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

Abstract

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.

Defining Sex-Specific Habitat Suitability for a Northern Gulf of Mexico Shark Assemblage

“…This species has been protected in the GoM since 2010, and populations in the GoM seem to be increasing as a result (Peterson et al, 2017). Our findings show very clear and interesting associations between sandbar sharks and Alabama's Artificial Reef Zone (AARZ), where depredation (i.e., the partial or complete removal of a hooked species by a non-target species) by sandbar sharks is common in hook and line fisheries (Drymon et al, 2019). In Western Australia, depredation by sharks is higher in areas receiving higher fishing pressure, perhaps indicting learned behavior by the sharks (Mitchell et al, 2018), which may also be the case for sandbar sharks inhabiting the AARZ.…”

Discerning the dietary habits of the smooth butterfly ray Gymnura lessae using two distinct methods, otolith identification and metagenetics

“…The specific protocols followed by the Genomics Core Laboratory for DNA extraction, PCR amplification and quality control, pooling and library preparation before Illumina sequencing and bioinformatics related to demultiplexing, read clustering and separation and identification into putative operational taxonomic units (OTU) can be found in the methods of Drymon et al . (). The universal metazoan primers MlcoIint‐F (primer sequence: 5′‐ GGWACWGGWTGAACWGTWTAYCCYCC‐3′; Leray et al ., ) and Jghc‐02198 (5′‐ TAIACYTCIGGRTGICCRAARAAYCA‐3′; Geller et al ., ) were used in PCR amplification and a G .…”

Kit‐Based Sampling by Trained Fishers Yields Successful DNA Identification of Depredating Shark Species in the Marianas

“…Previous proof-of-concept studies evaluating DNA bar coding of depredated fishes relied on researchers to swab the depredated target species (Drymon et al 2019;Fotedar et al 2019), whereas we demonstrate that volunteer fishers with minimal training can collect viable transfer DNA from depredated fishes. Our success suggests that a kit-based approach could be easily used in other fisheries where shark depredation occurs (e.g., high-seas longline fisheries) to more fully characterize depredating species and improve understanding of indirect and unaccounted mortality resulting from predation associated with NOTE commercial and recreational fishers.…”

“…Recent proof‐of‐concept studies have used transfer DNA to definitively identify depredating shark species via mitochondrial DNA (mtDNA) bar coding (Drymon et al 2019; Fotedar et al 2019). The epithelium of sharks is covered by a thin mucous layer known to contain their DNA (Lieber et al 2013).…”

“…When sharks bite their prey, some of this mucus is transferred to the prey and can be collected by swabbing the damaged catch for DNA analysis and identification. Previous studies that identified depredating species via transfer DNA used recreational fishing methods (Drymon et al 2019) or utilized experienced scientific staff to collect samples (Fotedar et al 2019). Using the baseline methodologies provided by these studies, we developed easy‐to‐use swab kits for collection of transfer DNA from shark‐damaged fish.…”