Fisheries Genomics Scientist Adam Ciezarek, and PhD researcher Josie Dix, are combining their expertise to help improve sustainable fishing — using genomics to bring new precision to marine science.
For billions of people worldwide, fish are a crucial source of protein. But with demand expected to increase 10% by 2032, global fish stocks are under growing pressure from both rising consumption and climate impacts such as warming seas, salinity changes, and pollution.
Effective management of fisheries is vital, to balance the needs of communities, industry, and the natural environment they rely on.
In the UK, commercial fishing is carefully managed through international negotiations and quotas - supported by scientific advice. Bodies like the International Council for the Exploration of the Seas (ICES) assess the health of fisheries across the Northeast Atlantic, supporting government policy across different nations.
Robust and accurate data are central to this, and it’s the focus of a new collaboration between Earlham Institute and the Centre for Environment, Fisheries and Aquaculture Science (Cefas) - developing high-quality pangenomic resources to inform sustainable fisheries management.
Since the 1990s, global aquaculture - the breeding and farming of fish and shellfish - has dramatically increased to help meet rising demand for healthy and sustainable food sources. At the same time capture fisheries - the fishing, harvesting, and capture of wild aquatic species from their natural environment - has plateaued, partly due to the exploitation of existing stocks.
In the UK, the picture is slightly different, with capture fisheries still vastly surpassing aquaculture for production.
What do we mean by fish stock?
A stock is a management concept , which is used to set quotas, policy and reporting, whereas a population is a biological unit defined by the genetic diversity, and structure within a species.
Sustainable fisheries require stock units to correspond closely with biological populations. Alignment between stocks and populations improves the accuracy of stock assessments and reduces uncertainty in fisheries advice and management decisions.
“We’re interested in whether fish species are genetically unique to the spatial boundaries they reside in,” says Josie Dix, PhD Researcher in the Haerty Group at Earlham Institute.
Her joint research project with Cefas is studying the population structure and genetic diversity of wild capture marine species around the UK and Ireland, starting with Atlantic Pollack (P. pollachius).
A mixed-catch species (caught in amongst other fish), pollack are significant for both commercial marine capture and marine ecosystem health.
But recent concern around declining populations of pollack in the Celtic Seas and English Channel led to ICES advice for zero catch in 2024 and 2025, causing significant challenges for commercial fishers in these mixed fisheries.
Previous studies of the population found little variation, but newer technologies and research methods, including long-read sequencing and pangenomics, are capable of providing the finer detail needed for defining population structure.
“We simply don’t have enough information about their population structure,” explains Josie. “For example, pollack off the west coast of Ireland may be genetically distinct from pollack off the south coast of England, and therefore may be harvested at a higher or lower rate than others, leading to uneven fishing pressures and a potential reduction or loss of vulnerable stocks.”
Drawing on a 2024 Cefas population study in which commercial fishers collected samples across the western English Channel, Josie and colleagues in the Technical Genomics Group at Earlham Institute are generating long-read sequences to develop pangenome resources for pollack, and investigate links between genetic diversity and spatial boundaries (their geographic territory).
“Understanding population structure across some wild capture fisheries species has been notably difficult because the signals can be very subtle and previous methods weren't always able to capture the level of detail required, explains Josie. “Third-generation sequencing (long-reads) combined with pangenome approaches can provide a high-resolution genomic lens to capture variation that species like pollack may have previously been missing.”
Traditional single reference genomes can introduce bias and miss important variation. In contrast, pangenomes - collections of genomes from multiple individuals within a species - provide a more complete picture of genetic diversity.
These methods are already transforming agriculture and plant sciences, and through the Earlham Institute’s Decoding Biodiversity programme, scientists are developing the tools required to build and analyse them.
We really want policy to be based on the absolute best information we possibly can. Developments in genomics move so fast that the collaboration with Earlham Institute allows both organisations to explore the very latest science and knowledge, aiming to generate a much stronger evidence base than if we each worked in isolation.
Dr Adam Ciezarek
As part of her PhD, Josie is working alongside Fisheries Genomics Scientists Dr David Murray and Dr Adam Ciezarek at Cefas.
Previously a Postdoctoral Researcher at Earlham Institute working on conservation genomics, Adam is now embedding genomics-led insights in the fishing sector to help ensure sustainable, healthy, and productive marine and freshwater ecosystems.
“Managing fisheries is incredibly complicated. Because of the interconnected nature of seas and ocean, fish mix, spawn, and feed across many different areas. At a genomic level, across large geographic scales we see fish looking identical. But in small genomic regions we may see very small but important differences that underpin biological processes or adaptations,” explains Adam.
“Although fishery management treats pollack as a single stock in the Celtic Seas and English Channel, there is very little known of the biological population structure in the area. And so the pangenome work Josie is leading on is really important as we may be missing a lot of important diversity with our current single-reference genome approach.” he adds.
Applying these methods to wild marine species is particularly valuable to capture hidden variation. Insights generated through Josie and Adam’s work are expected to play a key role in informing fisheries policy, supporting more sustainable and resilient management strategies.
“We really want policy to be based on the absolute best information we possibly can. Developments in genomics move so fast that the collaboration with Earlham Institute allows both organisations to explore the very latest science and knowledge, aiming to generate a much stronger evidence base than if we each worked in isolation,” says Adam.
Third-generation sequencing (long-reads) combined with pangenome approaches can provide a high-resolution genomic lens to capture variation that species like pollack may have previously been missing.
Josie Dix
Josie’s project builds on years’ of research at the Earlham Institute studying the diversity, hybridisation, and adaptations of aquaculture species in East Africa. Prior to starting her PhD Josie developed her genomics and bioinformatics skills with a UEA Masters’ course in the Haerty Group at Earlham Institute.
“I’ve always wanted to work with nature and conservation. In 2017 I started an undergraduate degree in Zoology, but at that stage I didn’t know which field I wanted to specialise in. Following a year’s break I started my MRes in Evolution and Genomics and I knew immediately I wanted to work at Earlham Institute,” she says.
“Their focus on genetics, and bioinformatics is amazing. I remember listening to a talk by a former colleague that was so inspiring that I could really see myself in that environment.”
As Josie says, the rapid development of third-generation sequencing, combined with developing methods such as pangenomes, is already generating significant new insights for questions in crops and agriculture, and now Josie is able to apply these cutting-edge methods to answer key questions in marine biology.
“I feel so passionate about conservation. My grandparents used to run a fish and chip shop, and I remember my grandad talking to me about the need to look after our fish, and make sure we’re fishing sustainably. Given the climate impacts our seas and fishes are experiencing at the moment I feel even more driven to make whatever difference I can in the field.”
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