Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots

Abstract

Trade restrictions for many endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, the variety of products and the complexity of import/export routes make trade monitoring challenging. We investigate the use of a portable, universal, DNA-based tool which would greatly facilitate in-situ monitoring. We collected shark and ray samples across the Island of Java, Indonesia, and selected 28 species (including 22 CITES-listed species) commonly encountered in landing sites and export hubs to test a recently developed real-time PCR single-assay originally developed for screening bony fish. We employed a deep learning algorithm to recognize species based on DNA melt-curve signatures. By combining visual and machine learning assignment methods, we distinguished 25 out of 28 species, 20 of which were CITES-listed. With further refinement, this method can provide a practical tool for monitoring elasmobranch trade worldwide, without the need for a lab or the bespoke design of species-specific assays.

Shark‐dust: Application of high‐throughput DNA sequencing of processing residues for trade monitoring of threatened sharks and rays

“…This has incentivized the use of genetic identification methods, which progressively made DNA-based inference a staple of wildlife forensics (Domingues et al, 2021). Of these, DNA barcoding (Shivji et al, 2002) and mini-barcoding (Fields et al, 2015) can robustly identify species in fresh and processed samples, while real-time qPCR (Cardeñosa et al, 2018), LAMP-based (But et al, 2020), and universal close-tube barcoding (Prasetyo et al, 2023) assays can detect target species in a matter of hours.…”

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

“…This has led to the rapid development of molecular technologies, which progressively made DNA-based inference a staple of wildlife forensics. Of these, DNA barcoding (Shivji et al 2002) and mini-barcoding (Fields et al 2015) can robustly identify species in fresh and processed samples, while real-time qPCR (Cardeñosa et al 2018), LAMP-based (But et al 2020) and universal close-tube barcoding (Prasetyo et al 2022) assays can detect target species in a matter of hours.…”