Conservation means Indonesian sharks must be captured by technology  

Beneath the shimmering surface of our world’s oceans lies an intricate web of marine life, where each species contributes an essential thread to the delicate fabric of our planet’s oceanic ecosystems. Yet, this equilibrium is now under dire threat, endangering the very tapestry of marine biodiversity through the spectre of extinction.

The tapestry, woven by countless organisms on Earth, is rapidly unravelling, experiencing an unprecedented and alarming decline. In just 50 years, our planet has borne witness to an astonishing 70% plummet in animal diversity, a stark and sobering testament to the profound and often detrimental impact of human activities on the natural world.

Among the most vulnerable inhabitants of our oceans are sharks and rays, collectively known as elasmobranchs. These remarkable creatures, once viewed as apex predators, now find themselves ensnared in a perilous struggle for survival.  

Characterised by sluggish growth, late maturation, and low reproductive rates, elasmobranchs face significant hurdles in replenishing their dwindling numbers.

The epicentre of this crisis is none more pronounced than in the waters of Indonesia. Indonesia boasts a remarkable one-fifth of the world’s shark and ray species diversity, with more than 220 documented species within its waters.

The sharks and rays are attracting tourists, with the economic value of shark tourism at least $22 million annually. But only 6 of these species are granted comprehensive protection against all forms of catch and trade – whale sharks (Rhincodon typus), giant manta rays (Mobula birostris), reef manta rays (Mobula alfredi) and 3 sawfish species.

Indonesia also prohibits the export of four globally endangered species – oceanic white-tip sharks (Carcharhinus longimanus) and three hammerhead shark species.

But Indonesia is also host to the world’s most extensive shark and ray fishery, yielding an annual average catch of 110,737 metric tons during the period spanning 2007-2017. While specific fishing communities may actively pursue these apex predators, a substantial portion of this tonnage is likely unintentional bycatch – as highlighted by a 2018 report from the Wildlife Conservation Society, which indicates that around 86% of Indonesian fisheries incidentally capture sharks and rays.

This plays a vital role in shaping the future of these creatures. However, there exist trade-offs between the goals of conservation and the socioeconomic significance of shark fishing within the nation. “We cannot think of it just from the perspective of shark and ray conservation,” Indonesian fisheries biologist Andhika Prasetyo told Mongabay in 2021. “People’s livelihoods and diets must also be considered.”

As a response to this challenge, Indonesian authorities have implemented a range of measures aimed at curbing the decline of elasmobranch populations. These strategies encompass an array of interventions, including the expansion of protected species, robust outreach programs, refinement of data collection and stock assessment methods, the establishment of marine protected areas, and the enactment of port state measures to counter illegal fishing activities.

There exist trade-offs between the goals of conservation and the socioeconomic significance of shark fishing.

Yet the effective oversight of trade is often limited to easily identifiable species, like the manta rays.  The recent efforts of these authorities, detailed in a newly published study, underscore a collective determination to safeguard these vital marine species from the precipice of extinction.

Amidst these trials, a glimmer of hope emanates from the convergence of science and technology. The advent of DNA-based diagnostic tools has catalyzed breakthroughs in the realm of wildlife identification, led by the FASTFISH-ID method.

A cutting-edge real-time PCR (polymerase chain reaction) technique, FASTFISH-ID provides a rapid and portable avenue for species identification. This novel approach harnesses fluorescent probes to pinpoint specific genetic markers within the DNA, working in tandem with the amplification of a universal DNA barcode segment.

The result is the creation of unique fluorescent signatures, individual to each species. Subsequently, a real-time PCR machine scrutinizes these signatures, equipping researchers and conservationists with the ability to identify species with remarkable precision.

Originally designed for teleost (bony) fish, the FASTFISH-ID method has now demonstrated its potential for elasmobranch identification.

In a bold move, researchers embarked on a mission to ascertain whether the existing FASTFISH-ID diagnostics could effectively generate a diverse array of fluorescent signatures, each distinctive and species-specific, for the 28 frequently traded elasmobranch species found in Indonesian waters.

They also wanted to investigate whether a deep machine learning approach could quantitatively assign these signatures to their respective species, independent of the visual fluorescence characteristics.

Meticulously sifting through data and discerning 33 incongruous runs, distinguished by poor probe-barcode hybridisation or irregular fluorescent signatures, the team yielded a triumphant result: the successful generation of 357 pairs of fluorescent signatures. This rich repository encompassed a diverse ensemble of 28 species, constituting 14 sharks and 14 rays. Astonishingly, this assortment featured 22 species acknowledged as CITES-listed, with 12 classified as sharks and 10 as rays.

Leveraging the amalgamation of barcode segments facilitated the identification of a myriad of species, unveiling unique signatures that set them apart – examples include pelagic thresher sharks (Alopias pelagicus), bigeye threshers (Alopias superciliosus), and longfin mako sharks (Isurus paucus). Furthermore, the discerning eye could visually differentiate 22 species, while the integration of a deep learning algorithm achieved an impressive 79.41% accuracy in species identification, highlighting its potential as a valuable supplementary identification tool. However, some species exhibited akin signatures in both barcode segments, leading to occasional misclassification.

Leveraging the amalgamation of barcode segments facilitated the identification of a myriad of species.

At the helm of this groundbreaking work is researcher Andhika P. Prasetyo, affiliated with the University of Salford. Prasetyo and his team firmly assert FASTFISH-ID as a promising technological avenue for identifying elasmobranch species, underscoring its advantages encompassing speed, portability, universality, and single nucleotide resolution. The capacity to analyse even processed products renders this method a vital asset for authorities, spanning fish inspectors, customs officials, and quarantine officers.

Despite its limitations, such as hybridization challenges and misassignments, Prasetyo and his fellow scientists harbor an optimistic belief that ongoing enhancements and database expansions will further amplify its efficiency and precision. Their shared vision is to harness this method as a potent tool to unravel the complexities of the shark and ray product trade, ultimately mitigating the consequential risk of extinction faced by these iconic and endangered taxa.