Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding |
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| Authors: | Alice Valentini Pierre Taberlet Claude Miaud Raphaël Civade Jelger Herder Philip Francis Thomsen Eva Bellemain Aurélien Besnard Eric Coissac Frédéric Boyer Coline Gaboriaud Pauline Jean Nicolas Poulet Nicolas Roset Gordon H Copp Philippe Geniez Didier Pont Christine Argillier Jean‐Marc Baudoin Tiphaine Peroux Alain J Crivelli Anthony Olivier Manon Acqueberge Matthieu Le Brun Peter R Møller Eske Willerslev Tony Dejean |
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| Affiliation: | 1. SPYGEN, Le Bourget‐du‐Lac Cedex, France;2. Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, France;3. Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, France;4. Laboratoire Biogéographie et Ecologie des Vertébrés, CEFE UMR 5175, Montpellier, France;5. Hydrosystems and Bioprocesses Research Unit, IRSTEA, Antony Cedex, France;6. RAVON, Nijmegen, The Netherlands;7. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark;8. Direction de l'Action Scientifique et Technique, ONEMA, Vincennes, France;9. Rh?ne‐Alpes Regional Direction, ONEMA, Bron, France;10. Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk, UK;11. Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada;12. Pole ONEMA/IRSTEA Hydroécologie des plans d'eau, Centre d'Aix‐en‐Provence, IRSTEA UR HYAX, Aix‐en‐Provence, France;13. Le Sambuc, Tour du Valat, Arles, France;14. Agence Centre‐Ouest, Ecosphère, Orléans, France;15. LNHE Department, EDF R&D, Chatou Cedex, France;16. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark |
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| Abstract: | Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90–0.99) vs. 0.58 (CI = 0.50–0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA‐based approach has the potential to become the next‐generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems. |
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| Keywords: | amphibian detection probability environmental DNA fish monitoring wildlife management |
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