CAFA Publications

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

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Climate Variability And Sardine Recruitment In The California Current: A Mechanistic Analysis Of An Ecosystem Model, Fisheries Oceanography

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

Author(s): D. Politikos, E.N. Curchitser, K.A. Rose, D.M. Checkley, J. Fiechter

Project PI: Jacox

Recruitment varies substantially in small pelagic fish populations. Understanding of the mechanisms linking environment to recruitment is essential for the effective management of fisheries resources. In this study, we used a fully coupled end-to-end ecosystem model to study the effect of climate variability on sardine recruitment in the California Current System during 1965–2006. Ocean variability was represented by ROMS hydrodynamic and NEMURO biogeochemical models, and sardine population dynamics was simulated through a full life cycle individual-based model. Model analysis was designed to elucidate how changes in abiotic and biotic conditions may impact the spawning habitats, early life stage survival, and ultimately recruitment of sardine. Our findings revealed the importance of spatial processes to shape early life stages dynamics. Shifts in spawning habitats were dictated by the spatial variations in temperature and the behavioral movement of adults. Additionally, the spatial match of eggs with warmer temperatures and larvae with their prey influenced their survival. The northward shifts in spawning locations and the accomplishment of good recruitment in warmer years agreed with existing knowledge. Egg production and survival during egg and yolk-sac larval stages were key factors to drive the long-term variations in recruitment. Finally, our analysis provided a quantitative assessment of climate impact on year-to-year variation in sardine recruitment by integrating multiple hypotheses.

Comparing And Synthesizing Quantitative Distribution Models And Qualitative Vulnerability Assessments To Project Marine Species Distributions Under Climate Change

Project: Climate velocity over the 21st century and its implications for fisheries management in the Northeast U.S.
Year: 2020

Author(s): Allyn, A. J., M. A. Alexander, B. S. Franklin, F. Massiot-Granier, A. J. Pershing, J. D. Scott, and K. E. Mills.

Project PI: Mills

Species distribution shifts are a widely reported biological consequence of climate-driven warming across marine ecosystems, creating ecological and social challenges. To meet these challenges and inform management decisions, we need accurate projections of species distributions. Quantitative species distribution models (SDMs) are routinely used to make these projections, while qualitative climate change vulnerability assessments are becoming more common. We constructed SDMs, compared SDM projections to expectations from a qualitative expert climate change vulnerability assessment, and developed a novel approach for combining the two methods to project the distribution and relative biomass of 49 marine species in the Northeast Shelf Large Marine Ecosystem under a “business as usual” climate change scenario. A forecasting experiment using SDMs highlighted their ability to capture relative biomass patterns fairly well (mean Pearson’s correlation coefficient between predicted and observed biomass = 0.24, range = 0–0.6) and pointed to areas needing improvement, including reducing prediction error and better capturing fine-scale spatial variability. SDM projections suggest the region will undergo considerable biological changes, especially in the Gulf of Maine, where commercially-important groundfish and traditional forage species are expected to decline as coastal fish species and warmer-water forage species historically found in the southern New England/Mid-Atlantic Bight area increase. The SDM projections only occasionally aligned with vulnerability assessment expectations, with agreement more common for species with adult mobility and population growth rates that showed low sensitivity to climate change. Although our blended approach tried to build from the strengths of each method, it had no noticeable improvement in predictive ability over SDMs. This work rigorously evaluates the predictive ability of SDMs, quantifies expected species distribution shifts under future climate conditions, and tests a new approach for integrating SDMs and vulnerability assessments to help address the complex challenges arising from climate-driven species distribution shifts.

Comparing Dynamic And Static Time-Area Closures For Bycatch Mitigation: A Management Strategy Evaluation Of A Swordfish Fishery

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

Author(s): Smith JA, et al

Project PI: Jacox

Time-area closures are a valuable tool for mitigating fisheries bycatch. There is increasing recognition that dynamic closures, which have boundaries that vary across space and time, can be more effective than static closures at protecting mobile species in dynamic environments. We created a management strategy evaluation to compare static and dynamic closures in a simulated fishery based on the California drift gillnet swordfish fishery, with closures aimed at reducing bycatch of leatherback turtles. We tested eight operating models that varied swordfish and leatherback distributions, and within each evaluated the performance of three static and five dynamic closure strategies. We repeated this under 20 and 50% simulated observer coverage to alter the data available for closure creation. We found that static closures can be effective for reducing bycatch of species with more geographically associated distributions, but to avoid redistributing bycatch the static areas closed should be based on potential (not just observed) bycatch. Only dynamic closures were effective at reducing bycatch for more dynamic leatherback distributions, and they generally reduced bycatch risk more than they reduced target catch. Dynamic closures were less likely to redistribute fishing into rarely fished areas, by leaving open pockets of lower risk habitat, but these closures were often fragmented which would create practical challenges for fishers and managers and require a mobile fleet. Given our simulation’s catch rates, 20% observer coverage was sufficient to create useful closures and increasing coverage to 50% added only minor improvement in closure performance. Even strict static or dynamic closures reduced leatherback bycatch by only 30–50% per season, because the simulated leatherback distributions were broad and open areas contained considerable bycatch risk. Perfect knowledge of the leatherback distribution provided an additional 5–15% bycatch reduction over a dynamic closure with realistic predictive accuracy. This moderate level of bycatch reduction highlights the limitations of redistributing fishing effort to reduce bycatch of broadly distributed and rarely encountered species, and indicates that, for these species, spatial management may work best when used with other bycatch mitigation approaches. We recommend future research explores methods for considering model uncertainty in the spatial and temporal resolution of dynamic closures.

Coupled modes of projected regional change in the Bering Sea from a dynamically downscaling model under CMIP6 forcing

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): Hermann, A. J., K. Kearney, W. Cheng, D. Pilcher, K. Aydin, K. K. Holsman, A. B. Hollowed.

Project PI: Hollowed

Three different global earth system models from the Coupled Model Intercomparison Project Phase 6 (CMIP6) were used to explore anticipated changes in the Bering Sea under high (SSP126) and low (SSP585) carbon mitigation scenarios (i.e. low and high emission scenarios), via dynamical downscaling. A multivariate pattern analysis, based on Empirical Orthogonal Functions applied to monthly time series, reveals strong coupling of changes across several biophysical variables and the global forcing itself, on both yearly and multidecadal time scales. Rising air and ocean temperatures from the global models are strongly coupled with rising regional temperatures and reduced ice cover/thickness, as well as strong changes to the phenology of the plankton food chain, including reduced biomass of large zooplankton in the fall. This method ultimately provides a compact way to estimate the changes to many regional attributes under a variety of global change scenarios. Application of this method to a broad ensemble of the CMIP6 global model air temperatures suggests that compared to present conditions, the Bering Sea shelf bottom temperatures in July will warm by an average of ∼4 degrees C by the end of the 21st century under SSP585, as compared with ∼1 degrees C under SSP126, with greatest warming focused on the outer northern shelf.

Decadal Changes In The Productivity Of New England Fish Populations

Project: Robust harvest strategies for responding to climate‐induced changes in fish productivity
Year: 2019

Author(s): Tableau, A., J.S. Collie, R. Bell, and C. Minto

Project PI: Collie

The Northwest Atlantic continental shelf is a large ecosystem undergoing rapid environmental changes, which are expected to modify the productivity of natural marine resources. Current management of most fished species assumes stationary production relationships or time-invariant recruitment rates. With linear state-space models, we examined the evidence of dynamic productivity for 25 stocks of the Northeast US shelf. We expanded the suite of options available within the state-space approach to produce robust estimates. Fifteen of the stocks exhibited time-varying productivity or changes in their maximum reproductive rate. Few productivity time series are related across the whole region, though adjacent stocks of the same species exhibited similar trends. Some links to region-wide environmental variables were observed. We demonstrate that fish recruitment can often be better predicted over a short-term horizon by accounting for dynamic productivity, which could be valuable for fisheries management. Improving predictions by incorporating environmental covariates or covariance among the stocks must be considered case by case and with caution, as their relationships may change over time.

Decision-Support Tools For Dynamic Management

Project: From physics to fisheries: A social-ecological management strategy evaluation for the California Current Large Marine Ecosystem
Year: 2019

Author(s): Welch, H, S Brodie, MG Jacox, SJ Bograd, EL Hazen

Project PI: Jacox

Spatial management is a valuable strategy to advance regional goals for nature conservation, economic development, and human health. One challenge of spatial management is navigating the prioritization of multiple features. This challenge becomes more pronounced in dynamic management scenarios, in which boundaries are flexible in space and time in response to changing biological, environmental, or socioeconomic conditions. To implement dynamic management, decision-support tools are needed to guide spatial prioritization as feature distributions shift under changing conditions. Marxan is a widely applied decision-support tool designed for static management scenarios, but its utility in dynamic management has not been evaluated. EcoCast is a new decision-support tool developed explicitly for the dynamic management of multiple features, but it lacks some of Marxan's functionality. We used a hindcast analysis to compare the capacity of these 2 tools to prioritize 4 marine species in a dynamic management scenario for fisheries sustainability. We successfully configured Marxan to operate dynamically on a daily time scale to resemble EcoCast. The relationship between EcoCast solutions and the underlying species distributions was more linear and less noisy, whereas Marxan solutions had more contrast between waters that were good and poor to fish. Neither decision-support tool clearly outperformed the other; the appropriateness of each depends on management purpose, resource-manager preference, and technological capacity of tool developers.

Drivers Of Subsurface Deoxygenation In The California Current System

Project: From physics to fisheries: A social-ecological management strategy evaluation for the California Current Large Marine Ecosystem
Year: 2020

Author(s): Evans, N, Schroeder, ID, Pozo Buil, M, Jacox, MG, Bograd, SJ

Project PI: Jacox

A confluence of subarctic, tropical, and subtropical water masses feed the California Current System (CCS), supporting a highly productive ecosystem and wide array of marine ecosystem services. Long-term declines in oxygen have been observed in this region, causing habitat compression and other ecosystem consequences. Here we quantify the water masses and processes causing deoxygenation in the subsurface CCS from 1993–2018, and we find that deoxygenation was caused both by changes in the advection of source waters and increased remineralization in the source waters. The historical deoxygenation trend can be attributed primarily (81%) to the Northern Equatorial Pacific Intermediate Water, the deep Pacific Equatorial Water mass transported in the California Undercurrent. We also find that advection and remineralization share nearly equal contributions to deoxygenation. This improved understanding of the mechanisms affecting the aerobic habitat of the CCS will inform projections of ecological impacts and mitigation of future deoxygenation.

Dynamic Habitat Use Of Albacore And Their Primary Prey Species In The California Current System

Project: From physics to fisheries: A social-ecological management strategy evaluation for the California Current Large Marine Ecosystem
Year: 2017

Author(s): Muhling, Barbara, et al.

Project PI: Jacox

Juvenile north Pacific albacore (Thunnus alalunga) forage in the California Current System (CCS), supporting fisheries between Baja California and British Columbia. Within the CCS, their distribution, abundance, and foraging behaviors are strongly variable interannually. Here, we use catch logbook data and trawl survey records to investigate how juvenile albacore in the CCS use their oceanographic environment, and how their distributions overlap with the habitats of four key forage species. We show that northern anchovy (Engraulis mordax) and hake (Merluccius productus) habitat is associated with productive coastal waters found more inshore of core juvenile albacore habitat, whereas Pacific sardine (Sardinops sagax) and boreal clubhook squid (Onychoteuthis borealijaponica) habitat overlaps more consistently with that of albacore. Our results can improve understanding of how albacore movements relate to foraging strategies, and why preyswitching behavior occurs. This has relevance for the development of ecosystem models for the CCS, and for the eventual implementation of ecosystem-based fishery management.

Dynamical downscaling of future hydrographic changes over the Northwest Atlantic Ocean

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

Author(s): Shin, S., and Alexander, M. A. 

Project PI: Curchister
DOI: http://

Projected climate changes along the U.S. East and Gulf Coasts were examined using the eddy-resolvingRegional Ocean Modeling System (ROMS). First, a control (CTRL) ROMS simulation was performed usingboundary conditions derived from observations. Then climate change signals, obtained as mean seasonalcycle differences between the recent past (1976–2005) and future (2070–99) periods in a coupled global cli-mate model under the RCP8.5 greenhouse gas trajectory, were added to the initial and boundary conditionsof the CTRL in a second (RCP85) ROMS simulation. The differences between the RCP85 and CTRLsimulations were used to investigate the regional effects of climate change. Relative to the coarse-resolutioncoupled climate model, the downscaled projection shows that SST changes become more pronounced nearthe U.S. East Coast, and the Gulf Stream is further reduced in speed and shifted southward. Moreover, thedownscaled projection shows enhanced warming of ocean bottom temperatures along the U.S. East and Gulf Coasts, particularly in the Gulf of Maine and the Gulf of Saint Lawrence. The enhanced warming was relatedto an improved representation of the ocean circulation, including topographically trapped coastal oceancurrents and slope water intrusion through the Northeast Channel into the Gulf of Maine. In response toincreased radiative forcing, much warmer than present-day Labrador Subarctic Slope Waters entered the Gulf of Maine through the Northeast Channel, warming the deeper portions of the gulf by more than 48ºC.

Ecosystem based fisheries management forestalls climate-driven collapse

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): Holsman, K. K., A. Haynie, A. B. Hollowed, A. J. Hermann, W. Cheng, A. Faig, J. Ianelli, K. Kearney, A. Punt, J. Reum

Project PI: Hollowed

Climate change is impacting fisheries worldwide with uncertain outcomes for food and nutritional security. Using management strategy evaluations for key US fisheries in the eastern Bering Sea we find that Ecosystem Based Fisheries Management (EBFM) measures forestall future declines under climate change over non-EBFM approaches. Yet, benefits are species-specific and decrease markedly after 2050. Under high-baseline carbon emission scenarios (RCP 8.5), end-of-century (2075–2100) pollock and Pacific cod fisheries collapse in >70% and >35% of all simulations, respectively. Our analysis suggests that 2.1–2.3 °C (modeled summer bottom temperature) is a tipping point of rapid decline in gadid biomass and catch. Multiyear stanzas above 2.1 °C become commonplace in projections from ~2030 onward, with higher agreement under RCP 8.5 than simulations with moderate carbon mitigation (i.e., RCP 4.5). We find that EBFM ameliorates climate change impacts on fisheries in the near-term, but long-term EBFM benefits are limited by the magnitude of anticipated change.

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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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