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Optimising recovery of DNA from minimally-invasive sampling methods: efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies
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  • Rémi Martin,
  • Katherine Mullin,
  • Nina White,
  • Nicole Grimason,
  • Robert Jehle,
  • John Wilkinson,
  • Pablo Orozco-terWengel,
  • Andrew Cunningham,
  • Simon Maddock
Rémi Martin
University of Wolverhampton Faculty of Science and Engineering

Corresponding Author:[email protected]

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Katherine Mullin
Cardiff University
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Nina White
Cardiff University
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Nicole Grimason
University of Wolverhampton Faculty of Science and Engineering
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Robert Jehle
University of Salford
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John Wilkinson
The Amphibian and Reptile Conservation Trust
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Pablo Orozco-terWengel
Cardiff University
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Andrew Cunningham
Zoological Society of London
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Simon Maddock
Newcastle University
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Abstract

Studies in evolution, ecology and conservation are increasingly based on genetic and genomic inferences. With increased focus on molecular approaches, ethical concerns about destructive or more invasive techniques need to be considered, with a push for minimally invasive sampling to be optimised. Buccal swabs have been increasingly used to collect DNA in a number of taxa, including amphibians. However, DNA yield and purity from swabs is often low, limiting its use. In this study we compare different types of swabs, preservation method and storage, and DNA extraction technique in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swab that we tested, Isohelix MS-02 and Rapidry swabs generated higher DNA yields than other swabs. When comparing storage buffers, ethanol is a better preservative than a non-alcoholic alternative. Dried samples resulted in similar or better final DNA yields than ethanol-fixed samples if kept cool. DNA extraction via a Qiagen™ DNeasy Blood and Tissue Kit and McHale’s salting out extraction method resulted in similar DNA yields but the Qiagen™ kit extracts contained less contamination. We also found that samples produce better DNA recovery if frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual sampled, access to cold storage facilities, and DNA extraction methodology. Maximising efficacy of all of these factors for better DNA recovery will allow buccal swabs to be used for genetic and genomic studies in a range of vertebrates.
29 May 2024Submitted to Ecology and Evolution
07 Jul 2024Review(s) Completed, Editorial Evaluation Pending
22 Jul 2024Editorial Decision: Revise Minor
13 Aug 20241st Revision Received
17 Aug 2024Assigned to Editor
17 Aug 2024Submission Checks Completed
17 Aug 2024Review(s) Completed, Editorial Evaluation Pending
29 Aug 2024Editorial Decision: Accept