Individual Identification of Prey in Carnivore Scats

Noninvasive genetic sampling is widely used in ecology and conservation to identify predators and their diets but recovering individual-level information from consumed prey remains largely unexplored. We evaluated whether individual prey can be reliably genotyped from carnivore scats and assessed limitations associated with degraded and mixed DNA sources. We developed a 31-locus SNP panel optimized for genotyping degraded elk (Cervus canadensis) DNA using amplicon sequencing. We validated prey genotyping by matching elk genotypes recovered from carnivore scats ('carcass scats') collected at cougar (Puma concolor) kill sites to genotypes from corresponding elk carcasses. We also genotyped scats collected throughout the study area, identified as containing elk using DNA metabarcoding ('survey scats'). To avoid misidentifying multiple individuals in a scat as a unique genotype, we evaluated artificial mixtures of prey DNA to assess the ability to detect and filter samples containing mixed DNA. Elk genotypes recovered from carcass scats matched associated carcass genotypes, confirming accurate recovery of individual prey DNA from carnivore scats. Genotyping success was 88% in fresh carcass scats and 74% in survey scats of unknown age. Heterozygosity excess filtering removed most mixed samples, although one of 24 mixtures with equal DNA contributions from two individuals produced a false unique genotype. Our results demonstrate that carnivore scats can serve as a reliable source of individual-level prey DNA under appropriate conditions. This method provides a new data stream on individual prey mortality, predation rates, and scavenging dynamics, processes that have previously been difficult to quantify without invasive capture and collaring techniques.