Bone appetit: DNA metabarcoding as a non-lethal alternative to morphological dietary assessment in Atlantic bonefish (Albula vulpes)

Traditional approaches to dietary assessment in fish necessitate the collection of stomach contents through either gastric lavage or lethal sampling. The Atlantic bonefish (Albula vulpes) is an economically important sportfish in the western central Atlantic region for which a minimally invasive, non-lethal alternative to morphological dietary assessment would be extremely useful. Here, we compare dietary DNA metabarcoding from cloacal swabs of 16 A. vulpes to dietary composition data obtained using traditional morphological classification techniques and metabarcoding of homogenized stomach contents. Further, we compare the performance of two commonly used barcoding genes (18S rRNA and COI) at inferring A. vulpes diet composition. We found that detection of taxa and the resolution of taxonomic annotation varied between markers, suggesting a multi-marker approach is likely to provide the most complete results. Importantly however, the number of dietary OTUs identified and the taxonomic composition of the core diet were not significantly different between molecular markers. Dietary compositions identified using metabarcoding approaches differed in both diversity and composition from matched dietary data obtained from morphologically analyzed stomach contents; however, the same core prey classes were identified using both methods, suggesting that metabarcoding does indeed offer a viable alternative to morphological dietary assessment. Importantly, dietary compositions identified by metabarcoding of cloacal swabs did not differ significantly from those identified by metabarcoding of stomach contents. Metabarcoding of minimally invasive cloacal swabs should be considered for dietary studies of bonefish and other fish species for which invasive or lethal sampling is problematic.