A comparison of protocols for isolating and extracting host DNA from caribou (Rangifer tarandus) fecal pellets

Fecal samples are valuable for wildlife genetic studies where invasive tissue sampling is difficult, expensive, or negatively impacts welfare. However, fecal DNA is challenging to work with due to high amounts of exogenous (non-host) DNA and PCR inhibitors. For conservation and management of caribou (Rangifer tarandus), feces may be used as a DNA source, but optimal extraction protocols remain unclear. We compared combinations of cell isolation methods (using a swab or toothpick, washing, or incubating in lysis buffer) and QIAGEN DNA extraction kits (QIAamp DNA Mini, Fast DNA Stool Mini, PowerSoil Pro) on fecal samples from a boreal caribou population in British Columbia, Canada. We assessed protocols based on total and target (host) DNA yields and PCR amplification success using a new qPCR assay. The most successful methods were further tested on samples from seven additional populations across three caribou ecotypes. All methods yielded at least 10 ng of caribou DNA per pellet, sufficient for most PCR-based genotyping protocols. In boreal caribou, the incubation isolation and QIAamp DNA Mini kit yielded the highest DNA quantities, while the wash isola-tion with Fast DNA Stool and PowerSoil kits yielded the highest host DNA proportions. Post-hoc validation, however, revealed that the wash isolation in combination with the QIAamp DNA Mini kit was more reliable for minimizing PCR inhibitors across populations while maximizing DNA yield. These results will inform feces-based genetic workflows in caribou, and offer a transferable framework for refining similar protocols in other species to advance non-invasive genetic monitoring more broadly.