Auke Bay Laboratories

Scientists at the Alaska Fisheries Science Center's Auke Bay Laboratories study commercially important fish species such as rockfish, sablefish, and salmon. They conduct research to better understand where fish live during each stage of life and pinpoint what makes them unique, down to their DNA. They also examine marine ecosystems that are essential fish habitats, focusing on ocean processes and chemistry, and food web interactions that impact fish survival.

Our goal is to estimate how many fish are in Alaska's waters through stock assessments. We also want to learn the overall health of fish species, the habitats they utilize, and the ecosystem upon which they depend. We do this through research surveys, laboratory experiments, and by updating mathematical models to gain the best information about Alaska's commercial fish. The data biologists collect is given to the North Pacific Fishery Management Council, Alaska Regional Office, fishing industries, state and federal regulators, and international groups. These groups make decisions on how much fish can be sustainably caught.

Marine Ecology and Stock Assessment Program

The Marine Ecology and Stock Assessment Program has three primary functions. We 1) conduct annual stock assessments to manage the fisheries resources in Alaska waters, 2) conduct annual surveys to assess the status of these resources, and 3) perform ecological research process studies to inform stock assessments and advance ecosystem-based fisheries management.

Specifically, we produce annual stock assessment and fishery evaluation reports for sablefish, rockfish, and sharks in Alaska. We use a variety of fish population models to integrate fishery catch, survey data, biological observations, and theoretical considerations to recommend annual fish quotas. We conduct an annual longline survey and tagging studies to provide information for the stock assessments for Pacific cod, skates, Perch, Pacific halibut and other flatfish. Field and laboratory studies provide important information on different aspects of fish life history such as recruitment (i.e., when a fish is large enough to be caught by a commercial fishery), movement, growth, maturity, and natural mortality. We integrate this ecosystem process research into our stock assessments to support ecosystem-based fisheries management. Our program also conducts research on essential fish habitat, benthic habitats, and cold water corals and the effects of fishing on these sensitive ecosystem components. In our work, we often collaborate with other scientists, both within NOAA and with external partners, and with fisheries managers, stakeholders, and the general public. The Salmon Ocean Ecology and Bycatch Assessment Program provide an annual pink salmon forecast.

Recruitment, Energetics, and Coastal Assessment Program

The Recruitment, Energetics, and Coastal Assessment Program develops and monitors indicators of ecosystem status and energy flow through different trophic levels in the marine food chain. Our analytical products can be used with survey data to assess the response of juvenile year classes (young age groups of fish) of fish to changing environmental conditions and to identify essential fish habitat. Young fish survival is key to understanding future fish population productivity. Our goal is to provide indicators of fish population productivity and protected resources population health (e.g., humpback whales) for resource managers use.

We conduct fully-integrated studies from sample collection to modeled results, and peer-reviewed publications. We conduct field projects in nearshore waters and laboratory experiments designed to understand how fish respond to environmental change. Our state-of-the-art chemistry lab is the Center's largest analytical laboratory. We perform broad-spectrum analyses on fish health and condition to better understand food webs and processes of ecosystem change and recruitment variability in Alaska's nearshore habitats. These analyses include indices for fish growth (RNA/DNA), nutritional status (proximate analysis, thiamine levels, bioenergetic measurements (diet, calorimetry) and prey resource identification (genomics, fatty acid analysis and compound-specific stable isotope analysis). We achieve our work through extensive collaborations within NOAA and with external partnerships.

Ecosystem Monitoring & Assessment Program

Ecosystem Monitoring and Assessment Program scientists collect information from Alaska's Large Marine Ecosystems including the Arctic, Eastern Bering Sea, and Gulf of Alaska. Through research surveys and other studies we collect data and information on temperature, salinity, oxygen, nutrients, phytoplankton (tiny plants), zooplankton (marine bugs), jellyfish, and fish. We use this information to understand what causes changes in the growth, fitness, and survival of fish including: walleye pollock, Pacific cod, Arctic cod, saffron cod, sablefish, rockfishes, salmon (i.e., Chinook, chum, sockeye, pink, and coho), arrowtooth flounder, and forage fishes such as Pacific herring, capelin, sandlance. Our research results are used to help develop Alaska marine ecosystem status reports and provide scientific advice to manage and protect marine resources and human communities.

Chinook and chum salmon are incidentally caught in federally managed fisheries in the Gulf of Alaska and Bering Sea. We combine data from fishery and non-fishery sources to study targeted catch rates, bycatch rates and how bycatch varies by area and different times of year. Bering Sea and Gulf of Alaska surveys focus on early marine ecology of salmon. Field stations (Little Port Walter and Auke Creek) conduct research on factors that affect marine migration, survival and shifts in age and physical characteristics of Chinook and other salmon. Samples of Chinook and chum salmon from the commercial fishing fleet and from tagged fish caught in salmon and non-salmon fisheries are used to determine the age and stock origin (i.e., the natal streams). Information from these data sets provide a better understanding of the impact of bycatch on specific stocks of salmon.

Genetics Program

The primary goal of the Alaska Fisheries Science Center Genetics Program is to utilize genetic tools to inform management of marine resources, primarily fish and crabs. Genetic tools have the advantage of identifying subtle clues that are not recognizable using typical experimental design. For example, DNA shed by marine species (environmental, or eDNA) can track the presence of species in the ocean, even without a net. DNA has been used to track the number of Atka mackerel contributing to a fertilized egg cluster (more than 2!) and can sometimes even help identify new species. 

Our three primary focal areas of research are: (1) conducting genetic stock identification on salmon caught as bycatch or in targeted fisheries to provide required information for regional, national, and international agreements and treaties, (2) investigating the stock structure and stock-specific distribution patterns of federally managed species to inform stock assessments and fisheries management, and (3) using environmental DNA and other molecular tools to understand species diversity, distribution, phenology, and ecology. In addition, we have recently started looking at how changes in the marine environment affect gene expression. Some of our current research includes determining the origin of Chinook and chum salmon stocks incidentally caught (bycatch) in the Bering Sea and Gulf of Alaska groundfish fisheries, investigating stock structure and adaptation of rockfish, Pacific cod, and sablefish, and using eDNA to investigate species diversity in a changing Arctic and in deep sea environments near coral aggregations. We are also looking at differences in the gene expression in red king, tanner, and snow crab under different ocean acidification conditions and plan to expand this research to fish.