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

Prasetyo, A; Cusa, M; Murray, J; Agung, F; Muttaqin, E; Maraini, S; McDevitt, A

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.

Citation

Prasetyo, A., Cusa, M., Murray, J., Agung, F., Muttaqin, E., Maraini, S., & McDevitt, A. (2022). Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots. bioRxiv, https://doi.org/10.1101/2022.11.30.518468

• Journal Article Type: Article
• Online Publication Date: Dec 5, 2022
• Publication Date: Dec 5, 2022
• Deposit Date: Feb 17, 2023
• Publicly Available Date: Feb 17, 2023
• Journal: bioRxiv
• DOI: https://doi.org/10.1101/2022.11.30.518468
• Publisher URL: https://doi.org/10.1101/2022.11.30.518468
• Additional Information: Access Information : This is a pre-print and has not been through the peer-review process. The link above should direct to the latest version of this pre-print.