Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats

Abstract

DNA metabarcoding has become a powerful technique for identifying species and profiling biodiversity with the potential to improve efficiency, reveal rare prey species, and correct mistaken identification error in diet studies. However, the extent to which molecular approaches agree with traditional approaches is unknown for many species. Here, we compare diets from wolf scats profiled using both mechanical sorting and metabarcoding of amplified vertebrate DNA sequences. Our objectives were: (1) compare findings from mechanical sorting and metabarcoding as a method of diet profiling and (2) use results to better understand diets of wolves on Prince of Wales Island, a population of conservation concern. We predicted metabarcoding would reveal both higher diversity of prey and identify rare species that are overlooked with mechanical sorting. We also posited that the relative contribution of Sitka black-tailed deer (Odocoileus hemionus sitkensis) and beaver (Castor canadensis) would be overestimated with mechanical sorting methods because of the failure to account for the full diet diversity of these wolves. We found that there was substantial overlap in the diets revealed using both methods, indicating that deer, beaver, and black bear (Ursus americanus) were the primary prey species. However, there was a large discrepancy in the occurrence of beaver in scats (54% and 24% from mechanical sorting and metabarcoding, respectively) explained by the high rate of false positives with mechanical sorting methods. Metabarcoding revealed more diet diversity than mechanical sorting, thus supporting our initial predictions. Prince of Wales Island wolves appear to have a more diverse diet with greater occurrence of rare species than previously described including 14 prey species that contribute to wolf diet. Metabarcoding is an effective method for profiling carnivore diet and enhances our knowledge concerning the full diversity of wolf diets, even in the extremely wet conditions of southeast Alaska, which can lead to DNA degradation. Given the increasingly efficient and cost-effective nature of collecting eDNA, we recommend incorporating these molecular methods into field-based projects to further examine questions related to increased use of alternate prey coinciding with changes in abundance of primary prey and habitat alteration.