Shark Genomics Seascapes

Illegal fishing in the Indian Ocean has drastically decreased reef shark populations and severely impacted ocean ecosystems. The loss of these important species leads to imbalance in the oceanic food web, leading to a decline in coral reef health and the loss of other marine organisms that depend on health reef environments.

Advanced DNA sequencing presents an opportunity to identify sub-populations of reef sharks across the entire Indian Ocean region. This study is working to create a Genomic Seascape, or comprehensive DNA catalogue, of reef shark populations within the Indian Ocean which will enable enhanced tracking of shark populations. By matching genetic signatures of illegally fished sharks with those of catalogued populations, the location of areas that are being targeted by illegal fisheries can be identified. These Genomic Seascapes can then be used as a management tool once lower cost, portable sequencing technology and genetic testing capacity is introduced at key fishing ports in the Indian Ocean.

Reefshark Genomescapes

Overfishing has severely depleted marine populations worldwide, including within protected areas. Illegal and unreported fishing are major contributors to this decline. Large-bodied apex predators such as sharks are among the most affected, with overfishing driving dramatic species declines and ecosystem destabilization through trophic downgrading. Key barriers to effective marine conservation and management include: data deficiencies that hinder population benchmarks and impact assessments; limited surveillance, which allows illegal fisheries to disproportionately target apex predators; and insufficient capacity in vulnerable nations to monitor and protect species within their waters.

Our study, led by Shaili Johri in collaboration with colleagues, communities, and institutions across 12+ countries, addresses these challenges through a novel genomic framework that enables assessment of shark population diversity and health while also improving fisheries traceability by detecting instances of illegal fishing across the Indian and Pacific Oceans. We present the Reefshark Genomescape, the first genome-wide reference database for Indo-Pacific reef sharks, which provides an assessment of genetic diversity, structure, and connectivity of two key species across their Indo-Pacific range and allows geographic assignment of fished individuals using population-specific genetic signatures.

We show that grey reef shark (Carcharhinus amblyrhynchos) populations exhibit high genetic diversity, strong population structure, and elevated Fst values, with previously unknown connectivity between the central and western Indian Ocean and clear isolation of populations in the Andaman Sea. In contrast, silvertip sharks (Carcharhinus albimarginatus) display high connectivity but show genomic signals of declining population health, supporting a reassessment of their IUCN status. Using supervised machine learning with Monte Carlo cross-validation, we assigned geographic origins to fished grey reef sharks with 96% accuracy.

These findings provide critical insights into the population structure, connectivity, and health of two ecologically important reef shark species, while establishing a robust method for assigning geographic origin. We anticipate this framework will support regional conservation assessments and targeted management. Moreover, by enabling the identification of fishing hotspots and detection of IUU fishing, it lays the groundwork for a broader traceability system in marine ecosystems. Much like the landmark elephant ivory tracing study, this approach has the potential to transform marine conservation globally.

Preprint: https://doi.org/10.1101/2025.09.22.676358

Preprint of Manuscript in review: http://dx.doi.org/10.2139/ssrn.5387526

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