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  • Coastwide Cooperative Pre-recruit Survey


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


Pre-Recruit Survey
Coastwide Cooperative Pre-recruit Survey
The Pre-recruit survey project is collaborative involving researchers from the FE Division based in 3 laboratories (Newport, Seattle and Hammond), scientists from the Southwest Fisheries Science Center (Santa Cruz), along with researchers from several universities (Oregon State University, University of Oregon, University of Washington, University of California, Santa Cruz). In concert with a similar SWFSC survey effort through California, the purpose of this project is to conduct annual surveys within the coastal ecosystem off Oregon and Washington to quantify the environmental conditions and biota found along the California Current and to elucidate ecosystem-level processes affecting managed and protected marine resources.

This project currently supports three main efforts:

1. An annual sampling regime of the hydrology, plankton, small fish, and predators along transects over the Continental Shelf from Oregon and Washington. This consistent survey has generated significant information on within- and between-year variability in the California Current Marine Ecosystem and has yielded valuable insights into the food web off our coast.

2. Collection of specimens for diet analysis, growth, containment load, and other studies related to the ecology and production of commercially important taxa and their relationships within the food web.

3. Parameters and ecological processes quantified during this effort are used in forecasts involving species, assemblages, and ecosystems and also to parameterize ecosystem models used to evaluate cumulative risks and managerial strategies.

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.

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.
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.
Understand how climate influences ecosystem variability
Effective ecosystem management will require an understanding of how climate variability and climate change will alter riverine, estuarine, and marine habitats and consequently how this will affect ecosystem status, function and recovery. Key research elements include better understanding of historical ecological variability through traditional (i.e., indigenous) sources, exploring the vulnerability of key species and biotic communities to expected habitat changes, including decreasing stream flow, increased flood frequency, increasing stream temperature, sea level rise, ocean acidification, shifts in ocean currents, and changed frequency and extent of deoxygenated zones. A secondary goal is to improve understanding of how ecosystems respond to year-to-year and decadal climate variability. Achieving these research goals will provide NOAA and state and local governments with the knowledge and tools needed to incorporate climate change and variability into management of living marine resources.


Acoustic automated analysis
Automated analysis and classification of biota in acoustic data
Bell M. Shimada
NOAA ship
Fish Eggs and larvae
Juvenile fishes
juvenile life history stage of fishes, typically during their first year of life
climate indicators
measures of climate relevant to management
ecosystem indicator
reflection of ecosystem status, may indicate either changes within an ecosystem or differences between ecosystems
food web
complex of interrelated food chains in an ecological community
small crustaceans of the order Euphausiacea
study of the oceans
target animals


CCIEA report to the PFMC
Ongoing assessment of the ecosystem prepared by CCIEA
Effects of warming ocean conditions on feeding ecology of small pelagic fishes in a coastal upwelling ecosystem: a shift to gelatinous food sources.
Paper in press in Marine Ecology Progress Series
Environmental and geographic relationships among salmon forage assemblages along the continental shelf of the California Current
Published a paper in Marine Ecology Progress Series
Major shifts in pelagic community structure in an upwelling ecosystem related to an unprecedented marine heatwave.
Paper published in Frontiers in Marine Science
Ongoing CalCOFI effort: State of the California Current
This is the CalCOFI report. This may transition, next year, to another publisher
Phenological and distributional shifts in ichthyoplankton associated with recent warming in the northeast Pacific Ocean.
Global Change Biology 24:259–272 (2018)
Winter ichthyoplankton as an indicator of salmon feeding conditions and survival
Published a paper in Marine Ecology Progress Series


Class Aves
Class Cephalopoda
Family Myctophidae
Family Penaeidae
penaeid shrimps
Genus Sebastes
Order Pleuronectiformes
Species Clupea pallasii
Pacific herring
Species Engraulis mordax
Californian anchovy, northern anchovy
Species Merluccius productus
North Pacific hake, Pacific hake, Pacific hake, whiting
Species Sardinops sagax
California pilchard, Japanese pilchard, Pacific sardine, South American pilchard, Southern African pilchard


Brandon Chasco
Internal Collaborator
Brian Burke
Project Group Lead
Brian Wells
Principal Investigator
Curtis Roegner
David Huff
Program Manager
Paul Chittaro
Internal Collaborator
Richard Brodeur