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Monitoring endangered freshwater biodiversity using environmental DNA

Authors

  • PHILIP FRANCIS THOMSEN,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
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    • These authors contributed equally to this study.

  • JOS KIELGAST,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
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    • These authors contributed equally to this study.

  • LARS L. IVERSEN,

    1. Freshwater Biology Section, Department of Biology, University of Copenhagen, Helsingørgade 51, DK-3400 Hillerød, Denmark
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  • CARSTEN WIUF,

    1. Bioinformatics Research Center (BiRC), Aarhus University, C. F. Møllers Alle 8, DK-8000 Århus, Denmark
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  • MORTEN RASMUSSEN,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
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  • M. THOMAS P GILBERT,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
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  • LUDOVIC ORLANDO,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
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  • ESKE WILLERSLEV

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
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Eske Willerslev E-mail: ewillerslev@snm.ku.dk

Abstract

Freshwater ecosystems are among the most endangered habitats on Earth, with thousands of animal species known to be threatened or already extinct. Reliable monitoring of threatened organisms is crucial for data-driven conservation actions but remains a challenge owing to nonstandardized methods that depend on practical and taxonomic expertise, which is rapidly declining. Here, we show that a diversity of rare and threatened freshwater animals—representing amphibians, fish, mammals, insects and crustaceans—can be detected and quantified based on DNA obtained directly from small water samples of lakes, ponds and streams. We successfully validate our findings in a controlled mesocosm experiment and show that DNA becomes undetectable within 2 weeks after removal of animals, indicating that DNA traces are near contemporary with presence of the species. We further demonstrate that entire faunas of amphibians and fish can be detected by high-throughput sequencing of DNA extracted from pond water. Our findings underpin the ubiquitous nature of DNA traces in the environment and establish environmental DNA as a tool for monitoring rare and threatened species across a wide range of taxonomic groups.

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