Unveiling Hidden Vulnerabilities: The Cape Snoek Genetic Diversity Study

Cape snoek, known scientifically as Thyrsites atun, has long been a beloved staple along South Africa's Western Cape coast. This pelagic fish, prized for its firm flesh perfect for braai and curries, supports small-scale fishing communities and provides affordable protein to low-income households. However, a groundbreaking genetic diversity study from Stellenbosch University (SU) reveals alarming vulnerabilities in local populations. Led by Dr. Sihle Mthethwa from SU's Department of Genetics, the research uncovers distinct genetic stocks with restricted gene flow, recent bottlenecks eroding diversity, and calls for tailored fisheries management to avert collapse.

The study challenges long-held assumptions of snoek as a single, resilient panmictic population. Instead, it identifies multiple isolated groups, making them prone to overexploitation despite seemingly sustainable overall catches. As catches decline and imports rise, this work underscores the urgent need for science-based conservation.

The Cultural and Economic Pillar: Cape Snoek in South African Life

Cape snoek migrates seasonally along the Benguela Current, arriving in autumn to thrill anglers at harbour walls—a tradition passed down generations. Historically stable catches fueled local economies, but recent declines have forced reliance on New Zealand barracouta imports, often mislabeled as local snoek. This shift threatens food security and coastal livelihoods, where snoek accounts for significant linefish harvests.

In South Africa's Traditional Linefish sector, snoek is a key species. The Department of Forestry, Fisheries and the Environment (DFFE) manages via vessel allocations rather than strict Total Allowable Catches (TAC) for many linefish. Recent 2026-2027 allocations slashed small-scale vessels from 547 to 77 nationwide, signaling broader pressures. Historical data from DFFE's 2025 status report notes linefish declines, with snoek catches dropping from peaks around 2,700 tonnes amid rising effort and environmental stressors.

Decoding the Genome: Methodology Behind the Stellenbosch Snoek Research

Dr. Mthethwa's PhD project sampled snoek from South Africa, New Zealand, Chile, and remote Southern Hemisphere islands, spanning time periods to track changes. Using advanced molecular genetics—likely Restriction site-Associated DNA sequencing (RAD-seq) or similar—researchers analyzed evolutionary history, gene flow (F_ST metrics), and population structure.

Key questions: Are South African Cape snoek and New Zealand barracouta the same species? How connected are global populations? Is the SA stock uniform? DNA markers revealed cryptic structure: distinct clades with limited interbreeding, even sympatric groups sharing habitats.

Global Genetic Tapestry: Distinct Snoek Stocks Across Oceans

Globally, Thyrsites atun forms isolated genetic clusters shaped by ocean currents and historical barriers. Restricted gene flow—low migration between regions—means populations evolve semi-independently. SA samples diverged from Indo-Pacific and Australasian kin, confirming New Zealand barracouta as conspecific but not interchangeable for local management.

This structure implies global fisheries treat snoek as meta-populations at risk; overharvesting one doesn't replenish others quickly. For SA importers, genetic verification prevents fraud, ensuring transparency.

Local Secrets: Multiple Stocks Along South Africa's Coast

Within South Africa, Cape snoek comprises at least two genetically discrete stocks, possibly three including a Namibian overlap. These coexist in Western Cape waters but rarely interbreed, per high F_ST values indicating isolation.

• Stock 1: West Coast/Benguela focus, vulnerable to upwelling variability.
• Stock 2: Agulhas Bank, influenced by warmer currents.
• Potential Stock 3: Northern extension shared cross-border.

Such cryptic diversity means uniform quotas risk depleting weaker stocks, as stronger ones mask declines.

Genetic Bottleneck: Evidence of Decline and Erosion

Temporal sampling shows a recent bottleneck: sharp drops in heterozygosity and effective population size (N_e). Factors include intensified fishing, climate-driven shifts (e.g., warmer waters altering prey), and habitat loss. Reduced diversity hampers adaptation to ocean acidification or El Niño events.

Dr. Mthethwa notes: “Genetic diversity and numbers have declined in recent generations,” echoing DFFE reports of falling catch per unit effort (CPUE).

Snoek Fishery Today: Declining Catches and Management Challenges

Linefish catches fell amid policy shifts post-2002 Marine Living Resources Act. Snoek, once abundant, sees volatile runs; 2025 DFFE data flags declines. Small-scale fishers report erratic shoals, blaming trawlers and poaching. DFFE's 2026 allocations prioritize sustainability, but critics decry impacts on 30,000 fishers.

Imports fill gaps, but ecological mismatches persist—NZ stock doesn't rebuild SA biomass. Climate change exacerbates: Benguela warming shifts prey like anchovy, starving predators.

Tailored Fisheries Management: Key Recommendations

The study urges stock-specific quotas, genetic tagging in assessments, and monitoring. Examples:

• Separate TAC/effort limits per stock.
• Marine Protected Areas (MPAs) safeguarding juveniles.
• International collaboration via ICCAT-like for Southern snoek.
• Labeling laws distinguishing imports.

Dr. Mthethwa: “Sustainable management must be based on genetic evidence, not just catch numbers.” Integrate eDNA for real-time tracking.

Stakeholder Voices: From Fishers to Policymakers

Small-scale fishers via Masifundise lament cuts threatening culture. DFFE emphasizes science-led recovery, citing rock lobster TAC hikes as success. Experts like SU's Prof. Aletta van der Merwe (genetics) praise integration of genomics in policy.

Broader views: WWF-SASSI rates snoek 'orange'—proceed with caution—urging consumers choose certified.

Stellenbosch University's Role in Marine Genetics Research

SU's Genetics Department pioneers stock delineation, from chondrichthyans to pelagics. This snoek work builds on mitogenome sequencing (e.g., 2023 Mitochondrial DNA B Resour.). Careers abound in research jobs blending genomics and ecology, vital for SA's blue economy.

For aspiring scientists, SU offers PhDs; explore academic CV tips.

Photo by Spekboom on Unsplash

Future Outlook: Safeguarding Snoek for Generations

With proactive measures, snoek stocks can rebound. Genetic insights enable resilient management amid climate threats. Ongoing monitoring, community co-management, and tech like AI stock modeling promise sustainability.

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