comprehensive phylogenetic tree of angraecoids at the genus level, including 280 species, we mapped the chromosome counts of 116 species in 35 genera. Accordingly, we inferred the ancestral haploid number of most Afroneotropical angraecoid genera, starting from x = 19, and we identified a total of three first step ascending dysploid events in Conchograecum(x= 21), Dendrophylax(x = 22) and in the ‘Aerangidinae’ (x= 25); and a single first-step descending dysploidy occurrence in Calyptrochilum(x = 17). Within the Aerangidinae clade nine independent second step descending dysploid events were identified, which define new generic and suprageneric synapomorphies, namely in Ancistrorhynchusand Microcoelia(x= 24); and in the Cyrtorchis-Tridactyleclade (x= 23). Furthermore, two secondary and one tertiary dysploid events were identified in Aerangisand Summerhayesia, respectively. Finally, nine neopolyploid events were identified in eight genera. These findings have allowed us to test whether there was a significant contribution of chromosome number evolution to the radiation of angraecoids in tropical Africa
Published: 2019

34. Mine versus Wild : a plant conservation checklist of the rich Iron-Ore Ngovayang Massif Area (South Cameroon)

Author: Bonaventure Sonké, Olivier Lachenaud, Hermann Taedoumg, Tariq Stévart, Gyslène Kamdem, Murielle Simo-Droissart, Vincent Droissart, Steven Dessein, Gilles Dauby, K Charlemagne Nguembou, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Libre de Bruxelles [Bruxelles] (ULB), Botanic Garden Meise, University of Yaoundé [Cameroun], Missouri Botanical Garden (USA), Université libre de Bruxelles (ULB), Meise Botanic Garden [Belgium] (Plantentuin), Missouri Botanical Garden, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, IUCN protected area categories, Rare species, Biodiversity, Endangered species, Rubiaceae, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Iron and gold exploitation, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, orchids, Endemism, Submontane forest, iron and gold exploitation, 2. Zero hunger, New records, 010604 marine biology & hydrobiology, new records, Forestry, endangered species, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Ex situ conservation, Orchids, submontane forest, Geography, Herbarium, Important Plant Area, Threatened species, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Background and aims – The rapid expansion of human activities in South Cameroon, particularly mining in mountainous areas, threatens this region’s exceptional biodiversity. To comprehend the effects of land-use change on plant diversity and identify conservation priorities, we aim at providing a first comprehensive plant checklist of the Ngovayang Massif, focusing on the two richest plant families, Orchidaceae and Rubiaceae.Location – The Ngovayang Massif Area (NMA) is located in the South Region of Cameroon. It is covered by lowland and submontane rainforest (100 to 1110 m elevation).Methods – We compiled a dataset of 6116 georeferenced herbarium specimens, of which 2787 belong to Rubiaceae and Orchidaceae. We used rarefaction methods to explore sampling and diversity patterns, and investigated the altitudinal distribution of rare and/or threatened taxa.Key results – The NMA, which houses about 1500 vascular plant taxa, is the richest documented area for Rubiaceae in Atlantic Central Africa (ACA) and the fifth for Orchidaceae, with respectively 281 and 111 taxa. Among these taxa, 178 (45%) are endemic to ACA and 67 (17%) are considered globally threatened according to IUCN categories and criteria. We show that higher elevation areas (> 750 m), which are also the main areas targeted for mining, are the richest in endangered and/or rare species. Three new records for Cameroon are reported here.Conclusion – The NMA represents an Important Plant Area of Cameroon as confirmed by its exceptional plant diversity (> 20% of the total Flora of Cameroon), by the concentration of many threatened and/or restricted range species (10 taxa are strict endemics of the massif) as well as by the threat on rare habitats (i.e. the submontane vegetation above ~750 m elevation). A management plan involving in situ and ex situ conservation actions is urgently needed to reduce the potential threats of future mining activities.
Published: 2019

35. Does pollination syndrome reflect pollinator efficiency in Silene nutans?

Author: Emna Lahiani, Isabelle De Cauwer, Pascal Touzet, Mathilde Dufay, Maryse Vanderplanck, Fabienne Van Rossum, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Meise Botanic Garden [Belgium] (Plantentuin), Fédération Wallonie-Bruxelles, Partenaires INRAE, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Botanic Garden Meise, Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, education.field_of_study, Silene, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Reproductive success, Pollination, Ecology, fungi, Population, Silene nutans, food and beverages, 15. Life on land, biology.organism_classification, Pollination syndrome, 010603 evolutionary biology, 01 natural sciences, Open pollination, Pollinator, education, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 010606 plant biology & botany, Nature and Landscape Conservation
Abstract: Despite the specialization of floral traits towards particular floral visitors (pollination syndrome), insect-pollinated plants can display generalist rather than specialist interactions with their pollinators. This is the case of several Silene species that were viewed as nocturnally pollinated but are factually visited, and then potentially pollinated, by both nocturnal and diurnal insects. This opens the question of the consistency of pollination syndromes and the impact of different pollinator assemblages on plant reproductive success. In this work, we measured diurnal and nocturnal pollinators’ contributions to pollination success (fruit and seed production) and offspring quality (seed mass and germination rate) of hermaphrodite plants in an artificial population of Silene nutans, by experimentally restricting pollinator access and controlling for floral and resource traits. We found that fruit and seed production was higher for nocturnal pollination, and that only very few seeds were produced by diurnal visitors. In our experimental system, plants did not benefit from being open during daytime, as they showed no fruit or seed production advantage in the open pollination treatment compared to the nocturnal one. Seeds generated from diurnal pollination were heavier but did not germinate better, so that the plant fitness proxy remained higher for nocturnal pollination than diurnal one, without any obvious evidence of a pollination mixed strategy. These data are in accordance with the nocturnal pollination syndrome of S. nutans, contrasting with several other studies carried out on other Silene species.
Published: 2020

36. Historical Aerial Surveys Map Long-Term Changes of Forest Cover and Structure in the Central Congo Basin

Author: Sofie Meeus, Jan Van den Bulcke, Piet Stoffelen, Hans Beeckman, Leen Van Hirtum, Filip Vandelook, Lisa Wingate, Koen Hufkens, Michael Amara, Hans Verbeeck, Thalès de Haulleville, Elizabeth Kearsley, Kim Jacobsen, Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Royal Museum for Central Africa [Tervuren] (RMCA), Botanic Garden Meise, and National Archives of Belgium
Subjects: Agriculture and Food Sciences, 0106 biological sciences, Technology, aerial survey, 010504 meteorology & atmospheric sciences, Aerial survey, 01 natural sciences, Remote Sensing, TROPICAL DEFORESTATION, Geosciences, Multidisciplinary, PHOTOGRAPHS, Reforestation, Geology, Vegetation, Geography, SfM, Physical Sciences, CO2, Life Sciences & Biomedicine, CNN, data recovery, Science, CONSERVATION, Atmospheric carbon cycle, Environmental Sciences & Ecology, Context (language use), Land cover, ANTHROPOGENIC DISTURBANCE, 010603 evolutionary biology, Aerial photography, Deforestation, RATES, congo basin, Imaging Science & Photographic Technology, cnn, 0105 earth and related environmental sciences, deep learning, Congo Basin, CARBON EMISSIONS, Science & Technology, Forestry, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, LAND-COVER, sfm, 13. Climate action, Earth and Environmental Sciences, cavelab, General Earth and Planetary Sciences, VEGETATION, SELF-SIMILARITY, Environmental Sciences
Abstract: Given the impact of tropical forest disturbances on atmospheric carbon emissions, biodiversity, and ecosystem productivity, accurate long-term reporting of Land-Use and Land-Cover (LULC) change in the pre-satellite era (
Published: 2020

37. Metabolomics fingerprint of coffee species determined by untargeted-profiling study using LC-HRMS

Author: Pierre Van Antwerpen, Cédric Delporte, Florence Souard, Jean-Michel Kauffmann, Nausicaa Noret, Bastien Dauvergne, Etienne A. Thévenot, Caroline Stevigny, Piet Stoffelen, Université Grenoble Alpes - UFR Pharmacie (UGA UFRP), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Pharmacognosie, de Bromatologie et de Nutrition Humaine, Université libre de Bruxelles (ULB), Meise Botanic Garden [Belgium] (Plantentuin), Laboratoire d'analyse des données et d'intelligence des systèmes (LADIS), Département Métrologie Instrumentation & Information (DM2I), Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire d'Ecologie Végétale et Biogéochimie, Laboratoire de Chimie Analytique et Instrumentale et Bioélectrochimie, Belgian National Fund for Scientific Research (FRS, No 3.4553.08 and T.0136.13 PDR)Universite Libre de Bruxelles (FER-207), ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), Botanic Garden Meise, Laboratoire d'Intégration des Systèmes et des Technologies (LIST), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST)
Subjects: 0301 basic medicine, Multivariate statistics, Workflow4metabolomics, CAFFEINE, Plant metabolomics, Ent kaurane diterpenoid, CHROMATOGRAPHY, Coffea, ARABICA, Coffee, 01 natural sciences, Mass Spectrometry, Analytical Chemistry, 03 medical and health sciences, LC-(HR) MS, Metabolomics, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RUBIACEAE, LEAVES, BIOSYNTHESIS, Ent-kaurane diterpenoid, Coffee bean, Chromatography, High Pressure Liquid, Rubiaceae, biology, business.industry, 010401 analytical chemistry, Univariate, Discriminant Analysis, General Medicine, MASS-SPECTROMETRY, biology.organism_classification, ROBUSTA, 0104 chemical sciences, Biotechnology, Metabolomics data, 030104 developmental biology, DISCRIMINATION, Data Interpretation, Statistical, CAMEROON, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [PHYS.PHYS.PHYS-DATA-AN]Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an], Food Science
Abstract: International audience; Coffee bean extracts are consumed all over the world as beverage and there is a growing interest in coffee leaf extracts as food supplements. The wild diversity in Coffea (Rubiaceae) genus is large and could offer new opportunities and challenges. In the present work, a metabolomics approach was implemented to examine leaf chemical composition of 9 Coffea species grown in the same environmental conditions. Leaves were analyzed by LC-HRMS and a comprehensive statistical workflow was designed. It served for univariate hypothesis testing and multivariate modeling by PCA and partial PLS-DA on the Workflow4Metabolomics infrastructure. The first two axes of PCA and PLS-DA describes more than 40% of variances with good values of explained variances. This strategy permitted to investigate the metabolomics data and their relation with botanic and genetic informations. Finally, the identification of several key metabolites for the discrimination between species was further characterized.
Published: 2018

38. Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action

Author: Florian Altermatt, Lyubomir Penev, Vasco Elbrecht, Jonas Zimmermann, Sofia Alexandra Ferreira Duarte, Alexander M. Weigand, Fedor Čiampor, Emre Keskin, Patricia Mergen, Martyn Kelly, Bas van der Wal, Simon Vitecek, Kat Bruce, Igor Liska, Filipe O. Costa, Daniel Hering, Alain Franc, Matthias F. Geiger, Yorick Reyjol, Diego Fontaneto, Jan Pawlowski, Zuzana Ciamporova-Zatovicova, Florian Leese, Kessy Abarenkov, Dirk Steinke, Ana Rotter, Belma Kalamujić Stroil, Kristian Meissner, Maria Kahlert, Torbjørn Ekrem, Agnès Bouchez, Ángel Borja, Universität Duisburg-Essen [Essen], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), University of Tartu, Department of Aquatic Ecology - (Dübendorf, Suisse), Swiss Federal Institute for Environmental Science and Technology [Dübendorf] (EAWAG), AZTI - Tecnalia, NatureMetrics, Norwegian University of Science and Technology [Trondheim] (NTNU), Slovak Academy of Sciences (SAS), University of Minho [Braga], Centre of Molecular and Environmental Biology - CBMA (Braga, Portugal), Universidade do Minho, Ruhr-Universität Bochum [Bochum], Swedish Museum of Natural History (NRM), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Botanic Garden Meise, Swedish University of Agricultural Sciences (SLU), University of Sarajevo, UNIVERZITET U SARAJEVU, Bowburn Consultancy, Ankara Üniversitesi, International Commission for the Protection of the Danube River [Vienna] (ICPDR), University of Guelph, University of Vienna [Vienna], Forschungsinstitut Senckenberg (SGN), Pensoft Publisher [Sofia], Agence Française pour la Biodiversité (AFB), National Institute of Biology [Ljubljana], Stichting Toegepast Onderzoek Waterbeheer [Amsterdam] (STOWA), Freie Universität Berlin, Musée National d'Histoire Naturelle de Luxembourg (MNHN), Universität Duisburg-Essen = University of Duisburg-Essen [Essen], Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Norwegian University of Science and Technology (NTNU), Universidade do Minho = University of Minho [Braga], Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Meise Botanic Garden [Belgium] (Plantentuin), UNIVERSITY OF SARAJEVO - UNIVERZITET U SARAJEVU, National Institute of Biology [Ljubljana] (NIB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, University of Duisburg-Essen, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), University of Zürich [Zürich] (UZH), Centre of Molecular and Environmental Biology (CBMA), University of Minho, Consiglio Nazionale delle Ricerche (CNR), Leibniz Institute for Animal Biodiversity, Partenaires INRAE, University of Sarajevo (UNSA), Ankara University, Vienna International Centre, International Atomic Energy Agency [Vienna] (IAEA), Meise Botanic Garden, Royal Museum of Central Africa, Finnish Environment Institute (SYKE), Université de Genève (UNIGE), The French Agency for Biodiversity, Stichting Toegepast Onderzoek Waterbeheer, Amersfoort, Senckenberg Research Institute and Natural History Museum, and Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, Directive, [SDV]Life Sciences [q-bio], ta1172, Framework, Legislation, Aquatic biomonitoring, Marine Strategy, 010603 evolutionary biology, 01 natural sciences, Freshwater ecosystem, Environmental legislation, 03 medical and health sciences, Marine Strategy Framework Directive, Water Framework Directive, Freshwater, 14. Life underwater, Bioassessment Biotic index Environmental legislation Freshwater Marine Marine Strategy Framework Directive Water quality Water Framework Directive, Environmental planning, Environmental quality, Bioassessment, Biotic index, Science & Technology, Marine, Ecology, Monitoring program, Engenharia e Tecnologia::Biotecnologia Ambiental, 030104 developmental biology, Geography, Water quality, Bioassessment Biotic index Environmental legislation, 13. Climate action, Identification (biology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biologie
Abstract: Aquatic biomonitoring has become an essential task in Europe and many other regions as a consequence of strong anthropogenic pressures affecting the health of lakes, rivers, oceans and groundwater. A typical assessment of the environmental quality status, such as it is required by European but also North American and other legislation, relies on matching the composition of assemblages of organisms identified using morphological criteria present in aquatic ecosystems to those expected in the absence of anthropogenic pressures. Through decade-long and difficult intercalibration exercises among networks of regulators and scientists in European countries, a pragmatic biomonitoring approach was developed and adopted, which now produces invaluable information. Nonetheless, this approach is based on several hundred different protocols, making it susceptible to issues with comparability, scale and resolution. Furthermore, data acquisition is often slow due to a lack of taxonomic experts for many taxa and regions and time-consuming morphological identification of organisms. High-throughput genetic screening methods such as (e)DNA metabarcoding have been proposed as a possible solution to these shortcomings. Such "next-generation biomonitoring", also termed "biomonitoring 2.0", has many advantages over the traditional approach in terms of speed, comparability and costs. It also creates the potential to include new bioindicators and thereby further improves the assessment of aquatic ecosystem health. However, several major conceptual and technological challenges still hinder its implementation into legal and regulatory frameworks. Academic scientists sometimes tend to overlook legal or socioeconomic constraints, which regulators have to consider on a regular basis. Moreover, quantification of species abundance or biomass remains a significant bottleneck to releasing the full potential of these approaches. Here, we highlight the main challenges for next-generation aquatic biomonitoring and outline principles and good practic, COST - European Cooperation in Science and Technology(CA15219). COST Action DNAqua-Net (CA15219), supported by the COST (European Cooperation in Science and Technology) programme
Published: 2018

39. Diversity and assemblage structure of tropical marine flora on lava flows of different ages

Author: Mayalen Zubia, Olivier De Clerck, Frederik Leliaert, Jean Pascal Quod, Harold Cambert, Stjepko Golubic, Christophe Vieira, Showe-Mei Lin, Shao-Lun Liu, Nicolas Loiseau, Mathieu Pinault, Claude Payri, L. Mattio, Université de la Polynésie Française (UPF), Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Universiteit Gent = Ghent University [Belgium] (UGENT), Botanic Garden Meise, Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Department of Biological Sciences (DBS), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Agence pour la Recherche et la Valorisation Marines - ARVAM (Ste Clotilde, La réunion-France), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Biological Science Center, Boston University [Boston] (BU), Institute of Marine Biology and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan University [Taiwan] (NTU), Tunghai University [Taichung], and Marex - Marine Expertise Company
Subjects: 0106 biological sciences, Lava, [SDE.MCG]Environmental Sciences/Global Changes, Plant Science, Ecological succession, Aquatic Science, Cyanobacteria, 010603 evolutionary biology, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Macroalgae, Canonical correspondence analysis, Dominance (ecology), 14. Life underwater, geography, geography.geographical_feature_category, biology, Piton de la fournaise, Ecology, 010604 marine biology & hydrobiology, Ephemeral key, Reunion island, Coral reef, 15. Life on land, biology.organism_classification, Seagrass, Volcano, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Recent volcanic lava flows extending into the ocean represent an ideal opportunity to study the long-term successional development of marine floral assemblages on the bare new substratum. We describe the floral assemblages of nine lava flows of different ages (prehistoric to 2007) at Piton de la Fournaise (Reunion Island, Indian Ocean) based on a survey of 37 stations. We identified 159 species including 148 macroalgae, 1 seagrass, and 10 cyanobacteria. Fifty-one of those represent new records for Reunion Island, and at least 9 taxa were identified as new to science. Recent lava flows were characterized by the dominance of ephemeral, opportunistic species, such as Pseudobryopsis hainanensis and Acrocladus dotyanus, while prehistoric lava flows were mainly characterized by perennial species, particularly Sargassum portierianum and Turbinaria ornata. A canonical correspondence analysis revealed that the environmental factor that most significantly correlated to the variation in floral assemblages was the distance to the most recent lava flow (2007). This factor was also highly correlated to coral cover. The composition of the different floral assemblages is discussed in relation to abiotic and biotic factors to explain ecological succession in a tropical environment.
Published: 2018

40. Phylogeography of a widely distributed species reveals a cryptic assemblage of distinct genetic lineages needing separate conservation strategies

Author: Pascal Touzet, Benjamin Brachi, Hélène Martin, Maarten J. M. Christenhusz, Fabienne Van Rossum, Solenn Le Cadre, Meise Botanic Garden, Partenaires INRAE, Centre des Archives de la Féderation Wallonie-Bruxelles & Espace d’expositions Temporaires, Mons, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Department of Environment and Agriculture, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), Plant Gateway, Botanic Garden Meise, Meise Botanic Garden [Belgium] (Plantentuin), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))
Subjects: 0106 biological sciences, 0301 basic medicine, Species complex, Outbreeding depression, [SDV]Life Sciences [q-bio], contact zones, Plant Science, Biology, phylogeography, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Refugium (population biology), Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, multiple refugia, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Phylogenetic tree, genetic restoration, Silene nutans, conservation, 15. Life on land, Ex situ conservation, biology.organism_classification, 030104 developmental biology, Evolutionary biology, Genetic structure, plastid (chloroplast) DNA
Abstract: International audience; Genetic structure in broadly distributed herbs may be shaped by past climate events, leading to distinct genetic lineages, and possibly to different Evolutionary Significant Units (ESUs). We identified the potential glacial refugia, postglacial (re)colonization routes, contact zones and ESUs in the widespread but locally rare Silene nutans to propose appropriate conservation strategies related to migration history-related genetic structure. We sequenced four plastid DNA markers from 136 populations covering S. nutans European distribution range. We built a network on concatenated sequences using statistical parsimony and performed Bayesian and Maximum Likelihood analyses to build a phylogenetic tree. Haplotype genetic diversity and between-population differentiation (G(ST), N-ST) were calculated. Based on 23 plastid haplotypes, populations were ascribed to seven strongly differentiated genetic lineages. Potential refugia were identified: in the Iberian and Italian Peninsulas, expanding to south-western France and the Alps, respectively; in south-central France, reaching England and Belgium; an eastern refugium, following a north-westward expansion; in the Balkans, expanding to north-eastern Italy, and in the Carpathians. Several contact zones were identified. Silene nutans consists of a cryptic assemblage of genetically distinct taxa, with at least seven ESUs. Evaluating the distribution range, the abundance, and the conservation status of each ESU is necessary for the preservation of the S. nutans species complex at European and regional levels. Ex situ conservation and genetic restoration involving plant translocations must consider the phylogeographic history and the distinct genetic lineages to avoid the introduction of poorly adapted plants and outbreeding depression leading to non-viable hybrid progeny, especially in contact zones.
Published: 2018

41. Alien futures: What is on the horizon for biological invasions?

Author: Dehnen-Schmutz, Katharina, Boivin, Thomas, Essl, Franz, J. Groom, Quentin, Harrison, Laura Jane, Touza-Montero, Julia Maria, Bayliss, Helen, Centre for Agroecology, Water and Resilience, Coventry University, Ecologie des Forêts Méditerranéennes [Avignon] (URFM 629), Institut National de la Recherche Agronomique (INRA), Department of Botany and Biodiversity Research, University of Vienna [Vienna], Botanic Garden Meise, Environment Department, Harper Adams University, Ecologie des Forêts Méditerranéennes (URFM), and BR/165/A1/TrIAS
Subjects: public health legislation, invasive alien species, [SDE.MCG]Environmental Sciences/Global Changes, biological invasions, global survey, gestion des invasions biologiques, future direction, prioritization, santé humaine, flux migratoire, human health, législation sanitaire, espèce exotique invasive, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, adaptation au changement climatique, gestion de l'eau, horizon scanning, changement environnemental, management, migratory stream
Abstract: Aim To collect and identify the issues that may affect the future global and local management of biological invasions in the next 20 to 50 years and provide guidance for the prioritisation of actions and policies responding to the management challenges of the future. Location Global Methods We used an open online survey to poll specialists and stakeholders from around the world as to their opinion on the three most important future issues both globally and at their respective local working level. Results The 240 respondents identified 629 global issues that we categorised into topics. We summarised the highest rated topics into five broad thematic areas: (1) environmental change, particularly climate change, (2) the spread of species through trade, (3) public awareness, (4) the development of new technologies to enhance management, and (5) the need to strengthen policies. The respondents also identified 596 issues at their respective local working levels. Management, early detection, prevention and funding-related issues all ranked higher than at the global level. Our global audience of practitioners, policy makers and researchers also elicited topics not identified in horizon scanning exercises led by scientists including potential human health impacts, the need for better risk assessments and legislation, the role of human migration and water management. Main conclusions The topic areas identified in this horizon scan provide guidance where future policy priorities for invasive alien species should be set. First, to reduce the magnitude and speed of environmental change and its impacts on biological invasions; second, to restrict the movement of potentially invasive alien species via trade; third, to raise awareness with the general public and empower them to act; and finally, to invest in innovative technologies that can detect and mitigate adverse impacts of introduced species.
Published: 2018

42. The genus Luticola (Bacillariophyta) on Ile Amsterdam and Ile Saint-Paul (Southern Indian Ocean) with the description of two new species

Author: Marc Lebouvier, Barbora Chattová, Myriam de Haan, Bart Van de Vijver, Masaryk University [Brno] (MUNI), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Botanic Garden Meise, University of Antwerp (UA), French Polar Institute [IPEV 136, 1167], ERASMUS scholarship, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Meise Botanic Garden [Belgium] (Plantentuin)
Subjects: 0106 biological sciences, Ochrophyta, Biogeography, Ecology (disciplines), Morphology (biology), Naviculales, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, diatoms, Diadesmidaceae, Genus, lcsh:Botany, lcsh:Zoology, morphology, lcsh:QL1-991, Bacillariophyta, Biology, Ecology, Evolution, Behavior and Systematics, Taxonomy, new species, Chromista, Bacillariophyceae, biology, Ecology, Luticola, 010604 marine biology & hydrobiology, Biodiversity, biology.organism_classification, lcsh:QK1-989, Indian ocean, Taxon, Geography, Diatom, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Five species of the terrestrial diatom genus Luticola D. G. Mann were found during a taxonomic survey of two small volcanic islands, Ile Amsterdam and Ile Saint-Paul (Southern Indian Ocean). Apart from the two already known Luticola species L. beyensii Van de Vijver et al. and L. subcrozetensis Van de Vijver et al., two new species are described: L. ivetana Chattova and Van de Vijver sp. nov. and L. vancampiana Chattova and Van de Vijver sp. nov. Finally, one, up to now unknown, Luticola species is briefly discussed and illustrated. Detailed morphological descriptions of these taxa are provided based on both light and scanning electron microscopy observations. Morphological features of the new species are compared to morphologically similar taxa, and notes on their ecology and biogeography are added.
Published: 2017

43. ConR: An R package to assist large-scale multispecies preliminary conservation assessments using distribution data

Author: Dauby, Gilles, Stévart, Tariq, Droissart, Vincent, Cosiaux, Ariane, Deblauwe, Vincent, Simo‐Droissart, Murielle, Sosef, Marc S. M., Lowry, Porter P., Schatz, George E., Gereau, Roy E., Couvreur, Thomas L. P., Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Libre de Bruxelles [Bruxelles] (ULB), Missouri Botanical Garden (USA), Botanic Garden Meise, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Department of Ecology and Evolutionary Biology, Center for Tropical Research, Institute of the Environment and Sustainability, University of California [Los Angeles] (UCLA), University of California-University of California, University of Yaoundé [Cameroun], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université libre de Bruxelles (ULB), Missouri Botanical Garden, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Meise Botanic Garden [Belgium] (Plantentuin), University of California (UC)-University of California (UC), and Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE)
Subjects: BIOLOGIE VEGETALE, Ecologie, extent of occurrence, threatened taxa, preliminary status, Santé publique, Environnement et pollution, IUCN, criterion B, area of occupancy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, distribution range, location, ComputingMilieux_MISCELLANEOUS, Original Research
Abstract: The Red List Categories and the accompanying five criteria developed by the International Union for Conservation of Nature (IUCN) provide an authoritative and comprehensive methodology to assess the conservation status of organisms. Red List criterion B, which principally uses distribution data, is the most widely used to assess conservation status, particularly of plant species. No software package has previously been available to perform large-scale multispecies calculations of the three main criterion B parameters [extent of occurrence (EOO), area of occupancy (AOO) and an estimate of the number of locations] and provide preliminary conservation assessments using an automated batch process. We developed ConR, a dedicated R package, as a rapid and efficient tool to conduct large numbers of preliminary assessments, thereby facilitating complete Red List assessment. ConR (1) calculates key geographic range parameters (AOO and EOO) and estimates the number of locations sensu IUCN needed for an assessment under criterion B; (2) uses this information in a batch process to generate preliminary assessments of multiple species; (3) summarize the parameters and preliminary assessments in a spreadsheet; and (4) provides a visualization of the results by generating maps suitable for the submission of full assessments to the IUCN Red List. ConR can be used for any living organism for which reliable georeferenced distribution data are available. As distributional data for taxa become increasingly available via large open access datasets, ConR provides a novel, timely tool to guide and accelerate the work of the conservation and taxonomic communities by enabling practitioners to conduct preliminary assessments simultaneously for hundreds or even thousands of species in an efficient and time-saving way., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2017

44. Ducatina umbilicata gen. et sp. nov., a remarkable Trapeliaceae from the subantarctic islands in the Indian Ocean

Author: Roar S. Poulsen, Alice Gadea, Ulrik Søchting, Maryvonne Charrier, Damien Ertz, Botanic Garden Meise, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut des Sciences Chimiques de Rennes (ISCR), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut Polaire Français Paul-Émile Victor, program 136 ‘Subanteco’, Fonds national de la Recherche Scientifique belge, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Meise Botanic Garden [Belgium] (Plantentuin), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Baeomycetales, Phylogenetic tree, Placopsis, Aspiciliopsis, 030108 mycology & parasitology, Biology, phylogeny, Thallus, Ascocarp, 03 medical and health sciences, taxonomy, Taxon, Phylogenetics, Genus, Botany, Taxonomy (biology), Orceolina, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Lichen, lichens, Ecology, Evolution, Behavior and Systematics, biodiversity
Abstract: The new genus and speciesDucatina umbilicatais described from Îles Crozet and Îles Kerguelen. This lichen is characterized by an umbilicate thallus with a black verrucose lower surface and a greyish to dark olivaceous smooth upper surface having large verrucae, large semi-immersed cephalodia, semi-immersed apothecia with a prominent thalline margin, simple, mainly ellipsoid ascospores of 23–42×12–25 µm and the presence of unknown chemical compounds. Phylogenetic analyses using nuLSU and mtSSU sequences placeDucatinain theTrapeliaceae(Baeomycetales). The new taxon is closely related toOrceolina antarcticaandO.kerguelensis, two other lichens endemic to these subantarctic islands, differing by its morphology and the lack of chemical compounds.Ducatinais the only genus in theTrapeliaceaeto develop a large umbilicate thallus.
Published: 2017

45. Seven recommendations to make your invasive alien species data more useful

Author: Teodora Trichkova, Helen E. Roy, Anastasia Christopoulou, Frances E. Lucy, Harry Helmisaari, Argyro Zenetos, Marie-Anne A. Rozenberg, Hans Peter Ravn, Diemer Vercayie, Tim Adriaens, Gareth Richards, Anna Gazda, Donald Hobern, Sonia Vanderhoeven, Ioannis Bazos, Olivera Petrović-Obradović, Ana Cristina Cardoso, Melanie Josefsson, Annie Simpson, Aaike De Wever, Peter Desmet, Elena Tricarico, Riccardo Scalera, Alain Roques, Quentin Groom, Dragana Marisavljevic, Tomasz Oszako, Jan Pergl, Céline Prévot, Lucinda Charles, Botanic Garden Meise, Research Institute for Nature and Forest (INBO), Core Science Analytics, Synthesis, and Libraries Program, United States Geological Survey (USGS), Aquatic and Terrestrial Ecology, Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences (RBINS), Department of Ecology and Systematics, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), EASIN, European Commission's Joint Research Centre, CABI Europe UK, Department of Forest Biodiversity, University of Agriculture in Krakow, Finnish Environment Institute (SYKE), Global Biodiversity Information Facility (GBIF), Swedish Environmental Protection Agency, Centre for Environmental Research Innovation and Sustainability (CERIS), Institute of Technology Sligo, Institute for Plant Protection and Environment, Forest Research Institute, Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences [Prague] (CAS), Faculty of Agriculture, Université nationale du Rwanda, DEMNA, Département de l’Étude du Milieu Naturel et Agricole, Service Public de Wallonie, Department of Geosciences and Natural Resource Management [Copenhagen] (IGN), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), Centre for Ecology and Hydrology, IUCN SSC Invasive Species Specialist Group, Università degli Studi di Firenze, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences (BAS), Natuurpunt, nstitute of Marine Biological Resources and Inland Waters, Hellenic Center for Marine Research (HCMR), Belgian Biodiversity Platform, Walloon Research Department for Nature and Agricultural Areas, Research Institute for Nature and Forest, National and Kapodistrian University of Athens = University of Athens (NKUA | UoA), CERIS, Centre for Environmental Research Innovation and Sustainability, Czech Academy of Sciences [Prague] (ASCR), and Unité de recherche Zoologie Forestière (UZF)
Subjects: 0106 biological sciences, Standardization, invasieve exoten, Computer science, Data management, Interoperability, open data, Introduced species, 01 natural sciences, data management plan, organisation des données, non-native, Invasive species (nature management), data interoperability, Data and Information, non-indigenous, Invasive species (management), B003-ecology, species directed nature management, statistics and modelling, gestion de données, Applied Mathematics, lcsh:T57-57.97, Data management plan, Invasive species (fauna management), data, exoten, standards, interoperabilité, lcsh:Probabilities. Mathematical statistics, Invasive species (species diversity), Statistics and Probability, espèce non indigène, [SDE.MCG]Environmental Sciences/Global Changes, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], 010603 evolutionary biology, Ecology and Environment, pest species, World Wide Web, plan de gestion, Controlled vocabulary, Relevance (information retrieval), espèce invasive, checklists, automation, business.industry, 010604 marine biology & hydrobiology, 15. Life on land, espèce introduite, Data science, Metadata, introduced species, invasieve soorten, 13. Climate action, lcsh:Applied mathematics. Quantitative methods, donnée, databanken, business, lcsh:QA273-280, plan de gestion de données
Abstract: Science-based strategies to tackle biological invasions depend on recent, accurate, well-documented, standardized and openly accessible information on alien species. Currently and historically, biodiversity data are scattered in numerous disconnected data silos that lack interoperability. The situation is no different for alien species data, and this obstructs efficient retrieval, combination, and use of these kinds of information for research and policy-making. Standardization and interoperability are particularly important as many alien species related research and policy activities require pooling data. We describe seven ways that data on alien species can be made more accessible and useful, based on the results of a European Cooperation in Science and Technology (COST) workshop: (1) Create data management plans; (2) Increase interoperability of information sources; (3) Document data through metadata; (4) Format data using existing standards; (5) Adopt controlled vocabularies; (6) Increase data availability; and (7) Ensure long-term data preservation. We identify four properties specific and integral to alien species data (species status, introduction pathway, degree of establishment, and impact mechanism) that are either missing from existing data standards or lack a recommended controlled vocabulary. Improved access to accurate, real-time and historical data will repay the long-term investment in data management infrastructure, by providing more accurate, timely and realistic assessments and analyses. If we improve core biodiversity data standards by developing their relevance to alien species, it will allow the automation of common activities regarding data processing in support of environmental policy. Furthermore, we call for considerable effort to maintain, update, standardize, archive, and aggregate datasets, to ensure proper valorization of alien species data and information before they become obsolete or lost.
Published: 2017

46. Lineages of Silene nutans developed rapid, strong, asymmetric postzygotic reproductive isolation in allopatry

Author: Martin, Hélène, Touzet, Pascal, Dufay, Mathilde, Godé, Cécile, Schmitt, Eric, Lahiani, Emna, Delph Lynda, F, van Rossum, Fabienne, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Indiana University [Bloomington], Indiana University System, Meise Botanic Garden [Belgium] (Plantentuin), Université libre de Bruxelles (ULB), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), and Botanic Garden Meise
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2017

47. Study in Agaricus subgenus Minores and allied clades reveals a new American subgenus and contrasting phylogenetic patterns in Europe and Greater Mekong Subregion

Author: Samantha C. Karunarathna, Komsit Wisitrassameewong, Jie Chen, Rui-Lin Zhao, Olivier Raspé, Kevin D. Hyde, Mao-Qiang He, Philippe Callac, Magalie Moinard, Luis A. Parra, A. De Kesel, Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Institut National de la Recherche Agronomique (INRA), State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences [Changchun Branch] (CAS), Center of Excellence in Fungal Research, Mae Fah Luang University [Thaïlande] (MFU), Avda, Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, World Agroforestry Center [CGIAR, Chine] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Botanic Garden Meise, Department of Biology, Faculty of Science, University of Isfahan, Unité de recherche Mycologie et Sécurité des Aliments (MSA), World Agroforestry Centre, China & East-Asia Office, and Naturalis journals & series
Subjects: 0301 basic medicine, taxonomie, [SDV]Life Sciences [q-bio], Subtropics, Agaricus sect. Minores, analyse phylogénétique, 03 medical and health sciences, taxonomy, Botany, Agaricaceae, Clade, Ecology, Evolution, Behavior and Systematics, divergence times, multi-gene phylogeny, Phylogenetic tree, biology, Species diversity, 15. Life on land, 030108 mycology & parasitology, biology.organism_classification, Evolutionary biology, Phylogenetic Pattern, Taxonomy (biology), agaricus, Subgenus, Research Article
Abstract: Within Agaricus subg. Minores, A. sect. Minores remains a little-studied section due generally to its delicate sporocarps often lacking taxonomically relevant morphological characters. To reconstruct the section, using the recent taxonomic system based on divergence times, and to evaluate the species diversity of A. sect. Minores in the Greater Mekong Subregion, 165 specimens were incorporated in phylogenetic analyses. A dated tree based on nuclear ITS, LSU and tef1-α sequence data allowed us to better circumscribe A. subg. Minores and to propose a new subgenus, A. subg. Minoriopsis, which is only known from tropical and subtropical regions of the Americas. A larger tree based on ITS sequences indicated that, with 81 phylogenetic species, the reconstructed section Minores is now one of the largest sections in the genus. Within A. subg. Minores, a new section, A. sect. Leucocarpi, and eleven new species are described from the Greater Mekong Subregion. Thirty-eight species of A. sect. Minores from this region of Asia were distributed in multiple clades that successively diverged over the past 24 million years. In contrast, species reported from Europe mostly grouped in a single non-tropical clade, suggesting a major species diversification following the middle Miocene climatic optimum.
Published: 2017

48. New epizoic diatom (Bacillariophyta) species from sea turtles in the Eastern Caribbean and South Pacific

Author: Andrzej Witkowski, Catherine Riaux-Gobin, Damien Chevallier, J. Patrick Kociolek, Pierre Compère, Luc Ector, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), lnstitute of Marine Sciences and Coastal Research, University of Szczecin, Department of Ecology and Evolutionary Biology [Boulder], University of Colorado [Boulder], Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Botanic Garden Meise, Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD)
Subjects: 0106 biological sciences, 0301 basic medicine, new species, Lesser Antilles, biology, Chelonia mydas, Host (biology), Ecology, 010604 marine biology & hydrobiology, 030108 mycology & parasitology, Aquatic Science, biology.organism_classification, 01 natural sciences, Tripterion, 03 medical and health sciences, Diatom, Taxon, Chelonicola, [SDE]Environmental Sciences, Juvenile, Society Archipelago, 14. Life underwater
Abstract: International audience; Obligately epizoic diatoms (Bacillariophyta) on vertebrates were first described from cetaceans, but turtles, both freshwater and marine, also host very specific floras. Several scrapings of juvenile Chelonia mydas have allowed the description of two new diatom taxa whose valves are asymmetrical about the transapical axis, Tripterion societatis sp. nov. and Chelonicola caribeana sp. nov. These taxa are very small and show some morphological plasticity. Such plasticity might suggest their inclusion in genera with slightly different characteristics from Tripterion and Chelonicola as originally delimited. Based on our observations, an emended diagnosis is proposed for Chelonicola.
Published: 2017

49. Beyong names: developing a names database and other applications for diatoms

Author: Kociolek, J.P., Balasubramanian, K., Blanco, Stéphane, Coste, Michel, Ector, L., Liu, Y., Kulikovskiy, M., Ludwig, T., Lundhom, N., Potapova, M., Rimet, Frédéric, Sabbe, Koen, Sar, E., Taylor, J., Van De Vijver, B., Wetzel, C.E., Williams, D.M., Witkowski, Anne, Witkowski, J., Vandepitte, L., Decock, W., Vanhoorne, B., UNIVERSITY OF COLORADO BOULDER USA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), AGHARKAR RESEARCH INSTITUT MAHARASHTRA IND, INSTITUT OF ENVIRONMENT LEON ESP, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), LIST BELVAUX LUX, HARBIN NORMAL UNIVERSITY HEILONGJIANG CHN, RUSSIAN ACADEMIC SCIENCE BOROK RUS, UNIVERSITY FEDERAL PARANA BRA, NATIONAL HISTORY MUSEUM COPENHAGEN DNK, BREXEL UNIVERSITY PHILADELPHIA USA, Institut National de la Recherche Agronomique (INRA), UNIVERSITY OF GHENT BEL, UNIVERSITY NACIONAL LA PLATA BUENOS AIRES ARG, NORTH WEST UNIVERSITY POTCHEFSTROOM ZAF, BOTANIC GARDEN MEISE BEL, University of Antwerp (UA), NATIONAL HISTORY MUSEUM LONDON GBR, University of Szczecin, and FLANDERS MARINE INSTITUT OOSTENDE BEL
Subjects: [SDE]Environmental Sciences
Abstract: International audience; Catalogue of diatom names resurrected: diatombase will be the new authority resource for diatom names and more.
Published: 2017

50. Taxonomy and phylogeny of the genus Steinera (Arctomiales, Arctomiaceae) in the subantarctic islands of Crozet and Kerguelen

Author: Roar S. Poulsen, Damien Ertz, Ulrik Søchting, Maryvonne Charrier, Botanic Garden Meise, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), French Polar Institute (Institut Polaire Francais Paul-Emile Victor), Fonds National de la Recherche Scientifique, Belgium (FNRS), Meise Botanic Garden [Belgium] (Plantentuin), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)
Subjects: 0301 basic medicine, Phylogenetic tree, Zoology, Massalongia, Plant Science, 15. Life on land, 030108 mycology & parasitology, Biology, Koerberiaceae, 03 medical and health sciences, Type species, Henssenia, Peltigerales, Phylogenetics, Genus, Convergent evolution, Taxonomy (biology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Lichen, Endemism, Ecology, Evolution, Behavior and Systematics, biodiversity
Abstract: The lichenized genus Steinera is revised for the archipelagos of Crozet and of Kerguelen, with a high level of endemism revealed. It is shown to represent a good example of convergent evolution between two different orders. Phylogenetic analyses using nuLSU, RPB1 and mtSSU sequences show that two different species groups can be recognized: Steinera s. str. belongs to the Arctomiaceae (Arctomiales) and is characterized notably by species having pluriseptate ascospores, and a second species group belongs to the Koerberiaceae (Peltigerales) and is characterized notably by simple ascospores sometimes having a plasma-bridge. The genus Henssenia is newly described to accommodate this latter group. The type species of Steinera is shown to have been erroneously treated in the past, with Steinera molybdoplaca being the type of Steinera and “ S .” glaucella belonging to the genus Henssenia . A sorediate morph is recorded for S. molybdoplaca and the results confirmed using a 4-gene phylogeny, including nuITS sequences. Some species previously described in the genera Arctomia and Massalongia from the Southern Hemisphere are shown to belong to Steinera s. str. Five new species are described: Steinera isidiata Ertz & R.S. Poulsen, S. membranacea Ertz & R.S. Poulsen, S. lebouvieri Ertz, S. pannarioides Ertz & R.S. Poulsen and Henssenia subglaucella Ertz & R.S. Poulsen along with seven new combinations: Steinera intricata (Ovstedal) Ertz, S . latispora (Ovstedal) Ertz, S. olechiana (Alstrup & Sochting) Ertz & Sochting, S . subantarctica (Ovstedal) Ertz, Henssenia glaucella (Tuck.) Ertz, R.S. Poulsen & Sochting, H. radiata (P. James & Henssen) Ertz and H. werthii (Zahlbr.) Ertz, R.S. Poulsen & Sochting. An epitype is chosen for Henssenia glaucella and a neotype for H. werthii . “ Steinera” symptychia has an isolated phylogenetic position in the Koerberiaceae and might represent a distinct, new genus. World-wide identification keys to the species of Henssenia and Steinera are provided.
Published: 2017

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