DNA barcoding increases the taxonomic resolution of shark diet analysis compared to morphological stomach contents identification

Abstract

Morphological identification of stomach contents is the most common methodology used for shark diet reconstruction. However, this approach often limits prey identification to low taxonomic levels (i.e., order or class) and is prone to inaccuracies due to subtle morphological differences among prey. Additionally, varying digestion rates can lead to the underrepresentation of soft-bodied prey, which degrade and become unrecognizable more quickly than hard-shelled organisms. We used both visual morphological analysis and DNA barcoding on each prey item collected from the stomachs of four coastal shark species (i.e., Atlantic sharpnose [Rhizoprionodon terraenovae], blacknose [Carcharhinus acronotus], blacktip [Carcharhinus limbatus], and bonnethead [Sphyrna tiburo]) in North Carolina. Stomachs were collected from 49 sharks, yielding 118 prey items for analysis. We then compared the results of both visual and genetic methods to assess whether DNA barcoding increased taxonomic resolution of prey. Each prey item was also assigned an equivalency category to quantify the level of agreement between the two methodologies. DNA barcoding more than doubled the number of prey identified to the species level compared to morphological identification, and dietary composition significantly differed between methods for all shark species. Additionally, equivalency categories were significantly correlated with shark species and prey taxa. Bonnetheads had the highest proportion of prey classified as a match between methods due to their dietary specialization on Atlantic blue crabs (Callinectes sapidus). The hard carapace of this species digests more slowly, making Atlantic blue crabs easier to identify during morphological analysis. Blacknose sharks had the highest proportion of prey with their comparative equivalency categorized as ‘unidentified general morphological’, where morphological and DNA results aligned, but prey remained unidentifiable through morphology alone. Incorporating DNA barcoding into dietary studies provides an inexpensive, accurate, and effective approach to improving prey identification in sharks and other taxa. Improved resolution of shark diets strengthens our understanding of their ecological roles and supports ecosystem-based management approaches for shark and marine ecosystem conservation.