Genetic Identification of Species Responsible for Depredation in Commercial and Recreational Fisheries

Depredation, the partial or complete removal of hooked fish (prey) by a nontarget predator species, is a cryptic interaction that negatively affects predators, prey, and fishing industries. However, these interactions are rarely observed, rendering positive identification of the predator nearly impossible. We therefore tested a genetic method for predator identification. Depredated remains from sharks and bony fish were sampled with buccal swabs. Genetic material was isolated from the swabs, which we hypothesized contained oral cells from the predator. A portion of the cytochrome-c oxidase subunit I locus was amplified using prey-specific blocking primers and sequenced in high depth using a metagenetics approach. We sequenced haplotypes from the remains of four sharks, where the predator was visually confirmed, and four bony fish, where the predator was unknown. For all interactions with known predators, our technique suggested the correct predator species. For all interactions where the predators were unknown, our technique suggested species previously confirmed as perpetrators in depredation events. Our findings provide a basis for the development of a genetic technique for predator identification, while highlighting challenges to be overcome before predator identification can be applied to large-scale fisheries.