Data from: Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Valentini, Alice; Taberlet, Pierre; Miaud, Claude; Civade, Raphaël; Herder, Jelger; Thomsen, Philip Francis; Bellemain, Eva; Besnard, Aurélien; Coissac, Eric; Boyer, Frédéric; Gaboriaud, Coline; Jean, Pauline; Poulet, Nicolas; Roset, Nicolas; Copp, Gordon H.; Geniez, Philippe; Pont, Didier; Argillier, Christine; Baudoin, Jean-Marc; Peroux, Tiphaine; Crivelli, Alain J.; Olivier, Anthony; Acqueberge, Manon; Le Brun, Matthieu; Møller, Peter Rask; Willerslev, Eske; Dejean, Tony

doi:10.5061/dryad.jm58p

Published October 23, 2015 | Version v1

Dataset Open

Data from: Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

1. SPYGEN; Savoie Technolac-Bât. Koala 17, Rue du Lac Saint-André-BP 274 Le Bourget-du-Lac Cedex 73375 France*
2. French National Centre for Scientific Research
3. Centre d'Ecologie Fonctionnelle et Evolutive
4. Hydrosystems and Bioprocesses Research Unit; IRSTEA; Antony Cedex 92761 France*
5. RAVON; Postbus 1413 Nijmegen 6501 BK The Netherlands*
6. University of Copenhagen
7. French National Agency for Water and Aquatic Environments
8. Trent University
9. Tour du Valat
10. Agence Centre-Ouest; Ecosphère; Orléans 45000 France*
11. Electricité de France (France)

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 into the environment. In this study, we tested if 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) versus 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.

Notes

OTU tables

Sequence reference database

Files containing the sequences for the reference databases for Batrachia and Teleostei species

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