CAFA Publications

Publications from CAFA funded projects. Sort by year, title, or project to view publications.

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Assessing the sensitivity of three Alaska marine food webs to perturbations: an example of Ecosim simulations using Rpath.

Project: The Alaska climate integrate modeling project phase 2: Building pathways to resilience, through evaluation of climate impacts, risk, and adaptation responses of marine ecosystems, fisheries, and coastal communities in the Bering Sea, Alaska
Year: 2020

Author(s): Whitehouse, G. A., K. Y. Aydin.

Project PI: Hollowed

Ecosystem modelling is a useful tool for exploring the potential outcomes of policy options and conducting experiments that would otherwise be impractical in the real world. However, ecosystem models have been limited in their ability to engage in the management of living marine resources due in part to high levels of uncertainty in model parameters and model outputs. Additionally, for multispecies or food web models, there is uncertainty about the predator-prey functional response, which can have implications for population dynamics. In this study, we evaluate the sensitivity of large marine food webs in Alaska to parameter uncertainty, including parameters that govern the predator-prey functional response. We use Rpath, an R implementation of the food web modeling program Ecopath with Ecosim (EwE), to conduct a series of mortality-based perturbations to examine the sensitivity and recovery time of higher trophic level groups in the eastern Chukchi Sea, eastern Bering Sea, and Gulf of Alaska. We use a Monte Carlo approach to generate thousands of plausible ecosystems by drawing parameter sets from the range of uncertainty around the base model parameters. We subjected the ecosystem ensembles to a series of mortality-based perturbations to identify which functional groups the higher trophic level groups are most sensitive to when their mortality was increased, whether the food webs returned to their unperturbed configurations following a perturbation, and how long it took to return to that state. In all three ecosystems, we found that the number of disrupted ensemble food webs was positively related to the biomass and the number of trophic links of the perturbed functional group, and negatively related to trophic level. The eastern Chukchi Sea was most sensitive to perturbations to benthic invertebrate groups, the eastern Bering Sea was most sensitive to shrimp and walleye pollock, and the Gulf of Alaska was most sensitive to shrimps, pelagic forage fish, and zooplankton. Recovery time to perturbations were generally less than 5 years in all three ecosystems. The recovery times when fish groups were perturbed were generally longer than when benthic invertebrates were perturbed, and recovery times were shortest when it was pelagic invertebrates. The single model ensemble approach produced simulation results that described a range of possible outcomes to the prescribed perturbations and provided a sense for how robust the results are to parameter uncertainty.

Interannual Variability of the Mid‐Atlantic Bight Cold Pool

Project: A high-resolution physical-biological study of the Northeast U.S. shelf: past variability and future change
Year: 2020

Author(s): Chen, Z., & Curchitser, E. N. 

Project PI: Curchister

The Mid-Atlantic Bight (MAB) Cold Pool is a bottom-trapped, cold (temperature below 10°C) and fresh (practical salinity below 34) water mass that is isolated from the surface by the seasonal thermocline and is located over the midshelf and outer shelf of the MAB. The interannual variability of the Cold Pool with regard to its persistence time, volume, temperature, and seasonal along-shelf propagation is investigated based on a long-term (1958–2007) high-resolution regional model of the northwest Atlantic Ocean. A Cold Pool Index is defined and computed in order to quantify the strength of the Cold Pool on the interannual timescale. Anomalous strong, weak, and normal years are categorized and compared based on the Cold Pool Index. A detailed quantitative study of the volume-averaged heat budget of the Cold Pool region (CPR) has been examined on the interannual timescale. Results suggest that the initial temperature and abnormal warming/cooling due to advection are the primary drivers in the interannual variability of the near-bottom CPR temperature anomaly during stratified seasons. The long persistence of temperature anomalies from winter to summer in the CPR also suggests a potential for seasonal predictability.

 Management strategy evaluation: Allowing the light on the hill to illuminate more than one species

Project: The Alaska climate integrate modeling project phase 2: Building pathways to resilience, through evaluation of climate impacts, risk, and adaptation responses of marine ecosystems, fisheries, and coastal communities in the Bering Sea, Alaska
Year: 2021

Author(s): Kaplan, I. C., S. K. Gaichas, C. C. Stawitz, P. D. Lynch, K. N. Marshall, J. J. Deroba, M. Masi, J. K. T. Brodziak, K. Y. Aydin, K. Holsman, H. Townsend, D. Tommasi, J. A. Smith, S. Koenigstein, M. Weijerman, J. Link.

Project PI: Hollowed

Management strategy evaluation (MSE) is a simulation approach that serves as a “light on the hill” (Smith, 1994) to test options for marine management, monitoring, and assessment against simulated ecosystem and fishery dynamics, including uncertainty in ecological and fishery processes and observations. MSE has become a key method to evaluate trade-offs between management objectives and to communicate with decision makers. Here we describe how and why MSE is continuing to grow from a single species approach to one relevant to multi-species and ecosystem-based management. In particular, different ecosystem modeling approaches can fit within the MSE process to meet particular natural resource management needs. We present four case studies that illustrate how MSE is expanding to include ecosystem considerations and ecosystem models as ‘operating models’ (i.e., virtual test worlds), to simulate monitoring, assessment, and harvest control rules, and to evaluate tradeoffs via performance metrics. We highlight United States case studies related to fisheries regulations and climate, which support NOAA’s policy goals related to the Ecosystem Based Fishery Roadmap and Climate Science Strategy but vary in the complexity of population, ecosystem, and assessment representation. We emphasize methods, tool development, and lessons learned that are relevant beyond the United States, and the additional benefits relative to single-species MSE approaches.

A Case Study In Connecting Fisheries Management Challenges With Models And Analysis To Support Ecosystem-Based Management In The California Current Ecosystem

Project: From physics to fisheries: A social-ecological management strategy evaluation for the California Current Large Marine Ecosystem
Year: 2021

Author(s): Tommasi, Desiree, et al

Project PI: Jacox

One of the significant challenges to using information and ideas generated through ecosystem models and analyses for ecosystem-based fisheries management is the disconnect between modeling and management needs. Here we present a case study from the U.S. West Coast, the stakeholder review of NOAA’s annual ecosystem status report for the California Current Ecosystem established by the Pacific Fisheries Management Council’s Fisheries Ecosystem Plan, showcasing a process to identify management priorities that require information from ecosystem models and analyses. We then assess potential ecosystem models and analyses that could help address the identified policy concerns. We screened stakeholder comments and found 17 comments highlighting the need for ecosystem-level synthesis. Policy needs for ecosystem science included: (1) assessment of how the environment affects productivity of target species to improve forecasts of biomass and reference points required for setting harvest limits, (2) assessment of shifts in the spatial distribution of target stocks and protected species to anticipate changes in availability and the potential for interactions between target and protected species, (3) identification of trophic interactions to better assess tradeoffs in the management of forage species between the diet needs of dependent predators, the resilience of fishing communities, and maintenance of the forage species themselves, and (4) synthesis of how the environment affects efficiency and profitability in fishing communities, either directly via extreme events (e.g., storms) or indirectly via climate-driven changes in target species availability. We conclude by exemplifying an existing management process established on the U.S. West Coast that could be used to enable the structured, iterative, and interactive communication between managers, stakeholders, and modelers that is key to refining existing ecosystem models and analyses for management use.

A coupled pelagic-benthic-sympagic biogeochemical model for the Bering Sea: documentation and validation of the BESTNPZ model (v2019.08.23) within a high-resolution regional ocean model.  Geooscientific Model Development

Project: The Alaska climate integrate modeling project phase 2: Building pathways to resilience, through evaluation of climate impacts, risk, and adaptation responses of marine ecosystems, fisheries, and coastal communities in the Bering Sea, Alaska
Year: 2020

Author(s): Kearney, K., A. Hermann, W. Cheng, I. Ortiz, and K. Aydin.

Project PI: Hollowed
DOI: http://

The Bering Sea is a highly productive ecosystem, supporting a variety of fish, seabird, and marine mammal populations, as well as large commercial fisheries. Due to its unique shelf geometry and the presence of seasonal sea ice, the processes controlling productivity in the Bering Sea ecosystem span the pelagic water column, the benthic sea floor, and the sympagic sea ice environments. The Bering Ecosystem Study Nutrient-Phytoplankton-Zooplankton (BESTNPZ) model has been developed to simulate the lower-trophic-level processes throughout this region. Here, we present a version of this lower-trophic-level model coupled to a three-dimensional regional ocean model for the Bering Sea. We quantify the model's ability to reproduce key physical features of biological importance as well as its skill in capturing the seasonal and interannual variations in primary and secondary productivity over the past several decades. We find that the ocean model demonstrates considerable skill in replicating observed horizontal and vertical patterns of water movement, mixing, and stratification, as well as the temperature and salinity signatures of various water masses throughout the Bering Sea. Along the data-rich central portions of the southeastern Bering Sea shelf, it is also able to capture the mean seasonal cycle of primary production. However, its ability to replicate domain-wide patterns in nutrient cycling, primary production, and zooplankton community composition, particularly with respect to the interannual variations that are important when linking variation in productivity to changes in longer-lived upper-trophic-level species, remains limited. We therefore suggest that near-term application of this model should focus on the physical model outputs, while model development continues to elucidate potential mechanisms controlling nutrient cycling, bloom processes, and trophic dynamics.

A Dynamic Ocean Management Tool To Reduce Bycatch And Support Sustainable Fisheries

Project: From physics to fisheries: A social-ecological management strategy evaluation for the California Current Large Marine Ecosystem
Year: 2018

Author(s): E.L. Hazen, K.L. Scales, S.M. Maxwell, D. Briscoe, H. Welch, S.J. Bograd, H. Bailey, S.R. Benson, T. Eguchi, H. Dewar, S. Kohin, D.P. Costa, L.B. Crowder, R.L. Lewison

Project PI: Jacox
DOI: 10.1126/sciadv.aar3001

Seafood is an essential source of protein for more than 3 billion people worldwide, yet bycatch of threatened species in capture fisheries remains a major impediment to fisheries sustainability. Management measures designed to reduce bycatch often result in significant economic losses and even fisheries closures. Static spatial management approaches can also be rendered ineffective by environmental variability and climate change, as productive habitats shift and introduce new interactions between human activities and protected species. We introduce a new multispecies and dynamic approach that uses daily satellite data to track ocean features and aligns scales of management, species movement, and fisheries. To accomplish this, we create species distribution models for one target species and three bycatch-sensitive species using both satellite telemetry and fisheries observer data. We then integrate species-specific probabilities of occurrence into a single predictive surface, weighing the contribution of each species by management concern. We find that dynamic closures could be 2 to 10 times smaller than existing static closures while still providing adequate protection of endangered nontarget species. Our results highlight the opportunity to implement near real-time management strategies that would both support economically viable fisheries and meet mandated conservation objectives in the face of changing ocean conditions. With recent advances in eco-informatics, dynamic management provides a new climate-ready approach to support sustainable fisheries.

A Dynamically Downscaled Ensemble Of Future Projections For The California Current System

Project: From physics to fisheries: A social-ecological management strategy evaluation for the California Current Large Marine Ecosystem
Year: 2021

Author(s): Pozo Buil, M, Jacox, et al

Project PI: Jacox

Given the ecological and economic importance of eastern boundary upwelling systems like the California Current System (CCS), their evolution under climate change is of considerable interest for resource management. However, the spatial resolution of global earth system models (ESMs) is typically too coarse to properly resolve coastal winds and upwelling dynamics that are key to structuring these ecosystems. Here we use a high-resolution (0.1°) regional ocean circulation model coupled with a biogeochemical model to dynamically downscale ESMs and produce climate projections for the CCS under the high emission scenario, Representative Concentration Pathway 8.5. To capture model uncertainty in the projections, we downscale three ESMs: GFDL-ESM2M, HadGEM2-ES, and IPSL-CM5A-MR, which span the CMIP5 range for future changes in both the mean and variance of physical and biogeochemical CCS properties. The forcing of the regional ocean model is constructed with a “time-varying delta” method, which removes the mean bias of the ESM forcing and resolves the full transient ocean response from 1980 to 2100. We found that all models agree in the direction of the future change in offshore waters: an intensification of upwelling favorable winds in the northern CCS, an overall surface warming, and an enrichment of nitrate and corresponding decrease in dissolved oxygen below the surface mixed layer. However, differences in projections of these properties arise in the coastal region, producing different responses of the future biogeochemical variables. Two of the models display an increase of surface chlorophyll in the northern CCS, consistent with a combination of higher nitrate content in source waters and an intensification of upwelling favorable winds. All three models display a decrease of chlorophyll in the southern CCS, which appears to be driven by decreased upwelling favorable winds and enhanced stratification, and, for the HadGEM2-ES forced run, decreased nitrate content in upwelling source waters in nearshore regions. While trends in the downscaled models reflect those in the ESMs that force them, the ESM and downscaled solutions differ more for biogeochemical than for physical variables.

Adaptation And Resilience Of Commercial Fishers In The Northeast United States During The Early Stages Of The Covid-19 Pandemic

Project: Adapting to changes in fishing opportunity portfolios: abundance, availability, and access
Year: 2020

Author(s): Smith, S. L., Golden, A. S., Ramenzoni, V., Zemeckis, D. R., & Jensen, O. P.

Project PI: Ramenzoni

Commercial fisheries globally experienced numerous and significant perturbations during the early months of the COVID-19 pandemic, affecting the livelihoods of millions of fishers worldwide. In the Northeast United States, fishers grappled with low prices and disruptions to export and domestic markets, leaving many tied to the dock, while others found ways to adapt to the changing circumstances brought about by the pandemic. This paper investigates the short-term impacts of the early months of the COVID-19 pandemic (March-June 2020) on commercial fishers in the Northeast U.S. to understand the effects of the pandemic on participation in the fishery and fishers’ economic outcomes, using data collected from an online survey of 258 Northeast U.S. commercial fishers. This research also assesses characteristics of those fishers who continued fishing and their adaptive strategies to the changing circumstances. Analysis of survey responses found the majority of fishers continued fishing during the early months of the pandemic, while a significant number had stopped fishing. Nearly all reported a loss of income, largely driven by disruptions of export markets, the loss of restaurant sales, and a resulting decline in seafood prices. Landings data demonstrate that while fishing pressure in 2020 was reduced for some species, it remained on track with previous years for others. Fishers reported engaging in a number of adaptation strategies, including direct sales of seafood, switching species, and supplementing their income with government payments or other sources of income. Many fishers who had stopped fishing indicated plans to return, suggesting refraining from fishing as a short-term adaptation strategy, rather than a plan to permanently stop fishing. Despite economic losses, fishers in the Northeast U.S. demonstrated resilience in the face of the pandemic by continuing to fish and implementing other adaptation strategies rather than switching to other livelihoods.

An Numerical Model Analysis of the Mean and Seasonal Nitrogen Budget on the Northeast U.S. Shelf.

Project: A high-resolution physical-biological study of the Northeast U.S. shelf: past variability and future change
Year: 2018

Author(s): Zhang. S., C. A. Stock, E. N. Curchitser, and R. Dussin

Project PI: Curchister
DOI: http://DOI:10.1029/2018JC014308

The supply of nitrogen is a primary limiting factor for the productivity of the Northeast United States (NEUS) continental shelf. In this study, a 12-year (1996–2007) retrospective physical-biogeochemical simulation over the Northwest Atlantic was used to analyze the mean and seasonal NEUS shelf nitrogen budget, including the connections between shelf subregions: the Gulf of Maine/Georges Bank (GoM/GB), and the Mid-Atlantic Bight (MAB). The model captures the primary mean and seasonal patterns of shelf circulation, nitrate, and plankton dynamics. Results confirm aspects of previous nitrogen budget analyses, including the dominance of offshore nitrogen influxes into the GoM/GB and the prominent role of riverine influxes and sedimentary denitrification in the MAB. However, detailed spatiotemporal analysis of nitrogen fluxes highlights the importance of dispersed inflows of shallow to intermediate depth waters (0–75 m), which can at times exceed the deep nitrogen influx emphasized in previous studies. A seasonal analysis shows a pronounced shift from the net import of nitrogen to the GoM/GB region during late fall and winter, to the net export of nitrogen from the region in the spring and early summer. The MAB, in contrast, consistently exports nitrogen to offshore waters. The prominence of the 0-75m nitrogen supply has implications for the roles of Labrador Slope Water and Atlantic Temperate Slope Water on the NEUS ecosystems, as Atlantic Temperate Slope Water has greater nitrate concentrations than Labrador Slope Water at depth but often less at the surface. Results suggest the need for further study of shallow to intermediate depth inflows beyond those from the Scotian Shelf, particularly during the fall/winter of net nitrogen inflow.

Are Long- Term Changes In Mixed Layer Depth Influencing North Pacific Marine Heatwaves?

Project: From physics to fisheries: A social-ecological management strategy evaluation for the California Current Large Marine Ecosystem
Year: 2021

Author(s): Amaya DJ, et al

Project PI: Jacox
DOI: 10.1175/BAMS-D-20-0144.1

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COCA FY2016 - Ecosystem Services for a Resilient Coast in a Changing Climate

  • 3 October 2016
COCA FY2016 -  Ecosystem Services for a Resilient Coast in a Changing Climate

NOAA’s Coastal and Ocean Climate Applications (COCA) program competitively selected four two-year projects totaling $1,105,115 in grants for the FY2016 Ecosystem Services for a Resilient Coast in a Changing Climate competition.

The COCA program addresses the needs of decision makers dealing with pressing climate-related issues in coastal and marine environments. The program supports interdisciplinary teams of researchers in the development and transition of climate-related research and information to advance decision-making in coastal communities and coastal and marine ecosystems. Outcomes of COCA projects inform the response and coping capacity of decision-making and management communities to climate variability and change.

As decision-makers along the coast plan for a changing climate, there is increased recognition of the importance of coastal ecosystems and their ecosystem services1. There is also an increased demand from managers and decision makers for information on valuing ecosystem services and mechanisms to incorporate this information into coastal decision-making.

For FY16, COCA held a competition to support interdisciplinary applied research projects focused on the  development and application of methodologies to value ecosystems services and natural and nature-based features (NNBF)2.  This competition is designed to build from research focused on ecosystem services funded in FY14. The goal of the FY16 projects is to support the integration of NNBF approaches into coastal adaptation efforts. 

Natural 'green barriers' help protect this Florida coastline and infrastructure from severe storms and floods. (Credit: NOAA).

The four new projects to be funded by the COCA program in 2016 are:

  • University of Massachusetts Boston – “Improving the Environment While Protecting Coasts: A Holistic Accounting of Ecosystem Services of Green Infrastructure and Natural and Nature-Based Features (NNBF) in an Urbanized Coastal Environment”

    • Lead Principal Investigator (PI): Ellen Douglas (University of Massachusetts Boston)

    • CO-PIs: Paul Kirshen (University of Massachusetts Boston), Kenneth Reardon (University of Massachusetts Boston), Jarrett Byrnes (University of Massachusetts Boston), Di Jin (Woods Hole Oceanographic Institution), Juanita Urban-Rich (University of Massachusetts Boston), Jack Wiggin (University of Massachusetts Boston), Cynthia Pilskaln (University of Massachusetts Dartmouth), David Levy (University of Massachusetts Boston), John Duff (University of Massachusetts Boston)

  • RAND – “Incorporating Interactive Visions and Bioeconomic Values of Ecosystem Services into Climate Adaptation: An Example from Jamaica Bay, Brooklyn / Queens, New York City”

    • Lead PI: Craig Bond (RAND)

    • Co-PIs: Philip Orton (Stevens Institute of Technology), Eric Sanderson (Wildlife Conservation Society)

  • Clark University – “Linking Coastal Adaptation Portfolios to Tidal Marsh Resilience and Sustainable Ecosystem Service Values: Transferable Guidance for Decisions under Uncertainty”

    • Lead-PI: Robert J. Johnston (Clark University)

    • Co-PIs: Matt Kirwan (College of William and Mary), Dana Marie Bauer (George Perkins Marsh Institute at Clark University), Anke D. Leroux (Monash University)

  • University of Chicago & University of Massachusetts at Dartmouth – “Kelp forests: Their Dynamics, Services, and Fate in a Changing Climate”

    • Lead PIs: Catherine Pfister (University of Chicago) and Mark Altabet (University of Massachusetts at Dartmouth)

    • Co-PIs: Liam Antrim (Olympic Coast National Marine Sanctuary), Helen Berry (Washington State Department of Natural Resources)

COCA is a program in the Climate and Societal Interactions Division of the Climate Program Office, within NOAA’s Office of Oceanic and Atmospheric Research. To learn more about COCA and it’s funding opportunities, visit:

For a full list of CPO’s grants and awards for 2016, visit:’s-Climate-Program-Office-awards-443M-to-advance-climate-research-improve-community-resilience.aspx

NOAA’s Climate Program Office helps improve understanding of climate variability and change in order to enhance society’s ability to plan and respond. NOAA provides science, data, and information that Americans want and need to understand how climate conditions are changing. Without NOAA’s long-term climate observing, monitoring, research, and modeling capabilities we couldn’t quantify where and how climate conditions have changed, nor could we predict where and how they’re likely to change. 





1Ecosystem services are the benefits (e.g. food, flood protection, opportunities for recreation) that ecosystems provide to people. Ecosystems and Human Well-Being: Current State and Trends: Findings of the Condition and Trends Working Group, Millennium Ecosystem Assessment. Rashid Hassan, Robert Scholes, Neville Ash (eds). Island Press, 2005.

2“Natural Features are created and evolve over time through the actions of physical, biological, geologic, and chemical processes operating in nature. Natural coastal features take a variety of forms, including reefs (e.g., coral and oyster), barrier islands, dunes, beaches, wetlands, and maritime forests. The relationships and interactions among the natural and built features comprising the coastal system are important variables determining coastal vulnerability, reliability, risk, and resilience. Nature-Based Features are those that may mimic characteristics of natural features but are created by human design, engineering, and construction to provide specific services such as coastal risk reduction. The combination of both natural and nature-based features is referred to collectively as nature and nature-based features (NNBF).” U.S. Army Corps of Engineers (USACE) in Use of Natural and Nature-Based Features (NNBF) for Coastal Resilience: Final Report.  



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