Universal Closed-Tube Barcoding for Monitoring the Shark and Ray Trade in Megadiverse Conservation Hotspots

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

doi:10.2139/ssrn.4292604

Cited by 1 publication

(1 citation statement)

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“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Prasetyo

Murray

Kurniawan

et al. 2023

Conservation Letters.

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Illegal fishing, unregulated bycatch, and market demand for certain products (e.g., fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity, and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, and are time‐consuming and/or species‐specific. Here, we performed high‐throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded “shark‐dust” samples from seven processing plants in the world's biggest shark landing site (Java, Indonesia), and identified 61 shark and ray taxa (representing half of all chondrichthyan orders), more than half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark‐dust sequences were found to belong to CITES‐listed species. We argue that this approach is likely to become a powerful and cost‐effective monitoring tool wherever wildlife is traded.

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