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

Prasetyo, A ORCID: https://orcid.org/0000-0002-7412-8432, Cusa, M, Murray, J, Agung, F, Muttaqin, E, Maraini, S and McDevitt, A ORCID: https://orcid.org/0000-0002-2677-7833 2022, 'Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots' , bioRxiv .

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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.

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