The Secret To Better Fisheries Management Is Hidden In Their DNA

DNA sequencing has gotten to be a lot less expensive and that has opened the door for many different uses. It is now relatively cheap to have your own DNA evaluated by services like 23andme or MyHeritage or Ancestry.com. You can learn about your ethnic background and even get connected with relatives you never knew. Sometimes there are surprises. While oral or written family histories are often incomplete or “sanitized,” the DNA record is fully transparent. It is also increasingly possible to learn about potential health risks you may have inherited.

There is an interesting application of DNA sequencing for tracking the “ethnicity” for ocean dwelling fish. Of course in that case it isn’t the fish who want the information – it’s the government agencies around the world who are responsible for managing ocean “fisheries” – the populations of wild fish that make up a significant part of the human food supply of protein and which provide healthy omega-3 fats and important minerals. According to a paper published in 2020 in the journal Nature titled “The Future of Food From the Sea,” humans currently derive 59 million metric tonnes of “food from the sea” of which 84% is from wild caught fisheries, and 16% is from “mariculture” – farmed fish and bivalves. That represents 17% of the global edible meat supply. By 2050 that amount is expected to increase to between 80 and 103 million metric tonnes, mostly through increases in mariculture. Even so, wild caught fish are still expected to provide between 56% and 71% of the 2050 total.

Alt protein graph

Humans have been harvesting ocean dwelling fish for centuries, and the ecosystems that support those fish are able to maintain a viable population even under a significant degree of human fishing pressure. However, there are historical examples of problematic overfishing such as the population of Atlantic cod that was once abundant off the coast of the US and Canada but which had collapsed by 1992.

Governments around the world have set up regulatory agencies to track important fish populations so that they can tell if they are being threatened by over-fishing. If that is happening, they can close the fishery in order to allow it to recover. Fish pay no attention to human boundaries and so there are many instances that require international cooperation. The United Nations has a Code of Conduct for Responsible Fishing and there are regional fisheries management organizations that work out the details. The system is not perfect, but at least for the developed world, fishing is largely a sustainable endeavor. However, there may be changes in ocean population dynamics linked to climate change and so the importance of monitoring and management is likely to increase.

Regulators have several tools that they use to monitor what is going on with fish population. For fish species that do a run up a clear fresh water river to spawn, it is possible to literally do sample counts of the fish as they are swimming upstream. They can do “acoustic surveys” that quantify general undersea movement in key locations, and then link that data to their own catch-based sampling to identify which species are involved. Regulators can measure the catch returned to shore by fisherman. Together these methods allow the regulators to do a reasonably good job of maintaining sustainable populations, but for some important species, it can be particularly difficult.

The complicating factor is that for somespecies of fish there are sub-populations called “stocks” that intermix in the open ocean for most of the year, but then go back at different times and or different places to “spawn.” That would be comparable to a diverse human society in which people still marry almost exclusively within their ethnic sub-community. For species like many salmon that have many distinct stocks which are caught as they go up their home rive, it is relatively easy to manage on a stock-by-stock basis by simply closing or opening fishing on a given river. For species that are harvested in the open ocean – stock-specific management is far more difficult. For instance there are six distinct stocks of Atlantic Cod.

The Georges Bank and Gulf of Maine stocks near the US are doing poorly as it one in the Celtic Sea. The stock in the North Sea is recovering, and the stocks in the Barents Sea and the shelves of Iceland are doing well (see map below). Particularly for the cod stocks on the eastern shore of the Atlantic, normal population sampling data only tells what is going on for the species as a whole, not the individual stock and so management decisions might not be able to strike the optimal balance between protection and supply.

For another important species, Herring, the situation is even more complicated. The map shown below describes the range of fourteen distinct herring stocks that regulators are trying to manage.

Many methods have been used in an attempt to track these distinct stocks ranging from attempts to find physical differences, to looking at their parasites, to physical tagging, but as a major recent study concluded:

“The reality is that confusion surrounding the population structure in herring across its distribution has persisted. This has prevented the identification of populations and hampered the delineation of stocks in many cases…”

In other words, these populations couldn’t really be optimally managed without a practical way to get the necessary stock-specific population estimates.

That made herring an ideal test case for the application of a DNA-based testing system that has been developed by the global animal health company Merck Animal Health in the US and Canada, also known as MSD Animal Health elsewhere including the EU, Latin America and Asia.

The starting point for this application of the technology was a Whole Genome Sequencing (WGS) of project conducted under the auspices of the Research Council of Norway (GENSINC: Genetic adaptations underlying population Structure IN herring). That step identified around 10 million “singular nucleotide polymorphisms” or SNPs that reflect the full genetic diversity within this species. Among those, academic researchers identified 800 more relevant SNPs that could be used to tell the difference between the herring stocks because they are connected with genetic differences that are “associated with ecological adaptation to different geographic areas and spawning conditions.” It was then necessary to get the list of markers down to a more practical number.

What followed was a major scientific study involving 17 cooperators from 6 countries was conducted in order to characterize the DNA of herring in existing and new ocean survey samples. This was a huge project looking at fish from fisheries surveys and commercial catches between 2014 and 2021. Their size, sex and maturity were recorded and a sample taken for DNA testing. 45 SNPs were chosen for the DNA testing and from the third quarter of 2019 to the end of the project in 2021 they shifted to having the samples sequence-tested using the DNA TRACEBACK®Fisheries Platform that is provided by Merck Animal Health, a commercial provider (they first confirmed that this service gave them the same genotype information as did their earlier lab method).

From that effort the authors determined that DNA testing gave them valuable new capabilities:

“If implemented as part of regular data collection on the MSHAS, the genetic stock identification method in the current study will enable the splitting of the survey indices into their constituent Division 6.a. populations, which has not previously been possible.”

There were two stocks for which the data suggested they were not actually distinct breeding populations and wouldn’t need to be tracked separately. The author’s overall conclusion was:

“What is clear is that the results of the current study have improved the capacity to delineate survey and assess the herring stocks in Division 6.a. and there is a need now to translate this into improved management.”

DNA-based stock-level monitoring may soon be expanded to other important species around the world, and Merck Animal Health is working with various researchers and regulators in that process, according to Ciaran Meghen, Science, Analytics and Quality lead for Merck Animal Health. Their list of projects includes Atlantic Salmon, Brown Trout, Cod, Herring, Horse Mackerel, Pacific Whiteleg Shrimp, Perch and Sprat. This entire field is an example of how advanced genetic technologies are helping with food supply sustainability challenges.