Genetics Shines New Light on Cod Populations and Distributions in Alaska

A team of researchers from NOAA's Alaska Fisheries Science Center, the University of Alaska-Fairbanks, and Alaska BioMap, Inc., recently published the most comprehensive population genetic assessment of Pacific cod . Pacific cod is a commercially and ecologically important species in the North Pacific Ocean, and this study identified four distinct genetic stocks. This research provides critical, novel information for setting appropriate stock boundaries for Pacific cod. It shows that our management boundaries generally align with the genetic structure across this region.

Genetic Stock Identification with a New Cost-Effective Tool

"We were interested in using advanced genetic techniques to determine genetic differences among Pacific cod from different regions in Alaska," said Sara Schaal, lead author of the study. "We collected samples from fish caught in known spawning grounds during the NOAA winter trawl surveys and from our fisheries partners within the Freezer Longline Coalition."

Schaal and her colleagues first conducted whole-genome sequencing, which identified four genetically distinct stocks of Pacific cod within the Gulf of Alaska and Bering Sea:

• Eastern Gulf of Alaska
• Western Gulf of Alaska/eastern Bering Sea
• Aleutian Islands
• Northern Bering Sea

Results highlight significant genetic mixing between Pacific cod spawning in the western Gulf of Alaska and the eastern Bering Sea. This aligns with satellite tag studies that showed high proportions of Pacific cod movement between these two regions outside of spawning season.

The stocks identified using genetics match current management areas, except for the eastern Bering Sea and western Gulf of Alaska, which are currently managed as separate stocks. However, these data show they cannot be distinguished at the genetic level. Additionally, results clearly delineate two distinct stocks within the Gulf of Alaska-with a break between the western and eastern Gulf of Alaska. This had been suggested by previous work, but was clearly shown in this new study.

Using the most informative genetic sites along the Pacific cod genome, the researchers designed, built, and implemented a panel of genomic markers using a method called Genotyping-in-the-Thousands by Sequencing (GT-Seq). This panel delineated the four genetically distinct stocks with greater than 90 percent confidence-proving it is extremely accurate for identifying Pacific cod stocks. The GT-seq panel will be a cost-effective and powerful way to investigate many research questions on the ecology of Pacific cod.

Limited Adult Seasonal Movement and Variable Juvenile Recruitment of Unique Genetic Stocks

The team used the GT-seq panel to determine the genetic stock for Pacific cod of unknown origin. Some of these were juveniles collected from nursery grounds throughout the Gulf of Alaska. Others were adults collected during the summer non-spawning season from NOAA summer bottom trawl surveys and the International Pacific Halibut Commission longline survey. "We were interested in how much mixing occurs between genetically distinct stocks during the periods when they are not concentrated on their spawning grounds," explained Dr. Schaal. So they applied the GT-seq panel to the samples from Pacific cod of unknown origin to ask two main questions:

1. What is the seasonal variation in stock-specific adult distribution?
2. What is the stock-specific distribution of juvenile Pacific cod throughout the Gulf of Alaska?

Applying the GT-seq panel to adult Pacific cod identified limited seasonal movement between the four distinct genetic stocks, except for the northern Bering Sea. In the northern Bering Sea, the researchers found significant mixing of the northern Bering Sea and western Gulf of Alaska/eastern Bering Sea stocks during non-spawning months. Future tagging efforts combined with GT-seq analysis would help to better understand movements between the northern and eastern Bering Sea. Tagging studies complement genetic data by providing additional information on fish movement.

GT-seq results from juvenile Pacific cod caught throughout the Gulf of Alaska indicated that larvae generally move westward along the Alaska Coastal Current toward Shelikof Strait. But this is not always the case. In some years, juveniles that are genetically a part of the western Gulf of Alaska/eastern Bering Sea stock appeared within coastal nursery grounds of the eastern Gulf of Alaska. This suggests that there is some eastward movement, which is potentially driven by eddy formations.

These data provide novel insights into passive movement of larvae. They will inform expectations of oceanographic models on early life stage Pacific cod movement in the Gulf of Alaska.

Conclusions

Pacific cod is an extremely important species both economically and ecologically in the Gulf of Alaska and Bering Sea. In 2024, the harvest totaled 374 million pounds valued at $106 million. This study shows that our management boundaries generally align with the genetic structure across this region, with the exception of the movement between the western Gulf of Alaska and the eastern Bering Sea.

Stock assessment modelers are already referencing these findings in conjunction with recent tagging work to ensure accurate management strategies for Pacific cod. Developing this cost-effective genetic tool is a critical asset that will increase the research we conduct on the ecology of Pacific cod. Ultimately, these advancements are incredibly valuable to help ensure the sustainability of these fish stocks and their fisheries.