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

Trade restrictions for endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, trade monitoring is challenging due to product variety and the complexity of import/export routes. 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 commonly encountered species (including 22 CITES-listed species) to test a recently developed real-time PCR single-assay originally developed for screening bony fish. In the absence of a bespoke elasmobranch identification online platform in the original FASTFISH-ID model, 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 25/28 species, 20 of which were CITES-listed. With further refinement, this method can improve monitoring of the elasmobranch trade worldwide, without a lab or species-specific assays.