Collaborative Marine Salmon Research Foundational for Understanding Climate Change Impacts and Bycatch

Research Priorities

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NOAA Fisheries has a long and varied history of salmon research in Alaska, much in close coordination with scientific partners, including the State of Alaska. 

Currently the Alaska Fisheries Science Center’s salmon research focuses on four strategic areas:

1. Understanding and addressing salmon bycatch in commercial pollock fisheries through fishery observer data collection and genetics research and collaborative work with the commercial fishing industry to identify more efficient ways to fish and reduce salmon bycatch. Future research topics in this area include pairing genetic stock composition data from bycatch analysis with environmental and salmon distribution data to predict stock-specific distributions to help the fleet avoid certain stocks (e.g., Western Alaska stocks). 
2. Providing information on the marine life-history (migration, growth, and survival) and ecology (diet, condition, and prey abundance) of salmon, and providing assistance to State of Alaska salmon fisheries management through pre-season forecast models of run size and harvest for select stocks of salmon.
3. Providing technical advice and data to support management of Alaskan salmon fisheries where U.S. treaty obligations exist under the Pacific Salmon Treaty, the Convention for the Conservation of Anadromous Stocks in the North Pacific Ocean and the High Seas Driftnet Enforcement Act.
4. Various special projects supporting Magnuson-Stevens Fishery Conservation and Management Act requirements (e.g., Essential Fish Habitat, National Standard 8, National Standard 1) and NOAA Fisheries Ecosystem-based Fishery Management Policy such as conducting ethnographic studies and related research to better understand how subsistence, commercial and recreational fishing communities are being impacted by climate change as part of its climate modeling projects for the Bering Sea and Gulf of Alaska. 

“Climate change is posing new challenges to resource managers. Our long-term observations and data coupled with our critical partnerships with the state, the fishing industry and coastal communities will help us navigate what lies ahead,” said Robert Foy, director, Alaska Fisheries Science Center.

Partnerships to Reduce Bycatch in Commercial Fisheries

NOAA Fisheries works with the commercial fishing industry and fisheries observers to both learn more about where fish that are caught in the commercial pollock fishery originate (U.S. or international waters) and explore technological solutions or other ways to reduce bycatch in these fisheries.

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Genetics Research May Help Fishermen Avoid Specific Stocks of Salmon

The Alaska Fisheries Science Center’s Genetics Program works to determine where fish caught as bycatch originate. They also are exploring ways to help the fishing industry avoid catching specific stocks of salmon.

In studying salmon bycatch, the Science Center’s Genetics Program has three primary research goals 

• Determine the geographic origin of salmon caught in federally managed groundfish fisheries that are collected by NOAA Fisheries observers to estimate stock-specific impacts of bycatch.
• Determine the number of adult Chinook salmon that would have returned to their natal rivers if not caught as bycatch (Adult Equivalency (AEQ) analyses).
• Merge stock ID with other data to predict stock-specific distributions and potentially help fishing fleets avoid certain stocks (e.g., western Alaska stocks).

There is 100% observer coverage in the Bering Sea pollock fishery. The large amounts of data from this fishery present a unique opportunity to understand the impacts and dynamics of bycatch. 

Scientists count all salmon caught in the fishery. They then collect random samples of both Chinook (1 in 10) and chum (1 in 30). For these samples, length, sex, genetic samples, and scale samples for aging are collected. Genetic stock identification is then conducted on all sampled Chinook salmon and a subset of the sampled chum salmon to determine the genetic stock compositions of the bycatch. Samples analyzed for genetics are also sent to the State for age analysis. 

“An important area of research for us is developing stock-specific distribution models,” said Wes Larson, Genetics Program Manager, Alaska Fisheries Science Center.

This effort will integrate all historical data and current environmental data collected during fishing and survey operations to attempt to understand stock-specific distributions and predict future distributions.

“We are really excited about the possibilities of being able to understand stock-specific abundance patterns across space and time so that the fleet can attempt to avoid certain stocks (i.e. dynamic bycatch avoidance),” said Larson. “By using new technologies we are also able to process genetic samples faster and share more timely information with the industry and the council.”

Understanding stock genetic structure is important to more effectively manage bycatch in U.S. fisheries. Genetic stock ID on sockeye salmon also provides a basis for Pacific Salmon Treaty harvest sharing arrangements between the U.S. and Canada.

Pollock Fishing Industry and NOAA Fisheries Work Together to Reduce Bycatch

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Another focal area for NOAA Fisheries is bycatch reduction. To accomplish this, Alaska Fisheries Science Center staff in the Marine Assessment and Conservation Engineering Program work closely with the commercial fishing industry and other scientists on numerous projects to reduce Pacific salmon bycatch in the Bering Sea pollock fishery.

“We collaborate with industry partners to test new technologies, methods, and ideas in support of bycatch mitigation,” said Noelle Yochum, Alaska Fisheries Science Center Conservation Engineering. “Fishing industry insights, experience and support in this research are essential. Progress in this area of research would not be possible without them.”

Some current areas of research to reduce salmon bycatch centers around the use of salmon excluders in trawls and studies on salmon behavior. 

A Closer Look at NOAA Fisheries State-Federal Partnership in Research Surveys

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NOAA Fisheries and the Alaska Department of Fish and Game have been working together for more than a decade to collect and analyze data from research surveys. This work provides the scientific basis for management of salmon fisheries by the state of Alaska that have U.S. international treaty obligations and implications. 

The northern Bering Sea surface trawl survey, which has been conducted since 2002, and the southeast coastal monitoring survey are two of these cooperative surveys. During these surveys, a variety of data are collected including information on oceanography, salmon prey availability, distribution, diet, size, condition and relative abundance of juvenile salmon, forage fish and juvenile groundfish, like pollock.  

NOAA Fisheries scientists also participate on the Alaska Department of Fish and Game's southeast Alaska survey. It provides an annual assessment of stock status and health of pink and Chinook during early marine residence.

NOAA Fisheries also collaborated with Alaska Department of Fish and Game and other research organizations as part of the North Pacific Anadromous Fish Commission’s International Year of the Salmon winter surveys in 2019, 2021 and 2022. These surveys were designed to improve our understanding of the winter survival of salmon in the Gulf of Alaska and the North Pacific Ocean.

“Marine surveys that provide information on the abundance and ecology of juvenile salmon can add insight into the relative importance of these critical survival periods as well as the resilience of salmon to changes in marine ecosystems, such as the emergence of marine heatwaves,” said Jim Murphy, fisheries biologist, Alaska Fisheries Science Center. “These surveys also provide important ecosystem data to inform and validate our developing climate models so we continue to sustainably manage commercial groundfish and crab stocks.”

“It’s a perfect match of superpowers,” said Katie Howard, fisheries biologist, Alaska Department of Fish and Game. Our expertise in Alaskan salmon population dynamics and genetics combined with NOAA Fisheries’ expertise in marine ecology and ecosystem dynamics has transformed what we understand about Alaskan salmon at sea. The surveys provide a valuable platform to leverage our respective expertise to aid resource management.”

Data collected during these surveys have enabled state and federal scientists to provide annual assessments of stock status and health of salmon during early marine residence and provide run-size and harvest forecasts for specific stocks of salmon. 

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Surveys Help Shed Light on Climate Impacts on Alaska Salmon Runs

The annual northern Bering Sea surface trawl and ecosystem survey, which will be conducted later this summer, helps scientists monitor abundance, condition and distribution of juvenile salmon in the ocean.

“There is a direct relationship between the abundance of juvenile Chinook salmon that we see in the northern Bering Sea surface trawl and ecosystem survey during the summer and the number of adult fish that return to the Yukon River to spawn three to four years in the future,” said Ed Farley, Ecosystem Monitoring and Assessment Program Manager, Alaska Fisheries Science Center.

This information is used to help establish pre-season fisheries management strategies and harvest expectations for subsistence fisheries in the Yukon River. The eastern Bering Sea pollock fishery operates under a strict cap on salmon bycatch that varies with the abundance of Chinook salmon that are harvested for subsistence. 

“So there is definitely interest from both these groups in our ability to predict the size of Chinook salmon runs,” said Farley.

The initial forecast model for Yukon River chum salmon, which is under development by Sabrina Garcia at the Alaska Department of Fish and Game, appeared to point to a similar relationship between juvenile and adult abundance that has been observed in Chinook salmon. However, the survival of juveniles has declined, which coincides with marine heatwaves in the Bering Sea and Gulf of Alaska. The condition, or fat reserves, of juvenile chum salmon has also declined with warming temperatures. Prey quality and quantity are thought to be an important factor defining critical marine survival periods of Yukon River chum salmon.

For instance, during 2016-2019 when ocean temperatures were warmer than average, scientists observed low abundance of certain high-fat zooplankton during the northern Bering Sea survey. These small planktonic animals form the base of the northern Bering Sea marine food chain for whales, seals, sea birds, walrus and young fish, like salmon and pollock. 

When scientists looked at what juvenile chum salmon were feeding on during warm years, they noticed a high proportion of Cnidaria (jellyfish and anemones) in their stomachs. This group of species has just half the caloric content of the zooplankton species that chum are known to eat. The chum caught in 2018 and 2019 were also smaller than average. 

“The prey quality, quantity and warm ocean temperatures while young salmon are in the ocean impacts their growth and fat reserves during the summer,” said Farley. “Young chum salmon got a one-two punch during the marine heatwave years (2014-2018).”

Juvenile western Alaska chum salmon spend their first summer at sea feeding and growing within the shelf waters of the northern Bering Sea. These salmon migrate offshore during late fall, and spend their winter in the Gulf of Alaska. Juvenile chum salmon fed on lower quality prey and were smaller in size during the extreme warm events of 2016 through 2019 along the northern Bering Sea shelf. They then migrated to the Gulf of Alaska where the second marine heatwave was occurring. Reduced fat reserves from summer and higher metabolic rates during winter, a period of reduced prey availability, likely led to high mortality of these fish.

Salmon are a vital component of marine ecosystems and the socio-economic framework of coastal communities throughout Alaska. “There is still a lot we need to learn and that is why this research is so important,” said Howard.

What’s Next?

Data collected through long-term surveys and winter surveys in the Gulf of Alaska as part of the International Year of the Salmon campaign will be analyzed to compare how salmon did during three consecutive years with varying ocean conditions 

• 2019—conditions were still relatively warmer than normal
• 2020—conditions were more moderate
• 2022—conditions were colder

The Alaska Department of Fish and Game are also putting additional resources towards the study of salmon survival in the marine environment and Howard is heading up that effort. The plan will be to build on the successful work with NOAA Fisheries studying juvenile fish in the Bering Sea and Gulf of Alaska.

All acknowledge that the work will take some time to better understand the impacts of climate change on salmon and young groundfish in Alaska. However, having more than 20 years of data from NOAA Fisheries surveys will help inform the effort. 

“Our science provides a critical jumping off point for the state’s new salmon program. The continued collaboration between our two agencies is essential to help resource managers, at the state, federal and international level, respond and adapt to changing ocean conditions to ensure the continued sustainability of Alaska commercial and subsistence fisheries,” said Farley.

Farley also sees lots of potential for NOAA Fisheries to advance its ecosystem studies and groundfish studies through this collaboration.

Science Underpinning U.S. Enforcement Actions to Address Illegal, Unreported and Unregulated Fishing and Maintain Prohibition on High Seas Driftnet Fishing for Salmon

To help the U.S. combat illegal, unreported and unregulated (IUU) fishing, NOAA Fisheries develops predictive models for high seas salmon distribution. These models are used by the U.S. Coast Guard to apprehend fishing vessels engaged in these activities. NOAA Fisheries scientists also conduct stock and species composition analysis of salmon collected on the high seas during enforcement actions to support domestic and other nation's salmon management efforts.

International Scientific and Technical Advice 

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For many years, NOAA Fisheries scientists have played a key role on a number of scientific and technical committees and working groups established through the Pacific Salmon Commission and the North Pacific Anadromous Fish Commission. Scientists also engage in and coordinate international research projects (e.g., International Year of the Salmon Survey). 

“We also provide data from our surveys to assist the U.S. and Canada in their management of Yukon River salmon, said Murphy. “For instance, the northern Bering Sea juvenile-based adult run-size forecasts models for Canadian-origin and Total Yukon stocks have become important components of the annual pre-season management and harvest planning for the Yukon River.”

Specifically, Alaskan fishery managers have used the Canadian-origin Chinook salmon forecast to inform planning discussions for one to three years in advance of harvest management. This forecast also has been used on an annual basis by U.S./Canada Yukon River Panel’s Joint Technical Committee as part of a multi-model approach to forecast adult run size since 2018.

NOAA Fisheries, Alaska Department of Fish and Game and the University of Alaska Southeast and Fairbanks are involved in collaborative research on Coho, pink and sockeye salmon at the Science Center’s Auke Creek field station. This research provides insights into the effects of climate variability on southeast Alaska salmon populations and influence of genetics on salmon behavior. Collected data on the out migration and returns of coho salmon at Auke Creek are also used by Alaska Department of Fish and Game for management under the Pacific Salmon Treaty.

Auke Creek and Little Port Walter Research

Other work that allows NOAA Fisheries to gain valuable insights on transboundary stock status, marine survival and catch origin is continued work at both the Alaska Fisheries Science Center's Auke Creek and Little Port Walter research stations. 

At the Auke Creek research station our scientists work with partners to study

• Climate variability effects on coho, pink, and sockeye salmon (Alaska Department of Fish and Game, University of Alaska Southeast, University of Alaska Fairbanks). 
• Genetics of salmon run timing, life-history strategies, and fisheries enhancement (Alaska Department of Fish and Game, University of Alaska Southeast, University of Alaska Fairbanks). 
• Coho salmon marine survival and harvest monitoring for the Alaska Department of Fish and Game's management in support of the Pacific Salmon Treaty.

At Little Port Walter salmon-specific research includes:

• Monitoring hatchery returns to augment data from other private hatcheries to inform the Treaty.

• Science to support hatchery operations in Alaska.

Community-based Efforts to Learn More about Salmon

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Since 2014, NOAA Fisheries, the Alaska Department of Fish and Game, the Native villages of  Emmonak and Alakanuk, and the Yukon Delta Fisheries Development Association have been working together to study smolt salmon on the Yukon River.  Each summer, local fishermen and NOAA Fisheries biologists work together. They set and retrieve salmon sampling nets, identify and count the catch, and measure water temperature and depth. They send salmon smolt samples to the NOAA Fisheries Auke Bay Laboratories where their diet, body condition, and genetic stock of origin are analyzed. Through this work the team is learning more about the impacts of freshwater on salmon smolts. They have observed declines in Chinook smolt abundance since 2018 and low chum salmon smolt abundance in 2021. This research supports both our efforts to address requirements under National Standards 8 and 1 and further ecosystem-based fisheries management.

More recently, NOAA Fisheries’ social scientists have initiated a couple of programs in the Bering Sea and the Gulf of Alaska to learn more about scientific and traditional observations of the impacts of climate change on salmon and other local subsistence and commercial fisheries. They are looking at how changes in returns are impacting communities, and if and how people are adapting to these changes. This will help inform ACLIM and GOACLIM scientists on indicator development (e.g., for size declines in Yukon Chinook spawner-recruit model) and projecting climate change impacts on fish stocks and communities in the Bering Sea and Gulf of Alaska. This information is helping NOAA Fisheries meet its obligations under National Standard 8. Specifically, helping to further understanding the effect of federal fisheries on salmon returns to communities and to minimize the social and economic impacts to those communities.

Salmon Essential Fish Habitat

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Another important area of NOAA Fisheries research is supporting our partners at the North Pacific Fishery Management Council by providing information to help refine salmon Essential Fish Habitat. This involves collaborating with the University of Alaska Fairbanks and NOAA Fisheries resource managers to develop models and improve estimates of the location and extent of salmon Essential Fish Habitat. 

NOAA Fisheries social and biological scientists work along the Yukon River through the ACLIM project, which will help inform these models. 

Specifically scientists will use spatio-temporal dynamic modeling to:

• Quantify occupancy and habitat use
• Identify static and dynamic physical and biological habitat attributes (length/weight) associated with salmon presence and density
• Explore multiple sources of information on salmon distribution, across life stages

Thiamine Deficiency Research 

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Vitamin B1 (Thiamine) is an essential molecule in cell function. Thiamine deficiency has been identified as a contributing factor in Chinook salmon population declines. Thiamine deficiencies have been linked to early mortality (i.e.,death in salmon egg, alevin and fry stages of development), neurological and immune impairment, poor swimming behavior and an inability to avoid predators.

“Scientists have observed thiamine deficiency in salmon found in the Great Lakes, the Baltic Sea, the California Central Valley and here in Alaska,” said Cody Pinger, research chemist, the Alaska Fisheries Science Center’s Recruitment Energetics and Coastal Assessment Program. “We are seeing evidence of thiamine deficiency impacts in Southeast Alaska hatcheries. We are also monitoring thiamine levels in adult and juvenile fish in Yukon River Chinook salmon and in their eggs.”

To understand what is driving this deficiency, scientists are developing novel new tools to monitor both thiamine and thiaminase levels in prey species across Alaska's large marine ecosystems, and studying the impact of climate-mediated metabolic stress on thiamine levels. Studies are being conducted with partners including Alaska Department of Fish and Game, U.S. Geological Survey, Yukon River Drainage FisheriesAssociation, Tr’ondëk Hwëch’in Government, and the U.S. Fish and Wildlife Service. This research further supports NOAA Fisheries efforts to advance Ecosystem-based Management.

Emerging Areas of Research

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Important areas for future research that NOAA Fisheries hopes to explore with its partners include 

• Conduct salmon biological and ecological research to retain competencies for current and future NOAA Fisheries’ Alaska Regional Office and North Pacific Fishery Management Council salmon management issues.
• Conduct research focused on the effect of increased heatwave frequency on salmon populations and adaptations to more variable marine ecosystems.
• Investigate role of thiamine deficiency in salmon eggs as contributor to low survival.
• Develop model-based forage fish indicators for the Center’s annual Ecosystem Status Reports and Forage fish stock assessment.
• Expand climate modeling to address community impacts and adaptation.
• Determine the role of salmon as predator and prey in dynamics of groundfish populations.
• Integrated Ecosystem Surveys with more focus on advanced technologies to collect data to understand the climate impact on ecosystem function, fish fitness, and survival (i.e., uncrewed monitoring systems, moorings, satellite, eDNA, artificial intelligence).
• Pair stock composition data from bycatch analysis w/ environmental and salmon distribution data to predict stock-specific distributions; support bycatch avoidance strategies by the pollock fleet and help to understand salmon ecology.

Additional Information

Salmon Research in Alaska