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Potapov AM, Chen TW, Striuchkova AV, Alatalo JM, Alexandre D, Arbea J, Ashton T, Ashwood F, Babenko AB, Bandyopadhyaya I, Baretta CRDM, Baretta D, Barnes AD, Bellini BC, Bendjaballah M, Berg MP, Bernava V, Bokhorst S, Bokova AI, Bolger T, Bouchard M, Brito RA, Buchori D, Castaño-Meneses G, Chauvat M, Chomel M, Chow Y, Chown SL, Classen AT, Cortet J, Čuchta P, de la Pedrosa AM, De Lima ECA, Deharveng LE, Doblas Miranda E, Drescher J, Eisenhauer N, Ellers J, Ferlian O, Ferreira SSD, Ferreira AS, Fiera C, Filser J, Franken O, Fujii S, Koudji EG, Gao M, Gendreau-Berthiaume B, Gers C, Greve M, Hamra-Kroua S, Handa IT, Hasegawa M, Heiniger C, Hishi T, Holmstrup M, Homet P, Høye TT, Ivask M, Jacques B, Janion-Scheepers C, Jochum M, Joimel S, Jorge BCS, Juceviča E, Kapinga EM, Kováč Ľ, Krab EJ, Krogh PH, Kuu A, Kuznetsova N, Lam WN, Lin D, Lindo Z, Liu AWP, Lu JZ, Luciáñez MJ, Marx MT, Mawan A, McCary MA, Minor MA, Mitchell GI, Moreno D, Nakamori T, Negri I, Nielsen UN, Ochoa-Hueso R, Oliveira Filho LCI, Palacios-Vargas JG, Pollierer MM, Ponge JF, Potapov MB, Querner P, Rai B, Raschmanová N, Rashid MI, Raymond-Léonard LJ, Reis AS, Ross GM, Rousseau L, Russell DJ, Saifutdinov RA, Salmon S, Santonja M, Saraeva AK, Sayer EJ, Scheunemann N, Scholz C, Seeber J, Shaw P, Shveenkova YB, Slade EM, Stebaeva S, Sterzynska M, Sun X, Susanti WI, Taskaeva AA, Tay LS, Thakur MP, Treasure AM, Tsiafouli M, Twala MN, Uvarov AV, Venier LA, Widenfalk LA, Widyastuti R, Winck B, Winkler D, Wu D, Xie Z, Yin R, Zampaulo RA, Zeppelini D, Zhang B, Zoughailech A, Ashford O, Klauberg-Filho O, Scheu S. Global fine-resolution data on springtail abundance and community structure. Sci Data 2024; 11:22. [PMID: 38172139 PMCID: PMC10764875 DOI: 10.1038/s41597-023-02784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024] Open
Abstract
Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.
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Affiliation(s)
- Anton M Potapov
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany.
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany.
- Department of Animal Ecology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, 37073, Germany.
| | - Ting-Wen Chen
- Department of Animal Ecology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, 37073, Germany
| | - Anastasia V Striuchkova
- Department of zoology and ecology, Institute of Biology and Chemistry, Moscow Pedagogical State University, Kibalchicha 6 B.3, Moscow, 129164, Russia
| | - Juha M Alatalo
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Douglas Alexandre
- Department of Soil Science, Centre for Agriculture and Veterinary Science, Santa Catarina State University (UDESC-Lages), Lages, SC, Brazil
| | - Javier Arbea
- CEPA Camargo, c/ Ria de Solia 3, ch. 39, 39610, Astillero, Spain
| | - Thomas Ashton
- Forest Research, Northern Research Station, Roslin, Midlothian, Scotland, EH25 9SY, United Kingdom
| | - Frank Ashwood
- Forest Research, Northern Research Station, Roslin, Midlothian, Scotland, EH25 9SY, United Kingdom
| | - Anatoly B Babenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskij prospekt 33, 119071, Moscow, Russia
| | | | | | - Dilmar Baretta
- Department Animal Science, University of Santa Catarina (UDESC), Chapeco, SC, 89815-000, Brazil
| | - Andrew D Barnes
- Te Aka Mātuatua - School of Science, University of Waikato, Private Bag 3105, Hamilton, 3204, New Zealand
| | - Bruno C Bellini
- Department of Botany and Zoology, Federal University of Rio Grande do Norte, Natal, 59078-970, Brazil
| | - Mohamed Bendjaballah
- Laboratoire de Biosystématique et Ecologie des Arthropodes, Faculté des Sciences de la Nature et de la Vie, Université Frères Mentouri Constantine 1, 25000, Constantine, Algeria
| | - Matty P Berg
- Section Ecology and Evolution, A-LIFE, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Community and Conservation Ecology group, GELIFES, University of Groningen, PO Box 72, 9700 AB, Groningen, The Netherlands
| | - Verónica Bernava
- Administración de Parques Nacionales, Calle Gral. San Martín y Padre Torrez (N3366), San Antonio, Misiones, Argentina
| | - Stef Bokhorst
- Systems Ecology, A-LIFE, Faculty of Science, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands
| | - Anna I Bokova
- Department of zoology and ecology, Institute of Biology and Chemistry, Moscow Pedagogical State University, Kibalchicha 6 B.3, Moscow, 129164, Russia
| | - Thomas Bolger
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, 4, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Mathieu Bouchard
- Department of wood and forest sciences, Université Laval, Québec, Qc, G1V 0A6, Canada
| | - Roniere A Brito
- Instituto de Biologia de Solo, Universidade Estadual da Paraíba, Rua Horácio Trajano de Oliveira, 666, João Pessoa/PB, 58071-160, Brazil
| | - Damayanti Buchori
- Department of Plant Protection, Bogor Agricultural University, Jalan Kamper, Kampus IPB Darmaga, 16680, Bogor, Indonesia
| | - Gabriela Castaño-Meneses
- Unidad Multidisciplinaria de Docencia e Investigación-Juriquilla, Facultad de Ciencias, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla, Querétaro, 76230, México
| | - Matthieu Chauvat
- Univ Rouen Normandie, INRAE, ECODIV USC 1499, F-76000, Rouen, France
| | - Mathilde Chomel
- FiBL France, Research Institute of Organic Agriculture, pole bio - ecosite du val de Drome, 26400, Eurre, France
| | - Yasuko Chow
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore, Singapore
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Aimee T Classen
- Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, Michigan, USA
- University of Michigan Biological Station, Pellston, Michigan, USA
| | - Jérôme Cortet
- CEFE, Université Paul-Valéry Montpellier 3, Université de Montpellier, CNRS, EPHE, IRD, route de Mende, 34000, Montpellier, France
| | - Peter Čuchta
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czech Republic
| | | | - Estevam C A De Lima
- Laboratório de Sistemática de Collembola e Conservação, Coleção de Referência de Fauna de Solo, Instituto de Biologia de Solo, Universidade Estadual da Paraíba, Campus V, Rua Horácio Trajano, 666, João Pessoa, Brazil
| | - Louis E Deharveng
- UMR7205, Museum national d'Histoire naturelle, 45 rue Buffon, 75005, Paris, France
| | - Enrique Doblas Miranda
- CREAF, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
- Universitat Autònoma de Barcelona, E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
| | - Jochen Drescher
- Department of Animal Ecology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, 37073, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
| | - Jacintha Ellers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Olga Ferlian
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
| | - Susana S D Ferreira
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Aila S Ferreira
- Laboratório de Sistemática de Collembola e Conservação, Coleção de Referência de Fauna de Solo, Instituto de Biologia de Solo, Universidade Estadual da Paraíba, Campus V, Rua Horácio Trajano, 666, João Pessoa, Brazil
| | - Cristina Fiera
- Institute of Biology Bucharest, Romanian Academy, Bucharest, Romania
| | - Juliane Filser
- University of Bremen, FB 02, UFT, General and Theoretical Ecology, Leobener Str. 6, D-28359, Bremen, Germany
| | - Oscar Franken
- Section Ecology and Evolution, A-LIFE, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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- Insect Ecology Laboratory, Department of Forest Entomology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
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- Département des sciences biologiques, Université du Québec à Montréal, C.P. 8888 succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada
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- Department of Geography and Spatial Information Techniques, Ningbo University, 315211, Ningbo, China
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- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, CNRS, Toulouse, 6, France
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- Département des sciences biologiques, Université du Québec à Montréal, C.P. 8888 succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada
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- Department of Environmental System Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto, 610-0394, Japan
| | - Charlène Heiniger
- University of Applied Sciences and Arts of Western Switzerland, Geneva, 150 route de Presinge, 1254, Jussy, Switzerland
| | - Takuo Hishi
- Kyushu University Forest, Kyushu University, 394 Tsubakuro, Sasaguri, Fukuoka, 811-2415, Japan
| | - Martin Holmstrup
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé 4, 8000, Aarhus C, Denmark
| | - Pablo Homet
- Departmento de Biogeoquímica, Ecología Vegetal y Microbiana/ Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas(CSIC), Avenida Reina Mercedes 10, 41012, Sevilla, Spain
| | - Toke T Høye
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé 4, 8000, Aarhus C, Denmark
| | - Mari Ivask
- Tartu College, Tallinn University of Technology, Puiestee 78, 51008, Tartu, Estonia
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi Str. 5, Tartu, 51006, Estonia
| | - Bob Jacques
- Department of Life Sciences, Aberystwyth University, Cledwyn Building, Penglais Campus, Aberystwyth, SY23 3DD, Wales, UK
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- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, 7701, South Africa
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- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103, Leipzig, Germany
- Department of Global Change Ecology, Biocenter, University of Würzburg, John-Skilton-Strasse 4a, 97074, Würzburg, Germany
| | - Sophie Joimel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR EcoSys, 91120, Palaiseau, France
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- Quantitative Ecology Lab, Department of Ecology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Edite Juceviča
- Institute of Biology, University of Latvia, O.Vācieša Street 4, Riga, LV-1004, Latvia
| | - Esther M Kapinga
- Agricultural University of Iceland, Hvanneyri, 311, Borgarbyggð, Iceland
| | - Ľubomír Kováč
- Department of Zoology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Košice, Slovakia
| | - Eveline J Krab
- Department of Soil and Environment, Swedish University or Agricultural Sciences, 750 07, Uppsala, Sweden
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| | - Paul Henning Krogh
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé 4, 8000, Aarhus C, Denmark
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- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi Str. 5, Tartu, 51006, Estonia
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- Department of zoology and ecology, Institute of Biology and Chemistry, Moscow Pedagogical State University, Kibalchicha 6 B.3, Moscow, 129164, Russia
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- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore, Singapore
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- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
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- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 3K7, Canada
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- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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- Department of Animal Ecology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, 37073, Germany
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- Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2. Cantoblanco, 28049, Madrid, España
| | - Michael T Marx
- Institute of Zoology, Johannes Gutenberg University Mainz, 55128, Mainz, Germany
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- Department of Animal Ecology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, 37073, Germany
| | - Matthew A McCary
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
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- Ecology & Zoology Group, School of Natural Sciences, Massey University, P.B, 11222, Palmerston North, New Zealand
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- Te Aka Mātuatua - School of Science, University of Waikato, Private Bag 3105, Hamilton, 3204, New Zealand
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- Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya, Yokohama, 240-8501, Japan
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- Department of Sustainable Crop Production (DI.PRO.VE.S.), Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
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- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Sydney, NSW, 2751, Australia
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- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus del Rio San Pedro, 11510 Puerto Real, Cádiz, Spain
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- Laboratorio de Ecología, Dept. Ecología y Recursos Naturales, Facultad de Cienicas, UNAM, Ave. Universidad 3000, Copilco, Coyoacán, 04510 CDMX, Mexico
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- Department of Animal Ecology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, 37073, Germany
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- Muséum National d'Histoire Naturelle, Department Adaptations du Vivant, UMR MECADEV, 4 avenue du Petit-Château, 91800, Brunoy, France
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- Department of zoology and ecology, Institute of Biology and Chemistry, Moscow Pedagogical State University, Kibalchicha 6 B.3, Moscow, 129164, Russia
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- Natural History Museum Vienna, 1. Zoology, Burgring 7, 1010, Vienna, Austria
- University of Natural Resources and Life Sciences, Department of Integrative Biology and Biodiversity Research, Institute of Zoology, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
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- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
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- Forest Research Institute of the Karelian Research Centre of the Russian Academy of Sciences11 Pushkinskaya St, 185910, Petrozavodsk, Karelia, Russia
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- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
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- Institute of Biology of Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, Moscow, Russia
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- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, Biology Building, University Campus, P.O.119, 54124, Thessaloniki, Greece
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- Department of Plant and Soil Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
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| | - Zhijing Xie
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- Laboratoire de Biosystématique et Ecologie des Arthropodes, Faculté des Sciences de la Nature et de la Vie, Université Frères Mentouri Constantine 1, 25000, Constantine, Algeria
| | | | - Osmar Klauberg-Filho
- Department of Soil Science, Centre for Agriculture and Veterinary Science, Santa Catarina State University (UDESC-Lages), Lages, SC, Brazil
| | - Stefan Scheu
- Department of Animal Ecology, Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, 37073, Germany
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2
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Bonin A, Guerrieri A, Ficetola GF. Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies. Mol Ecol Resour 2023; 23:368-381. [PMID: 36052659 DOI: 10.1111/1755-0998.13709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 08/08/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023]
Abstract
Clustering approaches are pivotal to handle the many sequence variants obtained in DNA metabarcoding data sets, and therefore they have become a key step of metabarcoding analysis pipelines. Clustering often relies on a sequence similarity threshold to gather sequences into molecular operational taxonomic units (MOTUs), each of which ideally represents a homogeneous taxonomic entity (e.g., a species or a genus). However, the choice of the clustering threshold is rarely justified, and its impact on MOTU over-splitting or over-merging even less tested. Here, we evaluated clustering threshold values for several metabarcoding markers under different criteria: limitation of MOTU over-merging, limitation of MOTU over-splitting, and trade-off between over-merging and over-splitting. We extracted sequences from a public database for nine markers, ranging from generalist markers targeting Bacteria or Eukaryota, to more specific markers targeting a class or a subclass (e.g., Insecta, Oligochaeta). Based on the distributions of pairwise sequence similarities within species and within genera, and on the rates of over-splitting and over-merging across different clustering thresholds, we were able to propose threshold values minimizing the risk of over-splitting, that of over-merging, or offering a trade-off between the two risks. For generalist markers, high similarity thresholds (0.96-0.99) are generally appropriate, while more specific markers require lower values (0.85-0.96). These results do not support the use of a fixed clustering threshold. Instead, we advocate careful examination of the most appropriate threshold based on the research objectives, the potential costs of over-splitting and over-merging, and the features of the studied markers.
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Affiliation(s)
- Aurélie Bonin
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,Argaly, Bâtiment Clean space, Sainte-Hélène-du-Lac, France
| | - Alessia Guerrieri
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France
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3
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Striuchkova A, Malykh I, Potapov M, Kuznetsova N. Sympatry of genetic lineages of Parisotomanotabilis s. l. (Collembola, Isotomidae) in the East European Plain. Zookeys 2022; 1137:1-15. [PMID: 36760483 PMCID: PMC9836473 DOI: 10.3897/zookeys.1137.95769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Parisotomanotabilis (Schaeffer, 1896) is one of the most abundant eurytopic species of springtails in temperate regions of the northern hemisphere, and is often used as a model species for studies on the genetics of soil microarthropod populations. Six genetic lineages (L0, L1, L2, L3, L4-Saltzwedel, L4-Hebert) are known which are distributed mainly parapatrically in Western and Central Europe. Individuals of P.notabilis from 21 locations on the East European Plain were analyzed. Three genetic lineages were found: L1, L2, L4-Hebert. In contrast to Western and Central Europe, the coexistence of two or three lineages was revealed in about half of the locations on the East European Plain. The most diverse genetic composition of P.notabilis populations was noted in natural forests and slightly disturbed habitats, while the least diverse was in places with a high anthropogenic influence.
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Affiliation(s)
- Anastasia Striuchkova
- Department of Zoology and Ecology, Institute of Biology and Chemistry, Moscow State Pedagogical University, Moscow, RussiaMoscow State Pedagogical UniversityMoscowRussia
| | - Irina Malykh
- Department of Zoology and Ecology, Institute of Biology and Chemistry, Moscow State Pedagogical University, Moscow, RussiaMoscow State Pedagogical UniversityMoscowRussia
| | - Mikhail Potapov
- Department of Zoology and Ecology, Institute of Biology and Chemistry, Moscow State Pedagogical University, Moscow, RussiaMoscow State Pedagogical UniversityMoscowRussia
| | - Nataliya Kuznetsova
- Department of Zoology and Ecology, Institute of Biology and Chemistry, Moscow State Pedagogical University, Moscow, RussiaMoscow State Pedagogical UniversityMoscowRussia
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4
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Specific and Intraspecific Diversity of Symphypleona and Neelipleona (Hexapoda: Collembola) in Southern High Appalachia (USA). DIVERSITY 2022. [DOI: 10.3390/d14100847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Collembola, commonly known as springtails, are important detritivores, abundant in leaf litter and soil globally. Springtails are wingless hexapods with many North American species having wide distributions ranging from as far as Alaska to Mexico. Here, we analyze the occurrence and intraspecific diversity of springtails with a globular body shape (Symphypleona and Neelipleona), in southern high Appalachia, a significant biodiversity hotspot. The peaks of high Appalachia represent ‘sky islands’ due to their physical isolation, and they host numerous endemic species in other taxa. We surveyed globular Collembola through COI metabarcoding, assessing geographic and genetic diversity across localities and species. Intraspecific diversity in globular Collembola was extremely high, suggesting that considerable cryptic speciation has occurred. While we were able to associate morphospecies with described species in most of the major families in the region (Dicyrtomidae, Katiannidae, Sminthuridae, and Sminthurididae), other families (Neelidae, and Arrhopalitidae) are in more pressing need of taxonomic revision before species identities can be confirmed. Due to poor representation in databases, and high intraspecific variability, no identifications were accomplished through comparison with available DNA barcodes.
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5
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Khan MU, Andleeb S, Khan MF, Mustafa RG. Molecular Characterization and Phylogenetic Analysis of Earthworm Species Collected from Different Soil Habitats of Poonch Division Azad Jammu and Kashmir Pakistan. J Oleo Sci 2022; 71:1349-1361. [PMID: 36047242 DOI: 10.5650/jos.ess21450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study aims to analyze molecular characterization and phylogenetic analysis of earthworm species collected from different soil habitats of Poonch division Azad Kashmir Pakistan by using CO1 gene partial sequencing methodology. Samples gathered randomly from 18 study sites (127 localities) by digging and hand sorting methods were preserved in pure ethanol at -20°C. The modified CTAB (Cetyltrimethyl ammonium bromide) method extracted high quality DNA from region of representative earthworm's caudal region. This extracted DNA was used to amplify the 700 bp partial region of the cytochrome oxidase I (COI) gene with LCO1490 and HCO2198 universal primers. All of the obtained amplified gene sequences were aligned, edited and analyzed using MEGA X software to characterize different species of earthworms. Thirty-eight (38) Barcoding sequences belonging to 11 different strains of earthworms were successfully generated. Their phylogenetic analysis revealed that 7 Barcoding sequences gave maximum similarity with the available online database, while the rest of the 4 sequences gave lower similarity than the maximum threshold level. The collected DNA barcode sequences were also clustered together by the maximum likelihood method and the resultant phylogenetic tree revealed they belong to different family lineages. Moreover the identified earthworm species have a close evolutionary link with the earthworm fauna of south and central Asia instead of Europe, which might be due to similar climate of both regions.
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Affiliation(s)
| | - Saiqa Andleeb
- Department of Zoology, University of Azad Jammu and Kashmir
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6
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Luan YX, Cui Y, Chen WJ, Jin JF, Liu AM, Huang CW, Potapov M, Bu Y, Zhan S, Zhang F, Li S. High-quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (Collembola). Mol Ecol Resour 2022; 23:273-293. [PMID: 35962787 PMCID: PMC10087712 DOI: 10.1111/1755-0998.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
The collembolan Folsomia candida Willem, 1902, is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal "standard" because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we obtained two high-quality chromosome-level genomes of F. candida, for a parthenogenetic strain (named as FCDK, 219.08 Mb, 25,139 protein-coding genes) and a sexual strain (named as FCSH, 153.09 Mb, 21,609 protein-coding genes), reannotated the genome of the parthenogenetic strain reported by Faddeeva-Vakhrusheva et al. in 2017 (named as FCBL, 221.7 Mb, 25,980 protein-coding genes), and conducted comparative genomic analyses of three strains. High genome similarities between FCDK and FCBL on synteny, genome architecture, mitochondrial and nuclear gene sequences support they are conspecific. The seven chromosomes of FCDK are each 25-54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large-scale inversions and translocations but no whole-genome duplication. The strain-specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to the broader environmental adaptation of parthenogenetic strains. In addition, FCDK has fewer strain-specific microRNAs than FCSH, and their mitochondrial and nuclear genes have diverged greatly. In conclusion, FCDK/FCBL and FCSH have accumulated independent genetic changes and evolved into distinct species since 10 Mya. Our work provides important genomic resources for studying the mechanisms of rapidly cryptic speciation and soil arthropod adaptation to soil ecosystems.
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Affiliation(s)
- Yun-Xia Luan
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yingying Cui
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | | | - Jian-Feng Jin
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ai-Min Liu
- Department of Pomology, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Cheng-Wang Huang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Yun Bu
- Natural History Research Center, Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai, China
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou, China
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7
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JANION-SCHEEPERS CHARLENE, DEHARVENG LOUIS. A shocking-red new species of Setanodosa Salmon, 1942 (Collembola: Brachystomellidae) from South Africa. Zootaxa 2022; 5154:483-495. [DOI: 10.11646/zootaxa.5154.4.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Indexed: 11/04/2022]
Abstract
A new species of Setanodosa, S. jacquesi sp. nov. is described from the Western Cape (South Africa). It differs from other species of the genus by its unique shocking red pigmentation, the number of vesicles in the post antennal organ, and the number of clavate tenent hairs on the tibiotarsi. A comparative table of the world Setanodosa and a key of Brachystomellidae species known from South Africa are provided. DNA barcoding results are provided for several Brachystomellidae species from South Africa, Australia and the sub-Antarctic to support our findings. It shows that a species provisionally identified as Brachystomella cf. platensis is unambiguously present in both South Africa and Australia.
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8
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Ross GM, Berg MP, Salmon S, Nielsen UN. Phylogenies of traits and functions in soil invertebrate assemblages. AUSTRAL ECOL 2022. [DOI: 10.1111/aec.13153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Giles M. Ross
- Hawkesbury Institute for the Environment Western Sydney University Locked Bag 1797 Penrith NSW 2751 Australia
| | - Matty P. Berg
- Department of Ecological Science Vrije Universiteit Amsterdam, De Boelelaan 1085 Amsterdam HV 1081 The Netherlands
- Community and Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences University of Groningen Nijenborgh 7 Groningen AG 9747 The Netherlands
| | - Sandrine Salmon
- Department of Living Adaptations UMR 7179 MECADEV, Muséum National d'Histoire Naturelle 1 Avenue du Petit Château, Brunoy Paris 91800 France
| | - Uffe N. Nielsen
- Hawkesbury Institute for the Environment Western Sydney University Locked Bag 1797 Penrith NSW 2751 Australia
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9
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Paiva DNA, Perdiz RDO, Almeida TE. Using near-infrared spectroscopy to discriminate closely related species: a case study of neotropical ferns. JOURNAL OF PLANT RESEARCH 2021; 134:509-520. [PMID: 33826013 DOI: 10.1007/s10265-021-01265-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/07/2021] [Indexed: 05/26/2023]
Abstract
Identifying plant species requires considerable knowledge and can be difficult without complete specimens. Fourier-transform near-infrared spectroscopy (FT-NIR) is an effective technique for discriminating plant species, especially angiosperms. However, its efficacy has never been tested on ferns. Here we tested the accuracy of FT-NIR at discriminating species of the genus Microgramma. We obtained 16 spectral readings per individual from the adaxial and abaxial surfaces of 100 specimens belonging to 13 species. The analyses included all 1557 spectral variables. We tested different datasets (adaxial + abaxial, adaxial, and abaxial) to compare the correct identification of species through the construction of discriminant models (Linear discriminant analysis and partial least squares discriminant analysis) and cross-validation techniques (leave-one-out, K-fold). All analyses recovered an overall high percentage (> 90%) of correct predictions of specimen identifications for all datasets, regardless of the model or cross-validation used. On average, there was > 95% accuracy when using partial least squares discriminant analysis and both cross-validations. Our results show the high predictive power of FT-NIR at correctly discriminating fern species when using leaves of dried herbarium specimens. The technique is sensitive enough to reflect species delimitation problems and possible hybridization, and it has the potential of helping better delimit and identify fern species.
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Affiliation(s)
- Darlem Nikerlly Amaral Paiva
- Universidade Federal do Oeste do Pará, Programa de Pós-graduação em Biodiversidade, Rua Vera Paz, s/n (Unidade Tapajós) Bairro Salé, Santarém, PA, 68040-255, Brazil.
| | - Ricardo de Oliveira Perdiz
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-graduação em Ciências Biológicas, Avenida André Araújo, Manaus, AM, 293669060-001, Brazil
| | - Thaís Elias Almeida
- Universidade Federal do Oeste do Pará, Programa de Pós-graduação em Biodiversidade, Rua Vera Paz, s/n (Unidade Tapajós) Bairro Salé, Santarém, PA, 68040-255, Brazil
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10
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Stevens MI, Greenslade P, D’Haese CA. Species diversity in
Friesea
(Neanuridae) reveals similar biogeographic patterns among Antarctic Collembola. ZOOL SCR 2021. [DOI: 10.1111/zsc.12490] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Mark I. Stevens
- Biological and Earth Sciences South Australian Museum Adelaide SA Australia
- School of Biological Sciences University of Adelaide Adelaide SA Australia
| | - Penelope Greenslade
- Environmental Management School of Science, Psychology and Sport Federation University Ballarat VIC Australia
- School of Biology Australian National University Canberra ACT Australia
| | - Cyrille A. D’Haese
- MECADEV UMR 7179 CNRS MNHN Muséum national d'Histoire naturelle Paris France
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11
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Skarżyński D, Smolis A, Kováč Ľ, Porco D. A new European species of Ceratophysella (Collembola, Hypogastruridae) revealed by morphological data and DNA barcodes. Zookeys 2021; 1021:1-18. [PMID: 33716539 PMCID: PMC7940320 DOI: 10.3897/zookeys.1021.63147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/26/2021] [Indexed: 12/05/2022] Open
Abstract
A new species, Ceratophysellastachi, from Denmark, Germany, Luxembourg, Norway, Poland, and Ukraine is described based on morphological data and DNA barcodes. It belongs to a small European group of species with type B chaetotaxy and strong tegumentary granulation with distinct fields of coarse granules: C.granulata Stach, 1949, C.lawrencei (Gisin, 1963), C.neomeridionalis (Nosek & Červek, 1970), C.scotica (Carpenter & Evans, 1899), and C.silvatica Rusek, 1964. It differs from all of them in the chaetotaxy of lateral parts of thoracic terga II–III (setae m6 present and one additional seta outside lateral sensillum m7 present or absent) that is exceptional within the whole C.armata-group. Notes on closely related species C.granulata are also given.
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Affiliation(s)
- Dariusz Skarżyński
- Institute of Environmental Biology, Department of Invertebrate Biology, Evolution and Conservation, University of Wrocław, Przybyszewskiego 65, 51-148, Wrocław, Poland University of Wrocław Wrocław Poland
| | - Adrian Smolis
- Institute of Environmental Biology, Department of Invertebrate Biology, Evolution and Conservation, University of Wrocław, Przybyszewskiego 65, 51-148, Wrocław, Poland University of Wrocław Wrocław Poland
| | - Ľubomír Kováč
- Department of Zoology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Moyzesova 11, 041 54, Košice, Slovakia Pavol Jozef Šafárik University Košice Slovakia
| | - David Porco
- Musée National d'Histoire Naturelle, 25 rue Munster, 2160, Luxembourg, Luxembourg Musée National d'Histoire Naturelle Luxembourg Luxembourg
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12
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Webster HJ, Emami-Khoyi A, van Dyk JC, Teske PR, Jansen van Vuuren B. Environmental DNA Metabarcoding as a Means of Estimating Species Diversity in an Urban Aquatic Ecosystem. Animals (Basel) 2020; 10:E2064. [PMID: 33171859 PMCID: PMC7695161 DOI: 10.3390/ani10112064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022] Open
Abstract
Adaptation to environments that are changing as a result of human activities is critical to species' survival. A large number of species are adapting to, and even thriving in, urban green spaces, but this diversity remains largely undocumented. In the current study, we explored the potential of environmental DNA (eDNA) to document species diversity in one of the largest green spaces in Johannesburg, South Africa. Using a novel metabarcoding approach that assembles short DNA fragments suitable for massively parallel sequencing platforms to the approximate standard ~710 bp COI barcoding fragment, we document the presence of 26 phyla, 52 classes, 134 orders, 289 families, 380 genera and 522 known species from the study site. Our results highlight the critical role that urban areas play in protecting the world's declining biodiversity.
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Affiliation(s)
- Heather J. Webster
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, Gauteng 2006, South Africa; (H.J.W.); (A.E.-K.); (P.R.T.)
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, Gauteng 2006, South Africa; (H.J.W.); (A.E.-K.); (P.R.T.)
| | - Jacobus C. van Dyk
- Department of Zoology, University of Johannesburg, Auckland Park, Gauteng 2006, South Africa;
| | - Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, Gauteng 2006, South Africa; (H.J.W.); (A.E.-K.); (P.R.T.)
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, Gauteng 2006, South Africa; (H.J.W.); (A.E.-K.); (P.R.T.)
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13
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Katz AD. Inferring Evolutionary Timescales without Independent Timing Information: An Assessment of "Universal" Insect Rates to Calibrate a Collembola (Hexapoda) Molecular Clock. Genes (Basel) 2020; 11:genes11101172. [PMID: 33036318 PMCID: PMC7600954 DOI: 10.3390/genes11101172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 01/04/2023] Open
Abstract
Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but the assumption of rate constancy is rarely evaluated prior to using secondary rate calibrations. Here I evaluate whether an insect mitochondrial DNA clock is appropriate for estimating timescales in Collembola—a group of insect-like arthropods characterized by high levels of cryptic diversity. Relative rates of substitution in cytochrome oxidase subunit 1 (COI) were inferred via Bayesian analysis across a topologically constrained Hexapod phylogeny using a relaxed molecular clock model. Rates for Collembola did not differ significantly from the average rate or from the rates estimated for most other groups (25 of 30), suggesting that (1) their apparent cryptic diversity cannot be explained by accelerated rates of molecular evolution and (2) clocks calibrated using “universal” insect rates may be appropriate for estimating evolutionary timescales in this group. However, of the 31 groups investigated, 10 had rates that deviated significantly from the average (6 higher, 4 lower), underscoring the need for caution and careful consideration when applying secondary insect rate calibrations. Lastly, this study exemplifies a relatively simple approach for evaluating rate constancy within a taxonomic group to determine whether the use of secondary rates are appropriate for molecular clock calibrations.
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Affiliation(s)
- Aron D. Katz
- Engineer Research Development Center, 2902 Newmark Dr., Champaign, IL 61826, USA;
- Department of Entomology, University of Illinois at Urbana-Champaign, 320 Morrill Hall, 505 South Goodwin Ave., Urbana, IL 61801, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
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14
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Ecosystem Birth Near Melting Glaciers: A Review on the Pioneer Role of Ground-Dwelling Arthropods. INSECTS 2020; 11:insects11090644. [PMID: 32961739 PMCID: PMC7564799 DOI: 10.3390/insects11090644] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 11/26/2022]
Abstract
Simple Summary Due to climate change, glaciers are retreating. On newly deglaciated ground, ecosystems gradually evolve through the process of primary succession. This gives scientists a unique opportunity to study how a new ecosystem is born. During the first few years, before plants establish, the barren ground of sand, silt, and stones close to the ice edge is conquered by a rich variety of insects, spiders, and other small animals. Many of these are predators and their prey are either transported by air or produced in situ. The real pioneers are, however, wingless springtails that graze on biofilm containing algae or cyanobacteria. Studies of two pioneer food webs showed differences in structure and function. In the one case, beetles, spiders, and harvestmen exhibit preferences for locally produced springtails, while predators in the other example relied mainly upon midges hatching from young ponds. Pioneer communities contain a mixture of generalists and specialists. Species composition vary under different climatic and geographical conditions, depending on the available candidate species in the surrounding areas. This study illustrates flexibility in the early phase of primary succession. Certain cold loving beetles, spiders, and springtails may become extinct if glaciers disappear completely. Abstract As glaciers retreat, their forelands represent “natural laboratories” for the study of primary succession. This review describes how certain arthropods conquer pristine ground and develop food webs before the establishment of vascular plants. Based on soil samples, pitfall traps, fallout and sticky traps, gut content studies, and some unpublished data, we compare early arthropod succession on glacial forelands of northern Europe (Iceland, Norway including Svalbard, and Sweden) and of the Alps (Austria, Italy). While macroarthropod predators like ground beetles (Coleoptera: Carabidae), harvestmen (Arachnida: Opiliones), and spiders (Arachnida: Araneae) have usually been considered as pioneers, assumed to feed on airborne prey, this review explains a different pattern. Here, we highlight that springtails (Collembola), probably feeding on biofilm made up of algae or cyanobacteria, are super-pioneers, even at high altitudes and under arctic conditions. We also point out that macroarthropod predators can use locally available prey, such as springtails or non-biting midges (Diptera: Chironomidae). Pioneer arthropod communities vary under different biogeographical and climatic conditions. Two pioneer food webs, from northern Europe and the Alps, respectively, differed in structure and function. However, certain genera and orders were common to both. Generalists and specialists live together in a pioneer community. Cold-adapted specialists are threatened by glacier melting.
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15
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Guzik MT, Stevens MI, Cooper SJB, Humphreys WF, Austin AD. Extreme genetic diversity among springtails (Collembola) in subterranean calcretes of arid Australia. Genome 2020; 64:181-195. [PMID: 32552081 DOI: 10.1139/gen-2019-0199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The subterranean islands hypothesis for calcretes of the Yilgarn region in Western Australia applies to many stygobitic (subterranean-aquatic) species that are "trapped" evolutionarily within isolated aquifers due to their aquatic lifestyles. In contrast, little is known about the distribution of terrestrial-subterranean invertebrates associated with the calcretes. We used subterranean Collembola from the Yilgarn calcretes to test the hypothesis that troglobitic species, those inhabiting the subterranean unsaturated (non-aquatic) zone of calcretes, are also restricted in their distribution and represent reciprocally monophyletic and endemic lineages. We used the barcoding fragment of the mtDNA cytochrome c oxidase subunit 1 (COI) gene from 183 individuals to reconstruct the phylogenetic history of the genus Pseudosinella Schäffer (Collembola, Lepidocyrtidae) from 10 calcretes in the Yilgarn. These calcretes represent less than 5% of the total possible calcretes in this region, yet we show that their diversity for subterranean Collembola comprises a minimum of 25 new species. Regionally, multiple levels of diversity exist in Pseudosinella, indicative of a complex evolutionary history for this genus in the Yilgarn. These species have probably been impacted by climatic oscillations, facilitating their dispersal across the landscape. The results represent a small proportion of the undiscovered diversity in Australia's arid zone.
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Affiliation(s)
- Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia
| | - Mark I Stevens
- Biological and Earth Sciences, South Australian Museum, SA 5000, Australia.,University of South Australia, Clinical and Health Sciences, SA 5000, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - William F Humphreys
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia, Affiliate.,School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
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16
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Sánchez-Vialas A, García-París M, Ruiz JL, Recuero E. Patterns of morphological diversification in giant Berberomeloe blister beetles (Coleoptera: Meloidae) reveal an unexpected taxonomic diversity concordant with mtDNA phylogenetic structure. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz164] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
AbstractDelimiting species boundaries is a complex challenge usually hindered by overlooked morphological diversification or misinterpretation of geographically structured phenotypic variability. Independent molecular data are extremely useful to characterize and understand such morphological diversity. Morphological and molecular variability of the non-phoretic and apterous, widely distributed, giant blister beetles of the genus Berberomeloe, were investigated within and between lineages across most of the distributional range of the genus. We used two mtDNA gene fragments to characterize genetic variability and to produce a time-calibrated phylogeny of the genus. Our results reveal several mitochondrial lineages, allopatrically, parapatrically and sympatrically distributed. Most clades are not distinguishable between each other based on morphometrics. However, no morphometric overlap is observed between two closely related clades, one of them occurring in sympatry with a distantly congeneric species (B. insignis), suggesting that sympatry could trigger morphological diversification. Although most species share a morphometric space, they can be morphologically identified by a combination of easily observed characteristic qualitative features. Based on the concordance between mtDNA clades and morphological units, we describe six new species of Berberomeloe (B. castuo sp. nov., B. comunero sp. nov., B. indalo sp. nov, B. yebli sp. nov., B. payoyo sp. nov. and B. tenebrosus sp. nov.), revalidate two taxa (B. maculifrons comb. nov. and B. laevigatus comb. nov.) and redefine B. majalis.
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Affiliation(s)
| | | | | | - Ernesto Recuero
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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17
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Godeiro NN, Pacheco G, Liu S, Gioia Cipola N, Berbel‐Filho WM, Zhang F, Gilbert MTP, Bellini BC. Phylogeny of Neotropical Seirinae (Collembola, Entomobryidae) based on mitochondrial genomes. ZOOL SCR 2020. [DOI: 10.1111/zsc.12408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Nerivânia Nunes Godeiro
- Department of Botany and Zoology Biosciences Center Federal University of Rio Grande do Norte Natal Brazil
- Department of Entomology College of Plant Protection Nanjing Agricultural University Nanjing China
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - George Pacheco
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Shanlin Liu
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Beijing Advanced Innovation Center for Food Nutrition and Human Health College of Plant Protection China Agricultural University Beijing China
| | - Nikolas Gioia Cipola
- Laboratório de Sistemática e Ecologia de Invertebrados do Solo Instituto Nacional de Pesquisas da Amazônia—INPA CPEN Manaus Brazil
| | | | - Feng Zhang
- Department of Entomology College of Plant Protection Nanjing Agricultural University Nanjing China
| | | | - Bruno Cavalcante Bellini
- Department of Botany and Zoology Biosciences Center Federal University of Rio Grande do Norte Natal Brazil
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18
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Parimuchová A, Žurovcová M, Papáč V, Kováč Ľ. Subterranean Deuteraphorura Absolon, 1901, (Hexapoda, Collembola) of the Western Carpathians - Troglomorphy at the northern distributional limit in Europe. PLoS One 2020; 15:e0226966. [PMID: 31940408 PMCID: PMC6961878 DOI: 10.1371/journal.pone.0226966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/08/2019] [Indexed: 11/18/2022] Open
Abstract
An integrative approach employing molecular, morphological and geographical data were applied to species delimitation among Deuteraphorura congeners occupying caves of the Western Carpathian Mts. A new species of Deuteraphorura from the Western Carpathians is described. D. muranensis sp. nov. belongs among species with 4 pso at the hind margin of the head and possesses highly troglomorphic features. It is conspicuous with its distinctly elongated claws and long, hair-like body chaetae. The status of the new species was confirmed by DNA barcoding based on the mitochondrial COI marker. Populations of D. kratochvili (Nosek, 1963), the most widespread species, were studied in detail. Both ABGD and PTP analyses brought results congruent with geography, i.e. the molecular and geographic distance of the populations were positively correlated. However, some molecular separation based on pairwise distance and the number of substitutions was indicated within two of the studied populations. Despite the indistinct morphological differences, the tested populations were well isolated both geographically and genetically, which indicates that each studied population may represent a cryptic species. The troglomorphy of cave Collembola at the northernmost border of the distribution of cave-adapted species in the Europe is discussed. It is clear that the level of troglomorphy is closely associated with conditions of the microhabitat occupied by the individual subterranean species. The results of our study enhance the importance of the Western Carpathians regarding the diversity pattern of obligate cave species in Europe.
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Affiliation(s)
- Andrea Parimuchová
- Department of Zoology, Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University, Košice, Slovakia
- * E-mail:
| | - Martina Žurovcová
- Institute of Entomology, Biology Centre AS CR v.v.i., České Budějovice, Czech Republic
| | - Vladimír Papáč
- State Nature Conservancy of the Slovak Republic, Slovak Caves Administration, Cave Care Department, Rimavská Sobota, Slovakia
| | - Ľubomír Kováč
- Department of Zoology, Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University, Košice, Slovakia
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19
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Zhang B, Chen TW, Mateos E, Scheu S, Schaefer I. DNA-based approaches uncover cryptic diversity in the European Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae). INVERTEBR SYST 2019. [DOI: 10.1071/is18068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA sequence data and phylogenies are useful tools for species delimitation, especially in taxa comprising cryptic species. The Lepidocyrtus lanuginosus species group (Collembola: Entomobryidae) comprises three morphospecies and distinct cryptic species. We applied three DNA-based methods to delimit species boundaries in the L. lanuginosus species group across central and southern Europe. Using cytochrome c oxidase subunit I and II, we identified gaps of genetic distances that indicate species boundaries and found 10 and 9 distinct genetic lineages in L. cyaneus and L. lanuginosus, respectively. The nuclear gene elongation factor 1-α delimited 89% of the lineages but 28S rDNA (D1–2 domain) was too conserved for this purpose. The phylogenetic trees showed that L. cyaneus and L. lanuginosus are polyphyletic, suggesting that body colour is insufficient for delimiting species in the L. lanuginosus species group. Our study challenges the current morphology-based species delimitation in the L. lanuginosus species group and suggests that molecular approaches are needed for fast and accurate determination of Collembola species in both taxonomic and ecological studies. Overall, the results suggest that wide geographic sampling combined with molecular phylogenetic approaches is needed to delimit species and to understand the full range of cryptic diversity in Collembola.
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20
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Grund R, Stolarski A, Stevens M. Rediscovery of Synemon selene (Lepidoptera: Castniidae) in the mid-north of South Australia. T ROY SOC SOUTH AUST 2018. [DOI: 10.1080/03721426.2018.1532270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Roger Grund
- South Australian Museum, Adelaide, Australia
| | | | - Mark Stevens
- South Australian Museum, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
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21
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Sun X, Bedos A, Deharveng L. Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae). PeerJ 2018; 6:e5021. [PMID: 29938135 PMCID: PMC6011825 DOI: 10.7717/peerj.5021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/29/2018] [Indexed: 01/30/2023] Open
Abstract
Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic species T. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life.
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Affiliation(s)
- Xin Sun
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Anne Bedos
- Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Museum national d'Histoire naturelle, Paris, France
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Museum national d'Histoire naturelle, Paris, France
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22
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Song C, Lin XL, Wang Q, Wang XH. DNA barcodes successfully delimit morphospecies in a superdiverse insect genus. ZOOL SCR 2018. [DOI: 10.1111/zsc.12284] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Chao Song
- College of Life Sciences; Nankai University; Tianjin China
| | - Xiao-Long Lin
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
| | - Qian Wang
- Tianjin key Laboratory of Aqua-Ecology & Aquaculture; Fisheries of College; Tianjin Agricultural University; Tianjin China
| | - Xin-Hua Wang
- College of Life Sciences; Nankai University; Tianjin China
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23
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Zhang F, Jantarit S, Nilsai A, Stevens MI, Ding Y, Satasook C. Species delimitation in the morphologically conservedCoecobrya(Collembola: Entomobryidae): A case study integrating morphology and molecular traits to advance current taxonomy. ZOOL SCR 2018. [DOI: 10.1111/zsc.12279] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Feng Zhang
- Department of Entomology; College of Plant Protection; Nanjing Agricultural University; Nanjing China
| | - Sopark Jantarit
- Excellence Center for Biodiversity of Peninsular Thailand; Faculty of Science; Prince of Songkla University; Hat Yai, Songkhla Thailand
- Princess Maha Chakri Sirindhorn Natural History Museum; Faculty of Science; Prince of Songkla University; Hat Yai, Songkhla Thailand
| | - Areeruk Nilsai
- Department of Biology; Faculty of Science; Prince of Songkla University; Hat Yai, Songkhla Thailand
| | - Mark I. Stevens
- South Australian Museum; Adelaide SA Australia
- School of Pharmacy and Medical Sciences; University of South Australia; Adelaide SA Australia
| | - Yinhuan Ding
- Department of Entomology; College of Plant Protection; Nanjing Agricultural University; Nanjing China
| | - Chutamas Satasook
- Princess Maha Chakri Sirindhorn Natural History Museum; Faculty of Science; Prince of Songkla University; Hat Yai, Songkhla Thailand
- Department of Biology; Faculty of Science; Prince of Songkla University; Hat Yai, Songkhla Thailand
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24
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Lukić M, Delić T, Zagmajster M, Deharveng L. Setting a morphological framework for the genus Verhoeffiella (Collembola, Entomobryidae) for describing new troglomorphic species from the Dinaric karst (Western Balkans). INVERTEBR SYST 2018. [DOI: 10.1071/is17088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recent research of cave Collembola in Dinaric karst resulted in discovery of high regional diversification of the genus Verhoeffiella Absolon, 1900. The most striking feature of Verhoeffiella species is the high number of troglomorphic traits, which makes this genus a good model for studying morphological diversification and adaptation in subterranean environments. We explore the expression of various morphological modifications assumed to be linked to subterranean life, through detailed descriptions of four new species and redescription of two species including the type species of the genus. Species delimitations are confirmed by single locus (cytochrome c oxidase I) tree-based (Poisson tree processes) and distance-based (automatic barcode gap discovery) species delimitation approaches, which gave identical results. Morphological changes classically considered as adaptive for cave life and new, potentially troglomorphic characters for Collembola are discussed. For several of these characters, high morphological diversity between species and large decoupling in the development of different traits within species are recorded. Such a decoupling is also illustrated in the finding of two cases of Verhoeffiella species pairs at different levels of troglomorphy living in syntopy. We further provide several new differential characters of specific and possibly generic or supra-generic importance and describe for the first time among Collembola an original ‘distal organ’ on Ant. IV.
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25
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Zhang F, Yu D, Stevens MI, Ding Y. Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae). INVERTEBR SYST 2018. [DOI: 10.1071/is18019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.
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26
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Affiliation(s)
- Jean-Marc Thibaud
- ISYEB, UMR 7205 CNRS, MNHN, UPMC, EPHE, MECADEV, UMR 7179 CNRS, Muséum national d'Histoire naturelle, Sorbonne Universités, case postale 50, 57 rue Cuvier, F-75231 Paris cedex 05 (France)
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27
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Sun X, Zhang F, Ding Y, Davies TW, Li Y, Wu D. Delimiting species of Protaphorura (Collembola: Onychiuridae): integrative evidence based on morphology, DNA sequences and geography. Sci Rep 2017; 7:8261. [PMID: 28811535 PMCID: PMC5557941 DOI: 10.1038/s41598-017-08381-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 07/12/2017] [Indexed: 12/15/2022] Open
Abstract
Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences. Twenty-two molecular putative species were consistently recovered across molecular and geographical analyses. Geographic criteria were was proved to be an efficient delimitation method for onychiurids. Further morphological examination, based on the combination of the number of pseudocelli, parapseudocelli and ventral mesothoracic chaetae, confirmed 18 taxa of 22 molecular units, with six of them described as new species. These characters were found to be of high taxonomical value. This study highlights the potential benefits of integrative taxonomy, particularly simultaneous use of molecular/geographical tools, as a powerful way of ascertaining the true diversity of the Onychiuridae. Our study also highlights that discovering new morphological characters remains central to achieving a full understanding of collembolan taxonomy.
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Affiliation(s)
- Xin Sun
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yinhuan Ding
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Thomas W Davies
- Centre for Geography, Environment and Society, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
| | - Donghui Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
- Key laboratory for vegetation ecology, ministry of education, Northeast Normal University, Changchun, 130117, China.
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
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28
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Phillips L, Janion-Scheepers C, Houghton M, Terauds A, Potapov M, Chown SL. Range expansion of two invasive springtails on sub-Antarctic Macquarie Island. Polar Biol 2017. [DOI: 10.1007/s00300-017-2129-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Cicconardi F, Borges PAV, Strasberg D, Oromí P, López H, Pérez-Delgado AJ, Casquet J, Caujapé-Castells J, Fernández-Palacios JM, Thébaud C, Emerson BC. MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species. Mol Ecol 2017; 26:3104-3115. [PMID: 28139037 DOI: 10.1111/mec.14037] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/12/2016] [Accepted: 12/24/2016] [Indexed: 11/26/2022]
Abstract
Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil-dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human-mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.
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Affiliation(s)
- Francesco Cicconardi
- Institute of Ecology, University of Innsbruck, Technikerstrasse 25, a-6020, Innsbruck, Austria
| | - Paulo A V Borges
- CE3C - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Departamento de Ciências Agrárias e Ambiente, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Dominique Strasberg
- UMR PVBMT, Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de La Réunion, 15 avenue René Cassin, CS 93002, 97 744, Saint Denis Cedex 9, Reunion Island, France
| | - Pedro Oromí
- Departamento de Biología Animal y Edafología y Geología, Universidad de La Laguna, C/Astrofísico Francisco Sánchez, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Heriberto López
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Antonio J Pérez-Delgado
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Juliane Casquet
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario 'Viera y Clavijo' - Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, 35017, Las Palmas de Gran Canaria, Spain
| | - José María Fernández-Palacios
- Island Ecology and Biogeography Research Group, Instituto de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Christophe Thébaud
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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30
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Saitoh S, Aoyama H, Fujii S, Sunagawa H, Nagahama H, Akutsu M, Shinzato N, Kaneko N, Nakamori T. A quantitative protocol for DNA metabarcoding of springtails (Collembola). Genome 2017; 59:705-23. [PMID: 27611697 DOI: 10.1139/gen-2015-0228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species). The two gene regions were then amplified using the selected primers, ligated with adapters for 454 technology, and sequenced. Examination of the natural community samples showed that 32 and 36 operational taxonomic units (defined at a 90% sequence similarity threshold) were recovered from the mtCOI and mt16S data, respectively, which were comparable to the results of the microscopic identification of 25 morphospecies. Further, sequence abundances for each collembolan species from the mtCOI and mt16S data of the mock communities, after normalization by using a species as the internal control, showed good correlation with the number of individuals in the samples (R = 0.91-0.99), although relative species abundances within a mock community sample estimated from sequences were skewed from community composition in terms of the number of individuals or biomass of the species. Thus, this protocol enables the comparison of collembolan communities in a quantitative manner by metabarcoding.
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Affiliation(s)
- Seikoh Saitoh
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Hiroaki Aoyama
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Saori Fujii
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
| | - Haruki Sunagawa
- c Okinawa Prefectural Agricultural Research Center, 820 Makabe, Itoman 901-0336, Japan
| | - Hideki Nagahama
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Masako Akutsu
- d Department of Electrical Engineering and Computer Science, School of Industrial and Welfare Engineering, Tokai University, Toroku 9-1-1, Higashi-ku, Kumamoto 862-8652, Japan
| | - Naoya Shinzato
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Nobuhiro Kaneko
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
| | - Taizo Nakamori
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
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Minor MA, Babenko AB, Ermilov SG. Oribatid mites (Acari: Oribatida) and springtails (Collembola) in alpine habitats of southern New Zealand. NEW ZEALAND JOURNAL OF ZOOLOGY 2016. [DOI: 10.1080/03014223.2016.1251950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Maria A. Minor
- Ecology Group, Institute of Agriculture and Environment, Massey University, New Zealand
| | - Anatoly B. Babenko
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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Raschmanová N, Žurovcová M, Kováč Ľ, Paučulová L, Šustr V, Jarošová A, Chundelová D. The cold-adapted population ofFolsomia manolachei(Hexapoda, Collembola) from a glaciated karst doline of Central Europe: evidence for a cryptic species? J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Natália Raschmanová
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Martina Žurovcová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Ľubomír Kováč
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Lenka Paučulová
- Institute of Biology and Ecology; Faculty of Science; P. J. Šafárik University; Košice Slovakia
| | - Vladimír Šustr
- Institute of Soil Biology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
| | - Andrea Jarošová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Daniela Chundelová
- Institute of Entomology; Biology Centre AS CR v. v. i.; České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
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33
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Bu Y, Ma Y, Luan YX. Paracerella Imadaté in China: the description of a new species and the analysis of genetic differences between populations (Protura, Acerentomata, Nipponentomidae). Zookeys 2016:1-11. [PMID: 27551203 PMCID: PMC4978016 DOI: 10.3897/zookeys.604.8737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/15/2016] [Indexed: 11/12/2022] Open
Abstract
The genus Paracerella Imadaté, 1980 is recorded from China for the first time, with the description of a new species, Paracerellasinensissp. n.Paracerellasinensis is characterized by four pairs of A-setae on tergite I, the presence of setae Pc and P3a on tergite VII, eight A-setae on tergite VIII, the presence of seta Pc on both sternites VI and VII, and 4/2 setae on sternite VIII, which are different from all other members of the genus. The key to the four species of the genus is updated. In addition, DNA barcodes of four populations are sequenced and their genetic differences are analyzed.
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Affiliation(s)
- Yun Bu
- Natural History Research Center, Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai, 200041, China; Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Yao Ma
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China; University of Chinese Academy of Sciences, Beijing, China
| | - Yun-Xia Luan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
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34
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von Saltzwedel H, Scheu S, Schaefer I. Founder events and pre-glacial divergences shape the genetic structure of European Collembola species. BMC Evol Biol 2016; 16:148. [PMID: 27423184 PMCID: PMC4947257 DOI: 10.1186/s12862-016-0719-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 07/04/2016] [Indexed: 11/19/2022] Open
Abstract
Background Climate oscillations in the Cenozoic reduced species richness and genetic diversity of terrestrial and aquatic animals and plants in central and northern Europe. The most abundant arthropods in temperate soils are Collembola that live in almost any soil-related habitat. Extant species show little morphological variation to Eocene fossils, suggesting persistence of species in stable habitats for millions of years. Collembola are able to evade adverse climatic conditions by moving into deeper soil layers and are tolerant to frost and draught. If these adaptations sufficed for surviving glacial periods remains open and needs to be investigated in a phylogeographic context, i.e. investigating spatial structure on molecular level. We investigated the molecular variation of three common species of Collembola at a pan-European scale to identify glacial refuges and post-glacial colonization patterns with three genetic markers. Results All genes revealed remarkable genetic structure between but not within populations, suggesting density dependent processes for establishment of populations (founder-takes-all principle), which is common for European animals and plants. In contrast to the post-glacial recolonization patterns of many aboveground organisms, divergence times of most geographic lineages indicate preservation of genetic structure since the Miocene. Conclusions Collembola survived severe climatic changes including those during Quatenary glaciation and kept high genetic variance across Europe. Likely the buffering of temperature oscilliations in soil and the ability to evade adverse climatic conditions due to cold-tolerance and horizontal migration enabled Collembola to evade strong selective pressure of abiotic forces. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0719-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Helge von Saltzwedel
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Strasse 28, 37073, Göttingen, Germany.
| | - Stefan Scheu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Strasse 28, 37073, Göttingen, Germany
| | - Ina Schaefer
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Strasse 28, 37073, Göttingen, Germany
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35
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Taylor SJ, Katz AD, Soto-Adames FN, Addison A, Hoese GB, Sutton MR, Toulkeridis T. New records and new species of springtails (Collembola: Entomobryidae, Paronellidae) from lava tubes of the Galápagos Islands (Ecuador). SUBTERRANEAN BIOLOGY 2016. [DOI: 10.3897/subtbiol.17.7660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Schneider C, Porco D, Deharveng L. Two new Megalothorax species of the minimus group (Collembola, Neelidae). Zookeys 2016:37-68. [PMID: 26877679 PMCID: PMC4740829 DOI: 10.3897/zookeys.554.6069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/25/2015] [Indexed: 11/12/2022] Open
Abstract
Two new Megalothorax species, Megalothorax potapovi sp. n. from the Russian Far East and Megalothorax sanguineus sp. n. from the French Pyrénées are described. The two new species have a set of morphological characters (including a smooth mucro) that places them among the minimus group sensu Schneider and D'Haese (2013). Megalothorax potapovi characteristics include dorsal protuberance on forehead, peculiar chaetotaxy of antenna III and strong lanceolate chaetae on body. Megalothorax sanguineus characteristics include strong red pigmentation, large network of integumentary channels on head and elongated apex of the two postero-distal spines of dens. The DNA barcodes (cytochrome oxidase subunit I-COI) of the two species are also provided and analyzed among a broader sampling of the genus in order to support further their specific status. A special focus is given to the labral morphological characteristics. Pseudopores-like elements are reported for the first time in the genus. Positions of the τ-chaetae near the dorsal sensory field of thorax II are compared for several species of the genus.
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Affiliation(s)
- Clément Schneider
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Museum national d'Histoire naturelle, Sorbonne Universités, 45 rue Buffon, CP50, F-75005 Paris, France
| | - David Porco
- Université de Rouen, Laboratoire ECODIV, Bâtiment IRESE A, Place Emile Blondel, 76821 Mont Saint Aignan Cedex, France
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Museum national d'Histoire naturelle, Sorbonne Universités, 45 rue Buffon, CP50, F-75005 Paris, France
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37
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Deep molecular divergence and exceptional morphological stasis in dwarf cannibal snails Nata sensu lato Watson, 1934 (Rhytididae) of southern Africa. Mol Phylogenet Evol 2016; 95:100-15. [DOI: 10.1016/j.ympev.2015.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 11/21/2022]
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38
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Greenslade P. Updating the New Zealand checklist of Collembola: a synonymy and new combinations. NEW ZEALAND JOURNAL OF ZOOLOGY 2015. [DOI: 10.1080/03014223.2015.1070882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Penelope Greenslade
- School of Applied and Biomedical Science, Faculty of Science, Federation University, Mt Helen, Ballarat, VIC, Australia; Department of Biology, Australian National University, Canberra, ACT, Australia; South Australian Museum, North Terrace, Adelaide, SA, Australia
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39
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Giska I, Sechi P, Babik W. Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated. BMC Evol Biol 2015; 15:217. [PMID: 26438011 PMCID: PMC4595309 DOI: 10.1186/s12862-015-0488-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/14/2015] [Indexed: 11/10/2022] Open
Abstract
Background The accurate delimitation of species is essential to numerous areas of biological research. An unbiased assessment of the diversity, including the cryptic diversity, is of particular importance for the below ground fauna, a major component of global biodiversity. On the British Isles, the epigeic earthworm Lumbricus rubellus, which is a sentinel species in soil ecotoxicology, consists of two cryptic taxa that are differentiated in both the nuclear and the mitochondrial (mtDNA) genomes. Recently, several deeply divergent mtDNA lineages were detected in mainland Europe, but whether these earthworms also constitute cryptic species remains unclear. This information is important from an evolutionary perspective, but it is also essential for the interpretation and the design of ecotoxicological projects. In this study, we used genome-wide RADseq data to assess the reproductive isolation of the divergent mitochondrial lineages of L. rubellus that occur in sympatry in multiple localities in Central Europe. Results We identified five divergent (up to 16 % net p-distance) mitochondrial lineages of L. rubellus in sympatry. Because the clustering of the RADseq data was according to the population of origin and not the mtDNA lineage, reproductive isolation among the mtDNA lineages was not likely. Although each population contained multiple mtDNA lineages, subdivisions within the populations were not observed for the nuclear genome. The lack of fixed differences and sharing of the overwhelming majority of nuclear polymorphisms between localities, indicated that the populations did not constitute allopatric species. The nucleotide diversity within the populations was high, 0.7–0.8 %. Conclusions The deeply divergent mtDNA sympatric lineages of L. rubellus in Central Europe were not reproductively isolated groups. The earthworm L. rubellus, which is represented by several mtDNA lineages in continental Europe, apparently is a single highly polymorphic species rather than a complex of several cryptic species. This study demonstrated the critical importance of the use of multilocus nuclear data for the unbiased assessment of cryptic diversity and for the delimitation of species in soil invertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0488-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iwona Giska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
| | - Pierfrancesco Sechi
- Institute of Ecosystem Study, Sassari, National Research Council, Traversa La Crucca 3, Regione Baldinca, 07100, Sassari, Italy.
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
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40
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Armani A, Giusti A, Guardone L, Castigliego L, Gianfaldoni D, Guidi A. Universal Primers Used for Species Identification of Foodstuff of Animal Origin: Effects of Oligonucleotide Tails on PCR Amplification and Sequencing Performance. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0301-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Janion-Scheepers C, Deharveng L, Bedos A, Chown SL. Updated list of Collembola species currently recorded from South Africa. Zookeys 2015:55-88. [PMID: 26019671 PMCID: PMC4440272 DOI: 10.3897/zookeys.503.8966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/05/2015] [Indexed: 11/12/2022] Open
Abstract
Understanding the abundance and richness of species is one of the most fundamental steps in effecting their conservation. Despite global recognition of the significance of the below-ground component of diversity for ecosystem functioning, the soil remains a poorly studied terrestrial ecosystem. In South Africa, knowledge is increasing for a variety of soil faunal groups, but many still remain poorly understood. We have started to address this gap in the knowledge of South African soil biodiversity by focusing on the Collembola in an integrated project that encompasses systematics, barcoding and ecological assessments. Here we provide an updated list of the Collembola species from South Africa. A total of 124 species from 61 genera and 17 families has been recorded, of which 75 are considered endemic, 24 widespread, and 25 introduced. This total number of species excludes the 36 species we consider to be dubious. From the published data, Collembola species richness is high compared to other African countries, but low compared to European countries. This is largely a consequence of poor sampling in the African region, as our discovery of many new species in South Africa demonstrates. Our analyses also show that much ongoing work will be required before a reasonably comprehensive and spatially explicit picture of South Africa’s springtail fauna can be provided, which may well exceed 1000 species. Such work will be necessary to help South Africa meet its commitments to biodiversity conservation, especially in the context of the 2020 Aichi targets of the Convention on Biological Diversity.
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Affiliation(s)
- Charlene Janion-Scheepers
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa ; School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Louis Deharveng
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 45 rue Buffon, F-75005, Paris, France
| | - Anne Bedos
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 45 rue Buffon, F-75005, Paris, France
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
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42
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Katz AD, Giordano R, Soto-Adames FN. Operational criteria for cryptic species delimitation when evidence is limited, as exemplified by North AmericanEntomobrya(Collembola: Entomobryidae). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12220] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aron D. Katz
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
- Illinois Natural History Survey; University of Illinois; 1816 South Oak Street Champaign IL 61820 USA
| | - Rosanna Giordano
- Department of Entomology; University of Illinois; 320 Morrill Hall 505 South Goodwin Avenue Urbana IL 61801 USA
| | - Felipe N. Soto-Adames
- Illinois Natural History Survey; University of Illinois; 1816 South Oak Street Champaign IL 61820 USA
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43
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Chown SL, Hodgins KA, Griffin PC, Oakeshott JG, Byrne M, Hoffmann AA. Biological invasions, climate change and genomics. Evol Appl 2015; 8:23-46. [PMID: 25667601 PMCID: PMC4310580 DOI: 10.1111/eva.12234] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/24/2014] [Indexed: 12/13/2022] Open
Abstract
The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species' geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.
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Affiliation(s)
- Steven L Chown
- School of Biological Sciences, Monash UniversityClayton, Vic., Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash UniversityClayton, Vic., Australia
| | - Philippa C Griffin
- Department of Genetics, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
| | - John G Oakeshott
- CSIRO Land and Water Flagship, Black Mountain LaboratoriesCanberra, ACT, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery CentreBentley, WA, Australia
| | - Ary A Hoffmann
- Departments of Zoology and Genetics, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
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Adams M, Raadik TA, Burridge CP, Georges A. Global Biodiversity Assessment and Hyper-Cryptic Species Complexes: More Than One Species of Elephant in the Room? Syst Biol 2014; 63:518-33. [DOI: 10.1093/sysbio/syu017] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, SA 5000, Australia
- School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tarmo A. Raadik
- Aquatic Ecology Section, Arthur Rylah Institute for Environmental Research, Department of Environment and Primary Industries, 123 Brown Street, Heidelberg, VIC 3084, Australia
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Futures, University of Canberra, ACT 2601, Australia and
| | - Christopher P. Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Arthur Georges
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Futures, University of Canberra, ACT 2601, Australia and
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45
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Cooper SJB, Watts CHS, Saint KM, Leijs R. Phylogenetic relationships of Australian Scirtidae (Coleoptera) based on mitochondrial and nuclear sequences. INVERTEBR SYST 2014. [DOI: 10.1071/is13046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Scirtidae is a cosmopolitan group of beetles with aquatic or saproxylic larvae. A large diversity of species has recently been described from Australia, but their systematics is uncertain. There is evidence that current genera are polyphyletic and that Australian species were wrongly placed in northern hemisphere genera. Here we investigate the systematics of Australian Scirtidae using molecular phylogenetic analyses of combined data from the mitochondrial cytochrome c oxidase subunit 1 (COI) and nuclear gene elongation factor 1-α (EF1-α) genes. We also assess the current taxonomy of Australian Scirtidae using partial COI sequences. Bayesian phylogenetic analyses of COI and EF1-α sequence data from 81 taxa show that the Australian genera Contacyphon, Pseudomicrocara and Prionocyphon are polyphyletic. There is no close relationship between Australian and Eurasian genera, with the exception of Scirtes. Phylogenetic analyses of partial COI data from Australian Scirtidae generally support the current α taxonomy, with the exception of several species that may be associated with species complexes. Geographically a high proportion of species lineages are restricted to relict patches of wet forest suggesting that they may be relict populations. The phylogeny and sequence data presented here provide a sound basis for further systematic and biogeographical studies of the Scirtidae.
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Porco D, Skarżyński D, Decaëns T, Hebert PDN, Deharveng L. Barcoding the Collembola of Churchill: a molecular taxonomic reassessment of species diversity in a sub-Arctic area. Mol Ecol Resour 2013; 14:249-61. [DOI: 10.1111/1755-0998.12172] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/09/2013] [Accepted: 09/13/2013] [Indexed: 11/30/2022]
Affiliation(s)
- David Porco
- EA 1293 ECODIV; Université de Rouen; UFR Sciences et Techniques; SFR SCALE; Bâtiment IRESE A Mont Saint Aignan Cedex 76821 France
| | - Dariusz Skarżyński
- Department of Evolutionary Biology and Ecology; Wrocław University; Przybyszewskiego 63/77 Wrocław 51-148 Poland
| | - Thibaud Decaëns
- EA 1293 ECODIV; Université de Rouen; UFR Sciences et Techniques; SFR SCALE; Bâtiment IRESE A Mont Saint Aignan Cedex 76821 France
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario; University of Guelph; 50 Stone Road East Guelph ON N1G 2W1 Canada
| | - Louis Deharveng
- Muséum National d'Histoire Naturelle; UMR7205; «Origine, Structure et Evolution de la Biodiversité»; 45 rue Buffon CP50 Paris 75005 France
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47
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Cicconardi F, Fanciulli PP, Emerson BC. Collembola, the biological species concept and the underestimation of global species richness. Mol Ecol 2013; 22:5382-96. [DOI: 10.1111/mec.12472] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/10/2013] [Accepted: 07/17/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Cicconardi
- Department of Physics; University of Rome “La Sapienza”; P.le A. Moro 5 Rome 00185 Italy
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panamá, República de Panamá
| | - Pietro P. Fanciulli
- Department of Life Sciences; University of Siena; Via Aldo Moro 2 Siena 53100 Italy
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; IPNA-CSIC; La Laguna Tenerife 38206 Canary Islands Spain
- School of Biological Sciences; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
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