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Surprising Findings in Genetic Study about Pacific Cod in Alaska

November 02, 2021

Scientists find strong evidence that adaptation to their local environment could potentially make some Pacific cod stocks more vulnerable to Climate Change than others.

Pacific cod and northern rockfish swimming among coral

Understanding genetic differences among fish stocks is an integral component of successful fisheries management strategies. Pacific cod are an important commercial fish species caught throughout Alaskan waters. Cod caught in the Gulf of Alaska and Bering Sea are managed as separate stocks. A new genetics study found that the relationship between the Bering Sea and Gulf of Alaska may be a bit more complicated than originally thought.

In this study, scientists looked at one region of the genome, which is an organism’s complete DNA, including all its genes. They found evidence to suggest that a genetic break between fish from Bering Sea and Gulf of Alaska may fall further to the east than is currently designated under existing management measures.

Scientists also found genetic evidence to suggest that local adaptation to environmental conditions may be critical to Pacific cod development and survival.

scientist on research vessel holding a Pacific cod
Ingrid Spies holding a Pacific cod during a NOAA Fisheries survey.

The Evolution of the Pacific Cod

Pacific cod is believed to have originated from an Atlantic cod ancestor that moved into the Pacific Ocean 4 million years ago. Today, Pacific cod are found throughout the Western Pacific. They are found in the Eastern Pacific along the Korean Peninsula. In the United States, their range extends from the Chukchi Sea to as far south as northern California. Populations at the southern edges of both the eastern and western Pacific show distinct genetic differences from northern populations.

Pacific cod undertake annual feeding migrations that are not well understood. However, scientists know that Pacific cod typically return to their natal spawning areas during winter months to reproduce. 

“While many of the genetic differences between Pacific cod populations can be explained by reproductive isolation caused by strong homing behavior, the mechanisms underlying these differences have not been specifically explored,” said Ingrid Spies, stock assessment scientist and geneticist with the Alaska Fisheries Science Center. “Such selective processes are increasingly relevant to the effective management of Pacific cod, given recent ocean warming events that have resulted in steep declines in Gulf of Alaska populations and anomalous summer feeding migrations into the northern Bering Sea.”

NOAA Fisheries scientists have found that these events emphasize sensitivity to temperature related to growth and survival in Pacific cod. There is a broad species range of Pacific cod, from the temperate climates of Korea and the Pacific Northwest to the arctic and subarctic conditions of the Bering and Chukchi Seas. This also suggests that local populations of cod are adapted to thermal profiles specific to their habitat. 

In this study, Spies and her colleagues looked at a specific gene region called zona pellucida or ZP3. They wanted to assess its role in geographic variation among Alaska’s two Pacific cod stocks. 

Scientists have studied ZP3 in other mammals and fish. In these species, ZP3 helps prevent polyspermy, in which two sperm fertilize a single egg. When this happens the embryo may die. ZP3 protects the embryo and aids in the fertilization process. In Antarctic fish eggs, ZP3 also produces an antifreeze protein that helps fish survive in colder water.

The Role of ZP3 in Defining Alaska Pacific Cod Stocks

Scientists examined the genetic structure of 230 samples collected from 16 spawning locations during the winter spawning season December-May (2003–2019). The samples were collected during this time when fish were spawning to avoid the chance of stock mixing. 

They found that the genetic structure of fish, at the ZP3 gene, from the Aleutian Islands, Bering Sea, Shumagin Islands, and Kodiak collections were similar and distinct from fish found in Prince William Sound and southward.

“The genetic differences between neighboring populations of Pacific cod at the ZP3 gene were extremely unexpected. They are similar to those found in  salmon populations, which return to very specific environments to spawn and are locally adapted to those environments. This is not often the case for marine fish,” said Wes Larson, a co-author on this study who leads the Alaska Fisheries Science Center Genetics program.

This suggests that large differences in habitats across small geographic areas are leading to very different selective pressures. For example, differences in water temperature may be affecting Pacific cod development at small spatial scales within the Gulf of Alaska. 

Further work is needed to study the role of ZP3 in Pacific cod found throughout the Gulf of Alaska. It could play a role in whether some populations of fish are more or less tolerant to warming ocean temperatures. Other work by NOAA Fisheries stock assessment scientists have found evidence that cod at early life stages are particularly vulnerable to temperature shifts. Warm temperatures also affect prey availability for both young and adult fish in the Gulf of Alaska.

Spies suspects that this may be the case as during and after the heatwave in the Gulf of Alaska (2014–2016). During that period, the population size of the Eastern Gulf of Alaska cod stock remained low but stable. In contrast, the cod stock in the Central Gulf of Alaska declined by about 30 percent per year, and by 23 percent per year in the Western Gulf of Alaska. 

“We also need wider-scale sampling of fish caught in winter and summer fisheries from the Shumagin Islands and Kodiak to have a more complete picture of genetic diversity across seasons. Currently these areas are managed as part of the Gulf of Alaska stock, but results from this work suggest that fish found here, at least during the winter, are more similar to fish found in the Bering Sea.”

Management Implications

Spies, Larson and colleagues plan to conduct further work to look at the whole genome of cod to refine stock structure and inform management. At this point only snapshots of the genome are available.Spies, Larson and colleagues plan to conduct further work to look at the whole genome of cod to refine stock structure and inform management. At this point only snapshots of the genome are available. While these snapshots (such as ZP3) are important, knowledge of the whole genome is necessary to provide managers with better information to make decisions about whether changes in management boundaries are warranted. 



Last updated by Alaska Fisheries Science Center on July 11, 2023