‘Shark dust’ helps researchers ID threatened species in Indonesia fish trade

Indonesia’s shark and ray trade is highly regulated but poorly monitored, opening the door for illegal activity alongside the legal sale and purchase of these fish and their products. Finding an easy and low-cost way to identify which species are being caught and where processing of restricted species occurs would greatly help improve trade monitoring.

The findings of a study recently published in the journal Conservation Letters could accomplish just that. In the study, researchers share a new technique of analyzing DNA from tiny fragments of skin and cartilage swept from the floors of fish-processing plants and export warehouses, which they dub “shark dust.” Shark dust provides unprecedented insight into the variety of shark and ray species that have been caught, processed and prepared at a given location.

All living things shed DNA, and that genetic material can track where they’ve been. “This is like the dried skin found in your living room,” says lead author Andhika Prasetyo, a marine researcher at Indonesia’s National Research and Innovation Agency (BRIN). The difference is that for humans, our living rooms are part of our “habitat,” whereas a processing plant or export office is decidedly not shark habitat.

Prasetyo and his colleagues applied metabarcoding, a method of analyzing mixtures of DNA sequences from a single sample, to shark dust. Metabarcoding is the same technology behind many recent advances in studying biodiversity through environmental DNA, the invisible biological fragments organisms shed in the soil, water and even air.

This research was part of Prasetyo’s Ph.D. at the U.K.’s University of Salford, and part of a larger multi-institutional collaboration that includes Indonesia’s Ministry for Maritime Affairs and Fisheries. Prior to beginning his position at BRIN, Prasetyo was an associate researcher at the ministry’s Center for Fisheries Research.

For their study, the research team collected 28 shark dust samples from seven processing plants across Indonesia’s main central island of Java. Though each sample contained just two tablespoons of dust, those 56 tablespoons combined contained the genetic sequences of 61 shark and ray species. About 84% of the genetic sequences in the samples belonged to CITES-listed species, meaning there are official restrictions in place on the international trade in these species. The top five CITES-listed sharks detected were the scalloped hammerhead (Sphyrna lewini), silky shark (Carcharhinus falciformis), smooth hammerhead (Sphyrna zygaena), spot-tail shark (Carcharhinus sorrah), and great hammerhead (Sphyrna mokarran). The top non-CITES species were zebra shark (Stegostoma tigrinum), tiger shark (Galeocerdo cuvier), Australian weasel shark (Hemigaleus australiensis), whitespotted whipray (Maculabatis gerrardi), and spotless smooth-hound shark (Mustelus griseus).

Some of the shark dust came from cryptic species rarely spotted at Javan landing sites. The smooth hammerhead, which isn’t very abundant in Indonesian waters but common in the Asian shark fin trade, is one example. The samples also contained DNA from knifetooth sawfish (Anoxypristis cuspidata) and manta and devil rays (Mobula spp.), each of which is fully protected under Indonesian law.

While DNA metabarcoding of shark dust is new, for the past several years scientists have been using DNA analysis to identify which species shark fins and other products come from. However, this approach requires testing individual tissue samples, which can be costly and logistically near-impossible to do at scale across a large geographic area like Indonesia. Prasetyo’s team wondered how their metabarcoding method would match up. To find out, they compared results from shark dust metabarcoding with DNA sampling of tissues collected from the seven processing sites. They found the shark dust samples provided evidence for 17 more genera than the tissue samples did, capturing a diversity of sharks moving through the trade that might have otherwise gone undetected.

According to shark scientist Demian Chapman, Prasetyo’s method is a useful complement to existing DNA testing techniques for shark trade monitoring. Chapman is a senior scientist and director of the Center for Shark Research at the Mote Marine Laboratory in the United States. He has published numerous studies on the shark fin trade in Asia and helped get several shark and ray species on CITES lists.

“It’s a great application, and certainly another tool in the toolset of those who are tasked with enforcing laws to protect these animals,” says Chapman, who wasn’t involved in the study. While shark dust fills an important gap in helping authorities narrow down where to search for illicit activity, he says, there remains a need for DNA testing of shark products to take illegal traders to court.

Prasetyo’s findings are already changing the way Indonesia’s fisheries ministry monitors the country’s trade in sharks and rays. “They are very happy, because they can imagine how easy [it will be] for them to do the detection,” Prasetyo tells Mongabay. To make the possibility a reality, Prasetyo is working to acquire seven DNA analysis machines the ministry can use to analyze shark dust. The plan is to distribute the machines across Indonesia, making testing more efficient; currently, any samples collected for metabarcoding must be sent to Jakarta. In the meantime, he and his colleagues have helped train ministry staff to collect both shark tissue and shark dust samples for DNA analysis.

If all goes according to plan and shark dust metabarcoding is widely adopted throughout Indonesia, it could be an important step toward stronger and more accurate enforcement of the country’s shark protection laws. And, according to Chapman, that possibility isn’t restricted only to Indonesia: “You could use this anywhere.”

Banner image: The top five CITES-listed sharks detected were the scalloped hammerhead, silky shark, smooth hammerhead, spot-tail shark, and great hammerhead. Image by Masayuki Agawa / Ocean Image Bank.

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Citations:

Prasetyo, A. P., Murray, J. M., Kurniawan, M. F., Sales, N. G., McDevitt, A. D., & Mariani, S. (2023). Shark‐dust: Application of high‐throughput DNA sequencing of processing residues for trade monitoring of threatened sharks and rays. Conservation Letters, 16(5). doi:10.1111/conl.12971

Cardeñosa, D., Fields, A. T., Babcock, E. A., Shea, S. K., Feldheim, K. A., & Chapman, D. D. (2020). Species composition of the largest shark fin retail-market in Mainland China. Scientific Reports, 10(1). doi:10.1038/s41598-020-69555-1