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Engel MS, Ceríaco LMP, Daniel GM, Dellapé PM, Löbl I, Marinov M, Reis RE, Young MT, Dubois A, Agarwal I, Lehmann A. P, Alvarado M, Alvarez N, Andreone F, Araujo-Vieira K, Ascher JS, Baêta D, Baldo D, Bandeira SA, Barden P, Barrasso DA, Bendifallah L, Bockmann FA, Böhme W, Borkent A, Brandão CRF, Busack SD, Bybee SM, Channing A, Chatzimanolis S, Christenhusz MJM, Crisci JV, D’elía G, Da Costa LM, Davis SR, De Lucena CAS, Deuve T, Fernandes Elizalde S, Faivovich J, Farooq H, Ferguson AW, Gippoliti S, Gonçalves FMP, Gonzalez VH, Greenbaum E, Hinojosa-Díaz IA, Ineich I, Jiang J, Kahono S, Kury AB, Lucinda PHF, Lynch JD, Malécot V, Marques MP, Marris JWM, Mckellar RC, Mendes LF, Nihei SS, Nishikawa K, Ohler A, Orrico VGD, Ota H, Paiva J, Parrinha D, Pauwels OSG, Pereyra MO, Pestana LB, Pinheiro PDP, Prendini L, Prokop J, Rasmussen C, Rödel MO, Rodrigues MT, Rodríguez SM, Salatnaya H, Sampaio Í, Sánchez-García A, Shebl MA, Santos BS, Solórzano-Kraemer MM, Sousa ACA, Stoev P, Teta P, Trape JF, Dos Santos CVD, Vasudevan K, Vink CJ, Vogel G, Wagner P, Wappler T, Ware JL, Wedmann S, Zacharie CK. The taxonomic impediment: a shortage of taxonomists, not the lack of technical approaches. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab072] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Michael S Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Luis M P Ceríaco
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, Portugal
| | - Gimo M Daniel
- Department of Terrestrial Invertebrates, The National Museum, Bloemfontein, South Africa; Department of Biological & Environmental Sciences, Walter Sisulu University, Mthatha, South Africa
| | - Pablo M Dellapé
- División Entomología, Universidad Nacional de la Plata, CONICET, Museo de La Plata, Paseo del Bosque s/n, La Plata, Buenos Aires, Argentina
| | - Ivan Löbl
- Muséum d’histoire naturelle, Département de Génétique et Evolution, Université de Genève, Geneva, Switzerland
| | - Milen Marinov
- Biosecurity Surveillance & Incursion Investigation Plant Health Team, Ministry for Primary Industries, Christchurch, New Zealand
| | - Roberto E Reis
- Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mark T Young
- School of GeoSciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Alain Dubois
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle,CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Ishan Agarwal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Pablo Lehmann A.
- Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil
| | - Mabel Alvarado
- Departamento de Entomología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Nadir Alvarez
- Muséum d’histoire naturelle, Département de Génétique et Evolution, Université de Genève, Geneva, Switzerland
| | | | - Katyuscia Araujo-Vieira
- Laboratório de Herpetologia, Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista-UNESP, Rio Claro, São Paulo, Brazil
| | - John S Ascher
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Délio Baêta
- Centro de Investigação em Biodiversidade e Recursos Genéticos - Rede de Investigação em Biodiversidade e Biologia Evolutiva, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Diego Baldo
- Instituto de Biología Subtropical (CONICET-UNaM), Posadas, Misiones, Argentina
| | - Suzana A Bandeira
- Instituto Nacional da Biodiversidade e Áreas de Conservação, Luanda, Angola
| | - Phillip Barden
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Diego A Barrasso
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Puerto Madryn, Chubut, Argentina
| | - Leila Bendifallah
- Laboratory of Soft Technologies, Valorization, Physico-Chemistry of Biological Materials and Biodiversity, Faculty of Science, University M’hamed Bougara of Boumerdes, Boumerdes, Algeria
| | - Flávio A Bockmann
- Department of Biology, FFCLRP/ Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Wolfgang Böhme
- Section of Herpetology, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Art Borkent
- 691-8th Ave SE, Salmon Arm, British Columbia, V1E 2C2, Canada
| | | | - Stephen D Busack
- Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
| | - Seth M Bybee
- Department of Biology and Monte L. Bean Life Science Museum, Brigham Young University, Provo UT, USA
| | - Alan Channing
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | | | - Maarten J M Christenhusz
- The Linnean Society of London, Burlington House, Piccadilly, London, UK; Royal Botanic Gardens, Kew, Richmond, UK; Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Jorge V Crisci
- División Plantas Vasculares, Universidad Nacional de la Plata, Museo de La Plata, Paseo del Bosque s/n, La Plata, Buenos Aires, Argentina
| | - Guillermo D’elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Luis M Da Costa
- Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Steven R Davis
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Carlos Alberto S De Lucena
- Pontifícia Universidade Católica do Rio Grande do Sul, Museu de Ciências e Tecnologia, Porto Alegre, Brazil
| | - Thierry Deuve
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle,CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | | | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales, ‘Bernardino Rivadavia’ – CONICET,Buenos Aires, Argentina
| | - Harith Farooq
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Adam W Ferguson
- Gantz Family Collection Center, Field Museum of Natural History, Chicago, USA
| | | | | | - Victor H Gonzalez
- Undergraduate Biology Program & Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Ismael A Hinojosa-Díaz
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ivan Ineich
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle,CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Sih Kahono
- Research Center for Biology, Indonesian Institute of Sciences, Jl, Raya Jakarta Bogor, Bogor, Indonesia
| | - Adriano B Kury
- Departmento Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - John D Lynch
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Valéry Malécot
- Institut Agro, Univ Angers, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Mariana P Marques
- Museu Nacional de História Natural e da Ciência da Universidade de Lisboa, Lisboa, Portugal
| | - John W M Marris
- Entomology Research Collection, Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | | | - Luis F Mendes
- Museu Nacional de História Natural e da Ciência da Universidade de Lisboa, Lisboa, Portugal
| | - Silvio S Nihei
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Sciences, Kyoto University, Kyoto, Japan
| | - Annemarie Ohler
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle,CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Victor G D Orrico
- Tropical Herpetology Laboratory, Universidade Estadual de Santa Cruz, Departamento de Ciências Biológicas, Ilhéus, Brazil
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, and Museum of Nature and Human Activities, Hyogo, Sanda, Japan
| | - Jorge Paiva
- Centre for Functional Ecology. Science for People and the Planet, University of Coimbra, Portugal
| | - Diogo Parrinha
- Museu Nacional de História Natural e da Ciência da Universidade de Lisboa, Lisboa, Portugal
| | | | - Martín O Pereyra
- Laboratorio de Genética Evolutiva ‘Claudio J. Bidau’, Instituto de Biología Subtropical (IBS, CONICET), Universidad Nacional de Misiones (UNaM), Posadas, Misiones, Argentina
| | - Lueji B Pestana
- Departamento de Biologia, Faculdade de Ciências da Universidade Agostinho Neto, Luanda, Angola
| | | | - Lorenzo Prendini
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Jakub Prokop
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | - Mark-Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Sara M Rodríguez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile,Valdivia, Chile
| | - Hearty Salatnaya
- Agrotechnology Study Program. Banau Tertiary Institute of Agricultural Enterprise, West Halmahera, Indonesia
| | - Íris Sampaio
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, Portugal
| | - Alba Sánchez-García
- Departament de Botànica i Geologia, Facultat de Ciències Biològiques, Universitat de València,Burjassot, València, Spain
| | - Mohamed A Shebl
- Department of Plant Protection, Faculty of Agriculture, Suez Canal University, Ismailia, Egypt
| | - Bruna S Santos
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Mónica M Solórzano-Kraemer
- Department of Palaeontology and Historical Geology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Ana C A Sousa
- Grutas da Moeda e Fátima Lda., São Mamede, Batalha, Portugal
| | - Pavel Stoev
- National Museum of Natural History, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Pablo Teta
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jean-François Trape
- Institut de Recherche pour le Développement (IRD), UMR MIVEGEC, Dakar, Senegal
| | | | - Karthikeyan Vasudevan
- CSIR-Centre for Cellular and Molecular Biology, Laboratory for the Conservation of Endangered Species, Attapur, Hyderabad, India
| | - Cor J Vink
- Department of Pest-management and Conservation, Lincoln University, Lincoln, New Zealand
| | - Gernot Vogel
- Society for Southeast Asian Herpetology, Heidelberg, Germany
| | | | | | | | - Sonja Wedmann
- Senckenberg Forschungsstation Grube Messel, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt/M., Germany
| | - Chifundera Kusamba Zacharie
- Laboratory of Herpetology, Zoology Section, Department of Biology, Centre of Research in Natural Sciences at Lwiro, South Kivu province, Democratic Republic of the Congo
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5
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Miralles A, Bruy T, Wolcott K, Scherz MD, Begerow D, Beszteri B, Bonkowski M, Felden J, Gemeinholzer B, Glaw F, Glöckner FO, Hawlitschek O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Stadler M, Weibulat T, Wilke T, Renner SS, Vences M. Repositories for Taxonomic Data: Where We Are and What is Missing. Syst Biol 2020; 69:1231-1253. [PMID: 32298457 PMCID: PMC7584136 DOI: 10.1093/sysbio/syaa026] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/20/2020] [Accepted: 03/24/2020] [Indexed: 12/05/2022] Open
Abstract
Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].
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Affiliation(s)
- Aurélien Miralles
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Teddy Bruy
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Katherine Wolcott
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Mark D Scherz
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Biology, Universität Konstanz, Universitätstraße 10, 78464 Konstanz, Germany
| | - Dominik Begerow
- Department of Geobotany, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Bank Beszteri
- Department of Phycology, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Center of Excellence in Plant Sciences (CEPLAS), Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674 Köln, Germany
| | - Janine Felden
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Leobenerstraße 8, 28359 Bremen, Germany
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Birgit Gemeinholzer
- Department of Systematic Botany, Justus Liebig University Gießen, Heinrich-Buff Ring 38, 35392 Giessen, Germany
| | - Frank Glaw
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Frank Oliver Glöckner
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Oliver Hawlitschek
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Scientific Infrastructure, Centrum für Naturkunde (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ivaylo Kostadinov
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Tim W Nattkemper
- Biodata Mining Group, Center of Biotechnology (CeBiTec), Bielefeld University, PO Box 100131, 33501 Bielefeld, Germany
| | - Christian Printzen
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| | - Jasmin Renz
- Zooplankton Research Group, DZMB – Senckenberg am Meer, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Nataliya Rybalka
- Department of Experimental Phycology and Culture Collection of Algae, University Göttingen, Nikolausberger-Weg 18, 37073 Göttingen, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Tanja Weibulat
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Gießen, Heinrich-Buff Ring 26, 35392 Giessen, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
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