Shark-dust: High-throughput DNA sequencing of processing residues unveils widespread trade in threatened sharks and rays

Abstract

Illegal fishing, unregulated bycatch, and market demand for certain products (e.g. fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, are time-consuming and/or species-specific. Here, we performed high-throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded "shark-dust" samples from seven processing plants in the world biggest shark landing site (Java, Indonesia), and identified 54 shark and ray taxa (representing half of all chondrichthyan orders), half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark-dust sequences were found to belong to CITES-listed species. We argue that this approach is likely to become a powerful and cost-effective monitoring tool wherever wildlife is traded. Keywords: Elasmobranchs, trade monitoring, DNA metabarcoding, environmental DNA, Indonesia

Environmental DNA as a tool to reconstruct catch composition for longline fisheries vessels

“…Both data-limited fisheries and IUU activity can result in a lack of adequate knowledge of what fish are being caught where and by whom, making it difficult to maintain the sustainability of fish stocks, ecosystems, and livelihood 6,10 . Currently, 4.5 million tons of reported catch is considered unidentified 1 , this figure does not include additional IUU catch (11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26) million tons per year) 9 .…”