Cape Snoek Genetic Study Reveals Distinct Populations and Vulnerability | Stellenbosch University

Unlocking the Genetic Secrets of Cape Snoek Populations

The Cape snoek (Thyrsites atun), a beloved staple in South African cuisine, especially along the Western Cape coast, is facing unprecedented challenges. A groundbreaking genetic study led by Dr. Sihle Mthethwa from the Department of Genetics at Stellenbosch University has revealed that local snoek populations consist of at least two genetically distinct groups that do not interbreed freely, despite their close proximity. This discovery underscores the fish's vulnerability, as declining genetic diversity coincides with noticeable drops in catches, making the species less resilient to environmental pressures and overfishing.

Snoek, known scientifically as Thyrsites atun—a pelagic predator in the nutrient-rich Benguela Current ecosystem—holds cultural and economic significance. From beach braais to commercial fisheries, it supports livelihoods and traditions. However, years of heavy exploitation have raised alarms, prompting researchers to delve into its genetic makeup for sustainable management insights.

Background on Cape Snoek: A Pelagic Icon of South African Waters

Cape snoek migrates seasonally along South Africa's west coast, arriving in autumn to feed on sardines and anchovies. Historically, catches peaked in the mid-20th century but have since plummeted. Fisheries data indicate a steady decline, with recent years showing reduced abundance ahead of peak seasons like Easter. The fish reaches sexual maturity around three years at 73 cm fork length, but overfishing targets larger individuals, disrupting reproduction.

In South Africa, snoek is not just food; it's a cultural emblem. Artisanal fishers and recreational anglers rely on it, while commercial operations supply markets. Yet, without understanding population structure, management efforts risk depleting isolated stocks irreversibly.

The Methodology: Advanced Genetic Analysis at Stellenbosch University

Dr. Mthethwa's research employed cutting-edge DNA sequencing techniques, including high-throughput genotyping and population genomics. Samples were collected from key fishing grounds around the Cape, analyzing thousands of genetic markers to map diversity and structure. This approach—known as restriction site-associated DNA sequencing (RAD-seq)—allows precise identification of subtle genetic differences, revealing barriers to gene flow.

• Sample collection from multiple sites along the coast.
• Genomic sequencing to assess heterozygosity and effective population size.
• Phylogenetic modeling to trace divergence.
• Comparison with global snoek populations from Chile and elsewhere.

Stellenbosch University's Genetics Department, renowned for marine population studies, provided the expertise. Previous work on species like dusky kob informed this project, highlighting declining trends in overfished stocks.

Key Findings: Distinct Genetic Groups and Low Diversity

The study identified at least two distinct genetic clusters within South African Cape snoek waters—one west of Cape Point and another east—showing limited mixing. Globally, snoek forms separate lineages, with South African stocks unique. Genetic diversity metrics revealed low heterozygosity, signaling inbreeding and small effective population sizes (Ne).

Dr. Mthethwa noted, “The DNA analyses reveal that Cape snoek in South Africa comprise at least two genetically distinct groups that do not interbreed freely despite their proximity.” This structure implies local depletion risks if fishing ignores stock boundaries.

Compared to historical data, current diversity is markedly lower, correlating with catch declines from historical highs to current lows.

Declining Catches: Evidence from Fisheries Records

South African snoek landings have fallen sharply. Department of Forestry, Fisheries and the Environment (DFFE) reports show commercial catches dropping over decades, with recreational sectors also affected. Recent pre-Easter concerns highlight stocks at critically low levels.

Factors include overexploitation, bycatch, and ecosystem shifts from climate change altering prey availability. Genetic bottlenecks exacerbate this, reducing adaptability.

Vulnerability Factors: Overfishing Meets Genetic Constraints

Low genetic diversity impairs resilience to stressors. Distinct populations mean uniform quotas could wipe out smaller groups. Climate-induced Benguela upwelling changes threaten migration patterns.

• Reduced Ne leads to inbreeding depression.
• Limited gene flow prevents recovery.
• High fishing pressure on adults skews demographics.

“Species less able to cope,” warns the research, urging targeted protections.Stellenbosch University press release

Implications for Fisheries Management and Policy

The findings advocate stock-specific quotas, marine protected areas (MPAs) around genetic hotspots, and monitoring via eDNA. DFFE could integrate genomics into total allowable catches (TACs).

Stakeholders, from small-scale fishers to exporters, must adapt. International parallels, like Chilean snoek management, offer lessons despite genetic separation.

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Stellenbosch University's Leadership in Population Genetics

SU's Genetics Department excels in applying genomics to conservation. Prof. Aletta Bester-van der Merwe's group has pioneered fish stock assessments, aiding species like kob. Facilities like the Central Analytical Facility support RAD-seq and mitogenomics.

This study exemplifies SU's commitment to interdisciplinary research, blending genetics, ecology, and policy for South Africa's blue economy.

Spotlight on Dr. Sihle Mthethwa: Driving Marine Conservation

Dr. Mthethwa, a rising star in marine genomics, completed this work as part of her doctoral research. Her passion for South African fisheries drives efforts to balance harvest with sustainability. “Genetics research wants to help protect Cape snoek,” she emphasizes.

Her contributions highlight opportunities in SA academia for genetics PhDs and postdocs.

Broader Ecological Context: Benguela Ecosystem Dynamics

Snoek thrives in the Benguela Current Large Marine Ecosystem (BCLME), shared with Namibia. Transboundary stocks require regional cooperation. Genetic data informs BCLME initiatives.

Photo by Anika De Klerk on Unsplash

Conservation Strategies and Future Outlook

Recommendations include:

• Genetic monitoring in annual surveys.
• MPAs to protect spawning grounds.
• Aquaculture trials for restocking.
• Public awareness for sustainable angling.

With proactive measures, snoek stocks could rebound, preserving this heritage species. Ongoing SU research promises more insights.

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