Optimising recovery of DNA from minimally invasive sampling methods: Efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies

Martin, Rémi; Mullin, K. E.; White, N. F. D.; Grimason, N.; Jehle, R.; Wilkinson, J. W.; Orozco‐terWengel, P.; Cunningham, A. A.; Maddock, S. T.

Abstract

Studies in evolution, ecology and conservation are increasingly based on genetic and genomic data. 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 are often low, limiting its use. In this study, we compare different types of swabs, preservation method and storage, and DNA extraction techniques in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swabs 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 compared to 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 have better DNA recovery if they are frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual animal 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.

• Journal Article Type: Article
• Acceptance Date: Aug 29, 2024
• Online Publication Date: Sep 12, 2024
• Publication Date: Sep 1, 2024
• Deposit Date: Sep 15, 2024
• Publicly Available Date: Sep 23, 2024
• Journal: Ecology and Evolution
• Electronic ISSN: 2045-7758
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 14
• Issue: 9
• Pages: e70294
• DOI: https://doi.org/10.1002/ece3.70294
• Keywords: genomics, anurans, genetic sampling techniques, DNA recovery