Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal (Halichoerus grypus) diet

Increasing grey seal (Halichoerus grypus) abundance in coastal New England is leading to social, political, economic, and ecological controversies. We studied grey seal feeding habits through next-generation sequencing of prey DNA using 16S amplicons from seal scat (N = 74) collected from a breeding colony on Monomoy Island in Massachusetts, U.S. and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised PCR assay. In contrast to current understanding of grey seal diet from hard parts and fatty acid analysis, we found no significant difference between male and female diet measured by alpha and beta diversity. Overall, we detected 24 prey groups, 18 of which resolved to species. Sand lance (Ammodytes spp.) was the most frequently consumed prey group, with a frequency of occurrence (FO) of 97.3%, consistent with previous studies, but Atlantic menhaden (Brevoortia tyrannus), the second most frequently consumed species (FO = 60....