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

Prasetyo, Andhika P; Cusa, Marine; Murray, Joanna M; Agung, Firdaus; Muttaqin, Efin; Mariani, Stefano; McDevitt, Allan D

Abstract

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 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. [Abstract copyright: © 2023 The Author(s).]

Citation

Prasetyo, A. P., Cusa, M., Murray, J. M., Agung, F., Muttaqin, E., Mariani, S., & McDevitt, A. D. (2023). Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots. iScience, 26(7), 107065. https://doi.org/10.1016/j.isci.2023.107065

• Journal Article Type: Article
• Acceptance Date: Jun 2, 2023
• Online Publication Date: Jun 7, 2023
• Publication Date: Jun 15, 2023
• Deposit Date: Jul 4, 2023
• Publicly Available Date: Jul 4, 2023
• Journal: iScience
• Print ISSN: 2589-0042
• Publisher: Cell Press
• Peer Reviewed: Peer Reviewed
• Volume: 26
• Issue: 7
• Pages: 107065
• DOI: https://doi.org/10.1016/j.isci.2023.107065
• Keywords: Aquatic science, Aquatic biology, Nature conservation, Ichthyology