Mapping Risk and Resilience Across Indo-Pacific Reefs with Shark Genomescapes

Abstract

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 causing dramatic species declines and ecosystem destabilization due to trophic downgrading. Key barriers to effective marine conservation and management include: Data deficiencies that hinder population benchmarks and impact assessments, limited surveillance, allowing illegal fisheries to disproportionately affect apex predators, and insufficient capacity in vulnerable nations to monitor and protect species within their waters. Our study 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, an assessment of genetic diversity, structure, and connectivity of two key species across their Indo-Pacific range and 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 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, our approach has the potential to transform marine conservation globally. Graphical AbstractWe developed the Reefshark Genomescape, a genomic framework for assessing shark population health and fisheries traceability across the Indo-Pacific. Genome-wide data from grey reef and silvertip sharks revealed contrasting patterns, unexpected connectivity, and genomic signals of decline. Geographic assignment of fished individuals reached 96% accuracy, enabling detection of illegal fishing and identification of hotspots. This framework strengthens regional management, supports IUCN reassessments, and lays the foundation for global marine traceability systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/676358v2_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@1eafd3aorg.highwire.dtl.DTLVardef@96ebd1org.highwire.dtl.DTLVardef@541d02org.highwire.dtl.DTLVardef@3c9ca2_HPS_FORMAT_FIGEXP M_FIG C_FIG