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Individual genotypes from environmental DNA: fingerprinting snow tracks of three large carnivore species
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  • Marta De Barba,
  • Molly Baur,
  • Frédéric Boyer,
  • Luca Fumagalli,
  • Marjeta Konec,
  • Christian Miquel,
  • Elena Pazhenkova,
  • Nadege Remollino,
  • Tomaž Skrbinšek,
  • Céline Stoffel,
  • Pierre Taberlet
Marta De Barba
University of Ljubljana Biotechnical faculty

Corresponding Author:[email protected]

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Molly Baur
University of Lausanne
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Frédéric Boyer
Universite Grenoble Alpes
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Luca Fumagalli
University of Lausanne
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Marjeta Konec
University of Ljubljana Biotechnical faculty
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Christian Miquel
Laboratoire d'Ecologie Alpine
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Elena Pazhenkova
University of Ljubljana Biotechnical faculty
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Nadege Remollino
University of Lausanne
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Tomaž Skrbinšek
University of Ljubljana, Biotechnical Faculty
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Céline Stoffel
University of Lausanne
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Pierre Taberlet
Université Joseph Fourier
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Abstract

Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wild animal populations. However, the use of eDNA samples for individual genotyping, as typically performed in non-invasive genetics, still remained unachieved. We present the first successful individual genotyping of eDNA obtained from snow tracks of three large carnivores: brown bear (Ursus arctos), European lynx (Lynx lynx) and wolf (Canis lupus). DNA was extracted using a protocol for isolating water eDNA and genotyped using amplicon sequencing of short tandem repeats (STR) and, for brown bear, a sex marker, on a high-throughput sequencing platform. Individual genotypes were obtained for all species, but genotyping performance differed among samples and species. Multilocus genotyping success for individual identification was higher for brown bear samples (6 over 7), than for wolf (7 over 10) and lynx (4 over 9) samples. The sex marker was genotyped in 5 out of 7 brown bear samples. Results for three species show that reliable individual genotyping, including sex identification, is now possible from eDNA in snow tracks, underlining its vast potential to complement the non-invasive genetic methods used for wildlife. To fully leverage the application of snow track eDNA, improved understanding of the ideal species- and site-specific sampling conditions, as well as laboratory methods promoting genotyping success are needed. This will also inform efforts to retrieve and type nuclear DNA from other eDNA samples, thereby advancing eDNA–based individual and population level studies.
28 May 2023Submitted to Molecular Ecology Resources
29 May 2023Submission Checks Completed
29 May 2023Assigned to Editor
29 May 2023Review(s) Completed, Editorial Evaluation Pending
19 Jun 2023Reviewer(s) Assigned
14 Aug 2023Editorial Decision: Revise Minor
02 Sep 20231st Revision Received
08 Sep 2023Submission Checks Completed
08 Sep 2023Assigned to Editor
08 Sep 2023Review(s) Completed, Editorial Evaluation Pending
28 Sep 2023Editorial Decision: Revise Minor
05 Nov 20232nd Revision Received
06 Nov 2023Submission Checks Completed
06 Nov 2023Assigned to Editor
06 Nov 2023Review(s) Completed, Editorial Evaluation Pending