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