DNA tool for tracing fish can improve quota decisions and sustainability

The often arbitrary and historical way that fish quotas in the North Atlantic have been assessed is set to change with the arrival of powerful new DNA tracing technology that allows scientists trace fish populations back to their origins with 95 per cent certainty.

The DNA Fisheries TraceBack platform, which has been developed by MSD Animal Health, promises to trace the origins of fish right back to their spawning waters in the same way that genetic technology has been developed to trace plant and animal origins.

“It’s a bit like genealogy or ancestry-type genetic analysis that you undertake if you want to know more about your family background,” says Irish scientist Ciaran Meghen, the science, analytics and quality lead for MSD Animal Health. “It’s analogous to ancestry.com or 23andme, but for fish,” he says.

Meghen is a former director of TCD spinout Identigen which was purchased by MSD in 2020, and was a key figure in the development of the Fisheries TraceBack platform, along with marine research collaborators working in both industry and academia.

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Identigen, which emerged from TCD genetics in 1996, developed tools to trace the genetic origins of animal food products. In 2013, technology the firm developed found horse DNA in more than a third of cheap frozen beefburger products. After changing the agri-food sector here, the company, now part of MSD, looked to the fishing industry.

The International Council for the Exploration of the Sea (ICES) a cross-national marine science body set up in 1902, is the authority that advises the European Commission on the setting of fishing quotas for commercial species of fish. In the absence of data, the ICES made quota decisions based on where a fish was located on a map when caught, or how much of a particular fish a fleet from a given nation landed in centuries past.

The TraceBack platform can enable the ICES to make better decisions on annual fishing quotas — using science and genetics rather than history and geography, Meghen says, while helping fisheries scientists to better understand what caught fish belong to what population and to determine how many fish can be caught sustainably in any location.

The platform can currently trace the genetic origins of eight of the 200 commercial fish species in the world. The goal is to upgrade it so that it can trace the top 50 species in the world, which together represent about 80 per cent of the world’s commercially important fisheries.

Species

Distinguishing between fish species is no easy task, says Dr Edward Farrell, chief scientific and sustainability officer with the Killybegs Fishermen’s Organisation, a group that has a keen interest in developing a more scientific basis for deciding fish quotas to ensure the health and sustainability of Ireland’s offshore fishing industry.

Taking herring as an example, Farrell says it is virtually impossible to distinguish between populations based on physical appearance and geographic location alone. This is important, because one type of herring might be on the brink of extinction — totally unknown to scientists — even though overall population numbers appear healthy.

“When we look at the difference between the herring population in the Irish Sea that spawns to the south of the Isle of Man and that in the Celtic Sea, that spawns mainly off Dunmore East, we find that they differ in only about three small parts of the genetic material, and in less than 20 individual bases,” says Farrell.

“Finding these is like finding a needle in a haystack but the advances in whole genome sequencing give us the power to do this now,” says Farrell.

“Simply put, in order to count fish accurately, you have to know where they come from and what population they belong to,” says Farrell. “Until recently this basic requirement has largely eluded fisheries scientists.”

The platform has been rolled out for tracking herring in the Celtic Sea and the next step is the waters off the west of Ireland

Herring populations have traditionally been divided into those supposedly living above 60 degrees north and those that live below that line, but this was an arbitrary division, says Farrell. “Genomic sequencing of herring populations found that they are very distinct and locally adapted to environmental conditions.”

The DNA tool developed by MSD Animal Health helps to separate these species of herring, with a very high degree of confidence, says Farrell. The idea is to get everyone using the same technology and data so that research bodies can work together to assess fish stocks.

The platform has been rolled out for tracking herring in the Celtic Sea and the next step is the waters off the west of Ireland. Other researchers are using it to trace herring in the Baltics, and the plan is to join up the data across all herring areas.

The Killybegs fishermen are keen to have a better, more scientific way to assess stocks could be found, in order to protect the long-term sustainability of the offshore fishery. “They have invested massively in boats and processing facilities over the years, and have one eye on the future, and the bigger picture,” says Farrell.

Future

The funding for genetic studies on fish is not as extensive as for genetic studies into human disease and medicine, which is one reason why scientists say it has taken so longer to develop a genetic tool for tracking fish in the offshore.

“We have put seven different species on this tool,” says Leif Andersson, a fisheries scientist at the University of Uppsala who collaborated on developing the platform.

“But the long-term goal would be to have every commercially exploited fish in Europe and around the world on a chip like this, so that any fishing industry, or government, could use this tool to monitor a fish population and maintain viable stocks of fish.”

The collapse of the once-thriving Newfoundland fishery in the early 1980s, where overfishing destroyed a fishing ground that still hasn’t recovered, must be avoided, says Andersson. “This was an enormously rich fishery, but completely collapsed.”

The fisheries platform could help avert such a situation while, in future, it could be taken a step further, says Andersson, with a simple-to-use, real-time onboard test.

“The ultimate goal is to develop a tool which could operate like a simple Covid-19 test, and test fish in real-time onboard ship to see what species they are. At the moment, the catches are landed and all the tests are done afterwards,” says Andersson. The tests he hopes for are technically possible even now, but are prohibitively expensive.

The price for failure will be that fisheries collapse or end up being unsustainable through overfishing, or lack of sufficient data on which to make good decisions. “You may end up wiping out a smaller population without realising it,” says Andersson.

The platform can help herring, Andersson’s main species of interest, and other species to avoid the kind of total collapse that happened to cod in the North Atlantic in 1992 — where numbers dropped back to 1 per cent of historical levels mainly due to overfishing.

“Herring are plankton feeders and are a really important prey for other fish, birds, and sea mammals like seals and whales,” says Andersson. “They are like a motor in the Atlantic ecosystem because they feed on plankton and then are fed on by other mammals, including humans.”