A Comparison of DNA Metabarcoding Cloacal Swabs and Stomach Contents for Shark Diet Reconstruction

ABSTRACT Metabarcoding fecal matter is increasingly common in dietary studies across a variety of taxa. This approach assumes that enough prey DNA remains detectable in the fecal DNA (fDNA) as the prey DNA becomes degraded while passing through the digestive tract. However, as prey DNA is degraded during digestion, diet reconstruction based on metabarcoding of fDNA could become incomplete, i.e., species for which DNA was highly degraded would not be detected. The purpose of this study was to test the use of cloacal swabs and metabarcoding fDNA for shark diet reconstruction. To do this, both stomach contents and cloacal swabs were collected from the same individual sharks and metabarcoded using two previously published primer sets targeting teleost fishes and crustaceans. Samples were collected from four coastal species of sharks in a temperate estuary: bonnethead ( Sphyrna tiburo ; n = 10), blacknose ( Carcharhinus acronotus ; n = 4), blacktip ( C. limbatus ; n = 4), and Atlantic sharpnose ( Rhizoprionodon terraenovae ; n = 5). We determined how well the fDNA represented the corresponding prey DNA from the stomach contents (stDNA) and found no statistical difference in taxonomic richness or diversity when comparing the two sample types. Our results indicate that the less invasive, non‐lethal method of DNA metabarcoding cloacal swabs provided higher taxonomic resolution than more common methods for studying trophic ecology (i.e., morphological stomach contents identification and trophic biomarkers such as stable isotope analysis) with no statistical difference in overall diet description between the two sample types.