Abstract
Metabarcoding is emerging as an alternative to morphological methods in noninvasive carnivore diet analysis based on scats. A number of metabarcoding markers have been developed but their comparative performance to recover DNA from scats remains mostly untested. We tested three markers covering a wide taxonomic range of prey items and compared them with the results of a morphological analysis. Morphological and genetic methods performed comparably regarding the identity of detected prey species, but the number of identified species varied strongly between markers. Only one, 12S-V5, amplified successfully in all samples and proved to be robust and reliable when working with the highly degraded DNA obtained from scats.