Co-amplification of cytochrome b and D-loop mtDNA fragments for the identification of degraded DNA samples

We propose a simple and effective approach to simultaneously co-amplify both cytochrome b and D-loop fragments to evaluate DNA preservation and to monitor possible contaminations in the analysis of degraded animal DNA samples. We have applied this approach to over 200 ancient salmon samples and 25 ancient whale DNA samples, clearly demonstrating its multiple benefits for analysis of degraded DNA samples, and the ease in which co-amplification can be optimized for different taxa. This simple, cost-efficient and genomic DNA-saving approach can be used routinely in the analysis of minute and degraded DNA samples in wildlife forensics, food inspection, conservation biology and ancient faunal remains.