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  • Development of Large PIT-Tag Antennas to Estimate Migration Timing and Survival for Adult Salmonids near Pile Dikes in the Columbia River Estuary


Northwest Fisheries Science Center (NWFSC) Fish Ecology FE - Estuarine and Ocean Ecology


Pile Dike PIT-tag Antennas
Development of Large PIT-Tag Antennas to Estimate Migration Timing and Survival for Adult Salmonids near Pile Dikes in the Columbia River Estuary
Stationary PIT-tag antennas are used to interrogate PIT-tagged fish throughout the Columbia River hydrosystem and in streams to evaluate fish passage and survival for both juvenile and adult fish. Pile dikes are common in the estuary and in some areas located less than 0.5 kms apart and can be a substantial obstacle for migrating fish along the shoreline. Fishermen often utilize the area near pile dikes to target adult fish believing they become more concentrated as they circumvent the outermost piling during their upstream migration. This strategy was similar to that used in the late 19th and early 20th centuries by designers of effective fish wheel leads utilized with great success until banned. Estuary PIT-tag data obtained with a pair-trawl characteristically shows an increase in detection rate of juvenile fish when passing just outside of these pile dikes.

A proto-type Pile Dike Antenna (PDA) system deployed near river kilometer 70 since 2011 has enabled collection of limited timing and species composition data for adult salmonids (primary target) entering the estuary and juvenile salmonids (secondary target) exiting the estuary. Expansion of such antenna systems to passively sample passing fish at various fixed locations in the estuary enable calculation of survival rates to Bonneville Dam for adult salmonids to better evaluate impacts by marine mammals. PDAs potentially provide full year detection capability for both adult and juvenile salmonids in the estuary.

Research Themes

Ecosystem approach to improve management of marine resources
The California Current Large Marine Ecosystem, Puget Sound and the Columbia River Basin are home to a wide range of freshwater and marine resources that provide a wealth of ecosystem goods and services. Ensuring the resiliency and productivity of the California Current and Pacific Northwest ecosystems requires an integrated understanding of their structure, function, and vulnerability to increased human population growth in coastal communities and competing uses of coastal waterways and oceans. The NWFSC‘s approach to understanding these large ecosystems integrates studies across ecosystems (terrestrial, freshwater, and marine) and scientific disciplines to inform resource managers responsible for conserving marine resources.
Recovery and rebuilding of marine and coastal species
The Pacific Northwest is home to several iconic endangered species, including Pacific salmon and killer whales, and several rockfish species. Mandates such as the Endangered Species Act, MagnusonStevens Act, and the Marine Mammal Protection Act, grant NOAA Fisheries the authority to manage the recovery of depleted species and stocks. The NWFSC contributes to species recovery through research, monitoring and analysis, providing NOAA managers and regional stakeholders the tools and information they need to craft effective regulations and develop sustainable plans for recovery.
Sustainable, safe and secure seafood for healthy populations and vibrant communities
Effective fisheries management provides economic opportunities and ensures the long-term sustainability of fisheries and the habitats on which they depend. The NWFSC seeks to improve the quality and quantity of data used in stock assessments, the methods for assessing stocks and ecosystem sustainability within the context of human modification of the environment. The NWFSC also provides state-of-the-art science and technology to support aquaculture while protecting and maintaining ecosystem health. Further, pathogens, toxins from harmful algal blooms (HABs), chemical contaminants and other stressors of marine ecosystems pose significant risks to health of both seafood resources and to humans. The NWFSC focuses on research to improve understanding of those risks, how to forecast them, and identify means to mitigate their impacts.

Research Foci

Assess ecosystem status and trends
Tracking the status of ecosystems across time and space is data intensive as it necessitates evaluating a broad range of trophic levels and environmental conditions from pre-European times to the present. Because ecosystems vary across space and time, the NWFSC must maintain a research focus on the design and implementation of monitoring programs that are capable of capturing this variability. Key research elements are the development and application of novel survey designs, the development of information rich metrics and indicators, and the development of novel spatiotemporal decision support models to facilitate the use of monitoring data in science based decision making. Long-term monitoring program design should be integrated with the development of ecosystem models and indicators to ensure that critical data are collected to support these efforts. An important management goal is the ability to quickly detect important changes in the state of ecosystems (e.g., presence of an invasive species) such that preventative actions can be taken as soon as possible; thus, key management questions and uncertainties should be identified as the structure of monitoring program design to facilitate the decision-making process. It is imperative that the NWFSC’s monitoring science strengths be applied to the design of ecosystem monitoring programs for species (e.g., salmon, rockfish) and ecosystems so that such programs are strategically designed to maximize useable information and minimize cost and effort.
Characterize ecological interactions (e.g. predation, competition, parasitism, disease, etc.) within and among species
Predator-prey interactions, inter- and intra-specific competition, and parasites and pathogens influence the survival, growth, and reproductive success of anadromous and marine fishes, marine mammals and other marine organisms. Moreover, anthropogenic stressors, such as pollution and fishing, can influence these interactions. Because of the complex nature of these interactions, addressing questions about ecological interactions will require novel field and laboratory studies and analyses. This includes ecosystem models, use of innovative technologies (e.g., otolith microchemistry and stable isotopes), integration of sample collection efforts with those of the Ocean Observing System entities on the west coast, and quantifying interactions among environmental stressors, species behavior and ecosystem processes.
Characterize the interaction between marine, freshwater, and terrestrial ecosystem components
Although many species migrate between connected aquatic, marine, estuarine and freshwater environments they are commonly studied and managed as separate ecosystems. Environmental conditions in both marine and freshwater areas are strongly influenced by flows of water, sediment, organic matter and nutrients among ecosystems. Moreover, many threats (e.g., pollution, habitat loss, climate change, etc.) to marine organisms cross land-sea boundaries. Successful management of aquatic systems thus requires an understanding of linkages among ecosystems, including study of how specific habitats (e.g., headwaters, floodplains, submerged aquatic vegetation, nearshore zones, plumes and frontal regions) contribute to the productivity and capacity of ecosystems, and how to prioritize ecosystem protection or restoration within the context of the entire freshwater-estuarinemarine ecosystem.
Characterize the population biology of species, and develop and improve methods for predicting the status of populations
To evaluate species status and recovery, it is necessary to understand key aspects of the population biology of the species in question. This includes basic information on abundance, age structure, recruitment, spatial distribution, life history and how the species interacts with its ecosystem. For some recovering species, including most overfished groundfish stocks, many ESA-listed Pacific salmon stocks, and high profile species such as Southern Resident killer whales, this basic information is often reasonably well understood. For other recovering species, such as Pacific eulachon and some ESA-listed rockfish species, even basic information (e.g. stock abundance) is unknown. Even for well-studied species, key information on survival rates for critical life stages and how the environment affects these vital rates is lacking. Without basic information on species dynamics, achieving other goals such as quantifying relationships between human activities and species recovery or even knowing if species recovery goals are being met will not be successful. The NWFSC, in partnership with regional stakeholders, including states, tribes and industry, is conducting research to collect and monitor critical demographic information for recovering species.
Describe the interaction between human activities, particularly harvest of marine resources, and ecosystem function
Humans are an integral component of ecosystems. These ecosystems provide goods and services such as fish and seafood harvests, but these activities and others such as habitat alteration, pollution, and ocean acidification, can have strong impacts. Understanding the nature of these interactions will require observational and experimental studies aimed at identifying ecosystem-level responses to human activities, both individually and cumulatively, as well as human responses to ecosystem changes. Modeling spatial choices for harvesting and other human activities that are affected by ecosystem integrity, for example, can support a better understanding of the effects of ecosystembased management actions.
Describe the relationships between human activities and species recovery, rebuilding and sustainability
Human activities play a major role in determining the status of species and stocks. Rebuilding and recovery therefore need to address how these activities affect their status. At the NWFSC, biophysical modeling is used to link specific human activities such as land use and pollution to habitat conditions, and then to link these conditions and other activities to particular life stages. These models can be used to quantitatively assess how human activities influence species abundance, productivity, distribution and diversity. Not surprisingly, altering human activities in some way is often necessary for species or stock recovery and rebuilding. It is therefore important to understand the socio-economic effects of alternative management structures. Gathering data on their economic costs and social impacts helps identify actions that are cost-effective. These actions will need to be resilient to potential changes in climate throughout the region. Research on how humans react to management strategies helps policy makers avoid those that lead to unintended consequences that can hinder rather than help recovery.
Develop methods to use physiological, biological and behavioral information to predict population-level processes
Understanding the biological processes occurring within organisms is a powerful way of understanding how environmental changes affect those organisms. Genetics, developmental, physiological and behavioral studies all provide important information for effective species recovery and rebuilding. Integrating this information into models is vital to predict how populations will respond to natural or human perturbations, and to assess the constraints to stock rebuilding efforts. For example, data on thermal tolerance and physiological responses to temperature can be used to explore changes caused by shifts in climate on reproductive behavior and productivity, viability, movement, habitat selection, and population dynamics. Similarly, data on contaminants that impact physiological processes (immune system, growth, development, reproduction, and general health) are critical in determining how these compounds affect population dynamics. Data on biological responses of organisms to ocean acidification are useful for understanding how acidification may affect individual development and survival. The NWFSC collects such information for several species that are of concern, targets of fisheries or otherwise important for overall ecosystem function. NWFSC scientists will continue to expand current efforts and develop methods to incorporate physiological, biological and behavioral data into population models in order to predict population-level processes from these individual level data.
Evaluate the effects of artificial propagation on recovery, rebuilding and sustainability of marine and anadromous species
Artificial propagation has the potential to provide benefits both to species recovery and to seafood sustainability. Artificial propagation also poses risks to wild species and ecosystems. In the past, the use of artificial propagation has been an important risk factor for several threatened and endangered species, particularly Pacific salmon. Assessing the effects of artificial propagation is complicated by the fact that programs vary widely in size, rearing practices, and goals. The NWFSC conducts critical research on the influence of artificial propagation on population dynamics, growth rate, ecology of infectious disease, and the evolutionary fitness of wild fish and other marine organisms. Results of this research are needed to support the recovery of fish populations and have been especially valuable in providing critical information for recent, larger scale habitat restoration activities such as the Elwha Dam removal. NWFSC will continue to conduct science that informs the discussion about whether to allow fish to recolonize naturally after barrier removal, or to supplement populations with hatchery fish and on the impacts of aquaculture on fishing pressure and practices, and on the surrounding environment and ecosystem.
Provide scientific support for setting annual catch limits and measure results of annual catch limit implementation
Effective fisheries management is dependent upon reliable estimates of current stock status and projections of likely future status. Work in this area focuses on several key research components. The first goal is to improve stock assessments and applications. NWFSC stock assessment scientists are currently using and developing state-of-the-art data collection and assessment methods. Priority research in this area includes continuing improvement of existing methods, development of methods for data-limited species and making these high-end techniques readily available to assessment scientists around the world. A second priority is to improve data for stock assessments. Stock assessments rely on both fishery-dependent and fishery-independent information. NWFSC scientists are involved in designing and implementing surveys, improving and enhancing data collection methods, including developing advanced technologies for ocean sampling, and evaluating the results of those surveys. Annual surveys are conducted to collect data on targeted species, habitats and ecosystems; the data are vital inputs to mathematical models used to inform management decisions. Third, NWFSC scientists measure and estimate fishery-related mortality for bycaught and discarded species. Reliable estimates of the numbers and distribution of non-target species affected by the fishery is a critical component of effective fisheries and protected resource management in the short-term (within season management measures) and long-term (e.g. restricted area definition). Scientists develop and improve data collection for this purpose, as well as improve analytical methods for estimating this catch.
Provide scientific support for the implementation of ecosystem-based management
Fisheries scientists and managers recognize the potential for ecosystem-based management to improve sustain the delivery of ecosystem goods and services, including sustainable fisheries resources. An Integrated Ecosystem Assessment (IEA) is one approach that examines all available information on relevant physical, chemical, ecological and human processes in relation to specified ecosystem management objectives. IEAs provide an efficient, transparent means of summarizing the status of ecosystem components, screening and prioritizing potential risks, and evaluating alternative management strategies against a backdrop of environmental variability. To perform IEAs of major ecosystems will require development of project components, including new and existing data, to develop a suite of indicators that characterize the ecosystem. Careful assessment of ecosystem indicators will provide a powerful means for assessing management efficacy and a basis for adapting and improving management practices. A major focus will be to produce the initial IEA of the California Current LME and then provide annual updates.
Support collaborative community-based data collection, dissemination, and analysis for fishers, fisheries management, science, marketing, seafood safety, and education
Data are no longer the sole province of the agency. As technologies advance, fishers are collecting and analyzing fleet data in near real time. Data collected by fishers are used by the fishing community to reduce bycatch, allocate fishery impacts, and trace products through the processing and marketing system. Fisher-collected data, in combination with survey and oceanographic data, satellite remote sensing, economic data, and sociocultural data provide improved understanding of fish stocks, fishing, and the near-shore ecosystem. Collaborative efforts increase the quantity and quality of data available to the agency for scientific analysis, modeling, fishery management, and conservation. Through cooperation with the science and management agencies, the fishing community stands to gain more control and flexibility of their fishing operations, including the potential for improved economic efficiency. Increased availability of fisheries data creates opportunities for education and outreach both in the school system and to the general public. Further, well-informed local leaders conversant in the latest fishery issues will help garner local support and fisher buy-in for improved information sharing. The NWFSC will work with industry groups to improve distributed data collection, compilation, and distribution for multiple uses in fisheries, management, science, marketing, and education.
Support effective catch share management and evaluation
Catch share programs use allocations of target and by-caught species to individuals, with the goal of improving the safety and profitability of the fishery while reducing environmental impacts, particularly with respect to bycatch. This type of Individual Transferable Quota program was implemented for the West Coast Groundfish fishery in 2011. While the catch share program itself is a management construct, evaluating its effects and providing key information about immediate harvest and bycatch status are science issues. Research to support this catch share program falls within four areas. First, identifying cost-effective monitoring systems is imperative. Currently, the West Coast groundfish fishery requires 100% observer coverage. Determining whether an electronic monitoring program that meets scientific, management, enforcement and fishery information needs and is cost-effective is a key priority. In collaboration with industry, states and fishers, NWFSC scientists are currently designing monitoring systems, evaluating their effectiveness and assessing trade-offs in information quality and costs for these programs. Second, catch share programs are designed to provide individual accountability and flexibility and increase the overall profitability of the fishery. Determining to what degree these goals are achieved, how changes are made and their impacts on fishing communities is a key element of improving management in the long-term. Third, NWFSC scientists are evaluating the biological, ecological and social impacts of the catch share program. As a result of increased flexibility, catch shares programs are also anticipated to alter human interactions with the ecosystem, in the timing of fishing activities, fishing intensity on at least some species, and potentially on the location of fishing activities. Any of these changes are likely to have cascading effects on the status of stocks and the systems upon which they depend. The NWFSC is actively working with NOAA and academic scientists to evaluate these effects. And last, it is important to improve data delivery systems for management. To provide the flexibility and accountability that a catch shares program promises, data must be available to fishers and managers in near-real-time. NWFSC scientists are working to improve existing database systems and add novel components allowing greater accessibility to data.


Chinook salmon
species of interest
Columbia River estuary
Columbia River estuary
PIT tag
Passive Integrated Transponder tags
Pacific salmon
species of interest
the quantity or amount of something
marine mammals
Includes whales, dolphins, seals, sea lions, manatees, walruses, sea otters and polar bears


Detection of PIT-tagged Adult and Juvenile Salmonids in the Columbia River Estuary using a stationary pile dike array, 2020


Genus Oncorhynchus
Species Oncorhynchus clarki
cuthroat trout
Species Oncorhynchus keta
chum salmon, dog salmon, Keta salmon
Species Oncorhynchus kisutch
Coho salmon, silver salmon
Species Oncorhynchus mykiss
rainbow trout, steelhead trout, syeelhead trout
Species Oncorhynchus nerka
kokanee, red salmon, sockeye salmon
Species Oncorhynchus tshawytscha
Chinook salmon, king salmon, spring salmon


Alex Borsky
External Collaborator
Erika Holcombe
External Collaborator
Gabriel Brooks
Internal Collaborator
Paul Bentley
Principal Investigator