NOAA Fisheries has identified a new way to deliver more timely genetic information to help resource managers and fishermen in their effort to reduce salmon bycatch in commercial groundfish fisheries.
Having access to information like this faster is particularly important given some concerns that salmon caught incidentally as bycatch may be contributing to a decline in Chinook and chum salmon runs, especially in western Alaska.
Understanding the Issue
Fishermen participating in fisheries off Alaska sometimes catch fish they do not want, cannot sell, or are not allowed to keep. These unwanted fish are collectively known as bycatch.
The Magnuson-Stevens Fishery Conservation and Management Act (MSA) requires that bycatch be minimized to the extent practicable. In the Alaska Region, the North Pacific Fishery Management Council and NOAA Fisheries have adopted measures to limit the catch of species taken incidentally in groundfish fisheries. Certain species, such as chum and Chinook salmon, are designated as “prohibited species” in groundfish fishery management plans because they are the target of other, fully utilized domestic fisheries.
The incidental catch of salmon in groundfish fisheries is closely monitored to ensure that all salmon are counted, and representative samples are analyzed using genetic tools to estimate what stocks are being caught.
Scientists at the Alaska Fisheries Science Center have been working to speed up genetic analyses and share results with industry to integrate stock-specific information into bycatch avoidance strategies.
“We’ve been working hard to deliver more comprehensive information faster so that it can be more efficiently integrated into the management process,” said Wes Larson, program lead for the Science Center's Genetics Program.
Technological Advancements in Genetic Stock Identification
The Science Center’s Genetics Program works to determine where salmon caught as bycatch originate. This information is vital to understand the impact of bycatch on various Chinook and chum salmon runs within the North Pacific. Scientists also are exploring ways to help the fishing industry avoid catching specific stocks through integrative analyses that combine large datasets to predict stock specific distributions.
In studying salmon bycatch, scientists hope to:
- 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 Analysis).
- Merge stock identification with other data to predict stock-specific distributions and potentially help fishing fleets avoid certain stocks (e.g., western Alaska stocks).
Genetic stock identification of the salmon bycatch from commercial trawl fisheries in the Bering Sea and Gulf of Alaska is completed each year to determine which salmon stocks are most affected by the fisheries. Stock composition reports are completed annually for chum and Chinook salmon in the Bering Sea and Gulf of Alaska.
Scientists use genetic information from chum and Chinook salmon bycatch in the pollock trawl fisheries to estimate the number and proportion of these salmon being caught.
For chum salmon, the contribution of six regional groups is estimated: Southeast Asia, Northeast Asia (Russia), Western Alaska, Upper/Middle Yukon (Yukon River fall chum), Southwest Alaska, and Eastern Gulf of Alaska/Pacific Northwest.
For Chinook salmon, the contribution of 11 regional groups is estimated: Russia, Coastal Western Alaska, Middle Yukon, Upper Yukon, North Alaska Peninsula, Northwest Gulf of Alaska, Copper River, Northeast Gulf of Alaska, Coastal Southeast Alaska, British Columbia, and West Coast United States.
During the past year, NOAA Fisheries geneticists have worked with Alaska Fisheries Information Network (AKFIN) to develop comprehensive databases for chum and Chinook salmon. These databases link observer collected information with genetic and age data.
Scientists have integrated new Genotyping-in-Thousands (GTseq) chemistry into the laboratory workflow. This method simultaneously generates genotypes (the genetic makeup of an organism) for thousands of individuals, subsequently increasing the statistical power needed to distinguish salmon sub-populations or stocks. As a result, they have been able to decrease turnaround time. They have also piloted the collection of dried DNA by fisheries observers for more efficient sampling and higher sample quality.
Additionally, Patrick Barry, a NOAA Postdoc, developed tools and software to more quickly process data, conduct additional analysis and streamline reports.
These advancements have allowed the genetics laboratory to deliver data much faster. For example, the lag time between bycatch occurrence and reporting of data has decreased by nearly a year for chum salmon. These advancements will be available for Chinook salmon starting in 2023.
This means that managers and industry have information from the most recent year when starting to fish. This should facilitate more effective stock-specific avoidance strategies. The stock-specific impacts of bycatch also can be estimated more quickly. This is important for informing management of different stock groupings.
Salmon Bycatch by the Numbers
Salmon bycatch levels vary from year to year due to changing environmental conditions, run sizes, fleet behavior, and other factors.
In 2021, in the Bering Sea/Aleutian Islands pollock directed fisheries bycatch mortality was an estimated 546,043 chum salmon and 13,783 (in pollock directed fisheries) and 15,895 (in all groundfish) Chinook salmon.
Genetic analysis indicated that 51,510 of the 545,883 chum salmon caught as bycatch in 2021 originated from rivers in western Alaska including the Yukon and Kuskokwim. These western Alaska fish represented 9.4% of the total chum bycatch.
During 2020, 18,195 of the 32,294 Chinook salmon caught in Bering Sea/Aleutian Islands groundfish fisheries were from western Alaska stocks including the Kuskokwim and Yukon. These fish represented 56.4% of the total Chinook salmon bycatch.
A Closer Look at Chum Salmon
In a given year, the largest stock found in the chum salmon bycatch is either Northeast Asia or Eastern Gulf of Alaska/Pacific Northwest (southern stocks including Southeast Alaska, British Columbia, Washington, and Oregon). In general, Asian fish are found more to the west and are caught earlier in the summer season, whereas Eastern Gulf of Alaska/Pacific Northwest fish are found further east and caught later in the year.
NOAA Fisheries is working to determine if there are certain times and areas where the pollock fishery is more likely to encounter Western Alaska chum salmon. Early work shows that in general, the proportion of Western Alaska chum salmon caught as bycatch is greater early in the summer and further east. However, these are initial estimates and further modeling is necessary to determine if these patterns are supported by available data.
A Closer Look at Chinook Salmon
During 2020, an estimated 32,294 Chinook salmon were taken in the bycatch of Bering Sea/ Aleutian Islands pollock trawl fisheries. The Chinook salmon bycatch estimate was 6% below the historical average (34,589) between 1991 and 2019. This is far below the highest overall Chinook bycatch in 2007 when an estimated 122,195 fish were taken.
The Bering Sea Chinook salmon bycatch has never approached 2007 levels since that year, and has stabilized near 20,000 fish. Regulatory changes contributed to this decrease, as the incidental harvest between 1991 and 2010 averaged 40,976 and after the implementation of Amendment 91 between 2011 and 2019, the average dropped to 19,328.
Western Alaska was the largest contributor to the bycatch in 2020 (52%). There were smaller contributions from British Columbia (15%), North Alaska Peninsula (13%), and West Coast US (7%). Since 2017, the contribution of British Columbia and West Coast US fish has been decreasing, while the proportion from Western Alaska stocks has been increasing.
The estimated numbers of Chinook salmon caught as bycatch from Coastal Western Alaska stocks has varied from a high of 17,421 in 2011 to a low of 4,635 in 2018. Total catches of Coastal Western Alaska stocks were relatively stable from 2012 to 2018 and were consistently below 8,000 fish. We anticipate that the number of Western Alaska Chinook salmon caught as bycatch in 2021 will be consistent with 2012-2018 data.
Adult Equivalency Models
Science Center scientists have developed models to better understand and help resource managers address bycatch impacts. These models, after accounting for natural mortality, produce estimates of the number of adult fish that would be expected to return to their natal rivers to spawn if they hadn’t been taken as bycatch in the Eastern Bering Sea pollock fishery.
The estimate of impact rates has averaged 1.9% since 2011 for the combined coastal Western Alaska stocks and 0.6% for the Upper Yukon River stock.
In 2021, the impact rate to the Western Alaska stock group was estimated as 2.64% and the impact rate to the upper Yukon was estimated as 1.10%. This means that bycatch accounted for < 3% of the total runs to each of these systems in 2021.
Run reconstructions that provide an estimation of total run size are more limited for chum salmon than for Chinook salmon in Western Alaska. A scientifically defensible run reconstruction includes a fairly thorough estimate of escapements (the number of fish that are not caught by fisheries and contribute to the spawning population) and harvests.
Run reconstructions are currently only available for Yukon River summer and fall chum salmon and Kwiniuk River chum salmon. This excludes large populations in Kuskokwim River and throughout Bristol Bay, Kotzebue Sound, and Norton Sound.
Unlike Chinook salmon, the lack of run reconstructions for large populations of Western Alaska chum salmon means that a good approximation of total Western Alaska chum salmon abundance cannot be provided at this time. However, the Science Center also has contracted Alaska Department of Fish and Game to age Chinook and chum salmon so that age data can be integrated into an updated adult equivalency analysis in the near future.
What’s Next?
Preventing and reducing bycatch is a shared goal of fisheries managers, fishermen, the environmental community, and subsistence users. The Science Center is involved in several research efforts to both learn more about bycatch impacts and reduce bycatch.
“We have reduced turnaround time for chum estimates by nearly a year and are attempting to do the same for Chinook next year. We also are collaborating with the commercial fishing industry to identify new ways of fishing, and to explore fishing gear modifications and new technologies to minimize bycatch in commercial trawl fisheries,” said Larson.
Additionally, the Genetics Program is working with partners from universities, state agencies, and industry to develop stock-specific distribution models. The goal of these models is to help predict where certain important stocks (e.g., Western Alaska) are found. This will help fishermen to avoid these stocks. This large effort integrates data from a large number of sources including genetics, fleet fishing patterns, environmental variables, surveys and more. These models will be developed and integrated into bycatch management over the next few years.
Center staff also are involved in a number of other studies in collaboration with the state of Alaska and Indigenous community members to learn more about salmon ocean survival, disease and how warming ocean temperatures are affecting salmon growth, development and survival in the Yukon-Kuskokwim River systems.
