Beneath the shimmering surface of our world’s oceans lies an intricate web of marine life, each species weaving an essential thread in the fabric of our planet’s delicate oceanic ecosystems. However, this balance is facing a crisis that jeopardizes the tapestry of marine biodiversity itself: extinction. Biodiversity, the rich tapestry of all life forms that roam our Earth, is now spiraling downwards in an unprecedented decline. In a mere span of five decades, the planet has been a witness to an astonishing 70% plummet in animal diversity, a stark and sobering testament to the profound impact of humans on the natural world.
Sharks and rays, collectively referred to as elasmobranchs, are emerging as some of the most vulnerable inhabitants of our oceans. Grappling with the mounting pressure of relentless fishing and overexploitation, the ramifications are far-reaching and have already been shown to be disrupting the fragile equilibrium of the marine ecosystems they call home. Whether as intentional targets or unfortunate by-catch, these magnificent animals are paying a heavy toll with many facing a risk of extinction. Characterized by slow growth, late maturity, and low reproductive rates, these species are struggling to replenish their numbers.
Urgent action is imperative… the very pulse of our planet’s heartbeat hangs in the balance.
And nowhere is the crisis more pronounced than in Indonesian waters, which hold the unfortunate distinction of recording the world’s largest volume of elasmobranch landings due to substantial bycatch. With nearly a quarter of the world’s elasmobranch species calling these waters home, Indonesia’s role in shaping the future of these species is undeniable. “Several measures have been established by the Indonesian authorities to reduce the decline of elasmobranch populations, such as: increasing the number of protected species, extensive outreach programmes, improvement of data collection and stock assessment, expansion of marine protected areas, as well as the establishment of port state measures to combat illegal fishing,” the authors of a new study explain.
But amongst these challenges, hope comes through the innovative intersection of science and technology. The advent of DNA-based diagnostic tools has paved the way for revolutionary breakthroughs in wildlife identification, and one such innovation is the FASTFISH-ID method. A cutting-edge real-time PCR (polymerase chain reaction) technique that offers a rapid and portable means of species identification. FASTFISH-ID operates on the principle of utilizing fluorescent probes to target specific genetic markers within a species’ DNA. This approach, coupled with the amplification of a universal DNA barcode segment, allows for the creation of distinct fluorescent signatures unique to each species. The real-time PCR machine then analyzes these signatures, enabling people to identify species with pretty remarkable accuracy.
It was originally developed for teleost (bony) fish but has potential for elasmobranch identification – and it is proving to be a game-changer. “We therefore chose to test whether the existing FASTFISH-ID diagnostics could produce a diverse range of fluorescent signatures unique and specific to each of the 28 elasmobranch species frequently found in Indonesian trade,” the authors propose. “And [investigate] whether a deep machine learning method could quantitatively assign signatures to the correct species, irrespective of the visual appearance of the fluorescence.”
By meticulously filtering out 33 incongruous runs characterized by deficient probe-barcode hybridization or irregular fluorescent signatures, a total of 357 pairs of fluorescent signatures were successfully generated. These signatures encompassed a diverse array of 28 species, encompassing 14 sharks and 14 rays. Remarkably, among these species, 22 were recognized as CITES-listed, with 12 falling under the category of sharks and 10 classified as rays. The utilization of combined barcode segments facilitated the discernment of numerous species, unveiling distinctive signatures that set them apart such as the pelagic thresher shark (Alopias pelagicus), bigeye thresher) (Alopias superciliosus), and longfin mako shark (Isurus paucus). Visual assessment of the signatures also distinguished 22 species, while a deep learning algorithm achieved an accuracy of 79.41% in identifying species, demonstrating its potential as a supplementary identification tool. However, some species displayed similar signatures in both barcode segments, leading to misassignments.
Through this work, led by researcher Andhika P. Prasetyo of the University of Salford believes the team has shown FASTFISH-ID to be promising technological method for identifying elasmobranch species, offering numerous advantages, including speed, portability, universality, and single nucleotide resolution. The ability to analyze even processed products also makes it an invaluable asset for authorities (i.e., fish inspectors, customs, and quarantine officers). Despite the current limitations, such as hybridization problems and misassignments, Prasetyo and the scientists believe that continuous improvements and expansion of the database will further enhance its efficiency and accuracy: “This method will help […] disentangle the complexity of the shark and ray product trade, and ultimately reduce the consequential risk of extinction for these endangered and iconic taxa.”
As we stand on the edge of an uncertain future, the combining of cutting-edge technology and dedicated conservation efforts offers a glimmer of hope for the well-being of these icons.
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