Validation of two swabbing methods to sample DNA for genotyping Atlantic bluefin tuna (Thunnus thynnus)

In fisheries, genetic based assignment of individuals to their population of origin can benefit efforts aimed at monitoring and managing stocks. Assignment combined with knowledge of the migration history of individuals can provide powerful insights into mechanisms of genetic mixing, for which refined sampling methods are required to minimise any impacts. In this study we tested two minimally invasive swabbing techniques for sampling DNA when attaching electronic satellite tags to Atlantic bluefin tuna (Thunnus thynnus) for migration studies. First, DNA was sampled by skin swabbing (hereafter skin swabs) individuals from which there were corresponding fin clip samples. Second, swabs were taken from the applicator poles used to attach electronic tags (hereafter pole swabs). Quantification of DNA from the different sources revealed decreasing yields moving from fin clips, to skin swabs, to pole swabs. The utility of the DNA obtained by both swabbing methods for individual genotyping was then assessed by sequencing of the mtDNA control region and genotyping of six microsatellite loci. In all cases successful genotyping was achieved. For mtDNA an 868 bp fragment was successfully amplified in all samples with 775 bp aligned across individuals revealing 26 haplotypes (overall haplotype diversity = 0.987). All six microsatellites were successfully amplified including a largest allele size of 291 bp. mtDNA and microsatellite genotypes for the skin swabs matched with the corresponding fin clip samples. Although no tissue replicates were available for the pole swab samples the genotypes obtained were unambiguous, consistent across repeated PCRs, and reported no evidence of PCR issues such as large allele drop out. Overall, the genetic data suggested high variability among individuals sampled, comparable to levels of genetic diversity seen within the species' Atlantic range. The study demonstrates that non-invasive sampling can be used to obtain DNA for population assignment studies and that valuable material can be sampled from tagging equipment.