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IntroductionUnderstanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes.MethodsThis study applies the NOAA (National Oceanic and Atmospheric Administration) Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions.ResultsOverall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges.DiscussionAs climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information can inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially effective to protect or restore.

Climate change may impact ocean ecosystems through a number of mechanisms, including shifts in primary productivity or plankton community structure, ocean acidification, and deoxygenation. These processes can be simulated with global Earth system models (ESMs), which are increasingly being used in the context of fisheries management and other living marine resource (LMR) applications. However, projections of LMR-relevant metrics such as net primary production can vary widely between ESMs, even under identical climate scenarios. Therefore, the use of ESM should be accompanied by an understanding of the structural differences in the biogeochemical sub-models within ESMs that may give rise to these differences. This review article provides a brief overview of some of the most prominent differences among the most recent generation of ESM and how they are relevant to LMR application.

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.

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.

As ecosystem-based fisheries management becomes more ingrained into the way fisheries agencies do business, a need for ecosystem and multispecies models arises. Yet ecosystems are complex, and model uncertainty can be large. Model ensembles have historically been used in other disciplines to address model uncertainty. To understand the benefits and limitations of multispecies model ensembles (MMEs), cases where they have been used in the United States to address fisheries management issues are reviewed. The cases include: (1) development of ecological reference points for Atlantic Menhaden, (2) the creation of time series to relate harmful algal blooms to grouper mortality in the Gulf of Mexico, and (3) fostering understanding of the role of forage fish in the California Current. Each case study briefly reviews the management issue, the models used and model synthesis approach taken, and the outcomes and lessons learned from the application of MMEs. Major conclusions drawn from these studies highlight how the act of developing an ensemble model suite can improve the credibility of multispecies models, how qualitative synthesis of projections can advance system understanding and build confidence in the absence of quantitative treatments, and how involving a diverse set of stakeholders early is useful for ensuring the utility of the models and ensemble. Procedures for review and uptake of information from single-species stock assessment models are well established, but the absence of well-defined procedures for MMEs in many fishery management decision-making bodies poses a major obstacle. The benefits and issues identified here should help accelerate the design, implementation, and utility of MMEs in applied fisheries contexts.

Changing ecosystem conditions present a challenge for the monitoring and management of living marine resources, where decisions often require lead-times of weeks to months. Consistent improvement in the skill of regional ocean models to predict physical ocean states at seasonal time scales provides opportunities to forecast biological responses to changing ecosystem conditions that impact fishery management practices. In this study, we used 8-month lead-time predictions of temperature at 250 m depth from the J-SCOPE regional ocean model, along with stationary habitat conditions (e.g., distance to shelf break), to forecast Pacific hake (Merluccius productus) distribution in the northern California Current Ecosystem (CCE). Using retrospective skill assessments, we found strong agreement between hake distribution forecasts and historical observations. The top performing models [based on out-of-sample skill assessments using the area-under-the-curve (AUC) skill metric] were a generalized additive model (GAM) that included shelf-break distance (i.e., distance to the 200 m isobath) (AUC = 0.813) and a boosted regression tree (BRT) that included temperature at 250 m depth and shelf-break distance (AUC = 0.830). An ensemble forecast of the top performing GAM and BRT models only improved out-of-sample forecast skill slightly (AUC = 0.838) due to strongly correlated forecast errors between models (r = 0.88). Collectively, our results demonstrate that seasonal lead-time ocean predictions have predictive skill for important ecological processes in the northern CCE and can be used to provide early detection of impending distribution shifts of ecologically and economically important marine species.

Management strategy evaluation (MSE) provides a simulation framework to test the performance of living marine resource management. MSE has now been adopted broadly for use in single-species fishery management, often using a relatively simple “operating model” that projects population dynamics of one species forward in time. However, many challenges in ecosystem-based management involve tradeoffs between multiple species and interactions of multiple stressors. Here we use complex operating models, multi-species ecosystem models of the California Current and Nordic and Barents Seas, to test threshold harvest control rules that explicitly address the linkage between predators and prey, and between the forage needs of predators and fisheries. Specifically, within Atlantis ecosystem models we focus on how forage (zooplankton) availability affects the performance of harvest rules for target fish, and how these harvest rules for fish can account for environmentally-driven fluctuations in zooplankton. Our investigation led to three main results. First, consistent with studies based on single-species operating models, we found that compared to constant F = FMSY policies, threshold rules led to higher target stock biomass for Pacific hake (Merluccius productus) in the California Current and mackerel (Scomber scombrus) in the Nordic and Barents Seas. Performance in terms of catch of these species varied depending partly on the biomass and recovery trajectory for the simulated stock. Secondly, the multi-species operating models and the harvest control rules that linked fishing mortality rates to prey biomass (zooplankton) led to increased catch variability; this stemmed directly from the harvest rule that frequently adjusted Pacific hake or mackerel fishing rates in response to zooplankton, which are quite variable in these two ecosystems. Thirdly, tests suggested that threshold rules that increased fishing when productivity (zooplankton) declined had the potential for strong ecosystem effects on other species. These effects were most apparent in the Nordic and Barents Seas simulations. The tests of harvest control rules here do not include uncertainty in monitoring of fish and zooplankton, nor do they include uncertainty in stock assessment and implementation; these would be required for full MSE. Additionally, we intentionally chose target fish with strong mechanistic links to particular zooplankton groups, with the simplifying assumption that zooplankton biomass followed a forced time series. Further developing and testing of ecosystem-level considerations can be achieved with end-to-end ecosystem models, such as the Atlantis models applied here, which have the added benefit of tracking the follow-on effects of the harvest control rule on the broader ecosystem.

The Dungeness crab (Metacarcinus magister) fishery is one of the highest value fisheries in the US Pacific Northwest, but its catch size fluctuates widely across years. Although the underlying causes of this wide variability are not well understood, the abundance of M. magister megalopae has been linked to recruitment into the adult fishery 4 years later. These pelagic megalopae are exposed to a range of ocean conditions during their dispersal period, which may drive their occurrence patterns. Environmental exposure history has been found to be important for some pelagic organisms, so we hypothesized that inclusion of recent environmental exposure history would improve our ability to predict inter-annual variability in M. magister megalopae occurrence patterns compared to using “in situ” conditions alone. We combined 8 years of local observations of M. magister megalopae and regional simulations of ocean conditions to model megalopae occurrence using a generalized linear model (GLM) framework. The modeled ocean conditions were extracted from JISAO’s Seasonal Coastal Ocean Prediction of the Ecosystem (J-SCOPE), a high-resolution coupled physical-biogeochemical model. The analysis included variables from J-SCOPE identified in the literature as important for larval crab occurrence: temperature, salinity, dissolved oxygen concentration, nitrate concentration, phytoplankton concentration, pH, aragonite, and calcite saturation state. GLMs were developed with either in situ ocean conditions or environmental exposure histories generated using particle tracking experiments. We found that inclusion of exposure history improved the ability of the GLMs to predict megalopae occurrence 98% of the time. Of the six swimming behaviors used to simulate megalopae dispersal, five behaviors generated GLMs with superior fits to the observations, so a biological ensemble of these models was constructed. When the biological ensemble was used for forecasting, the model showed skill in predicting megalopae occurrence (AUC = 0.94). Our results highlight the importance of including exposure history in larval occurrence modeling and help provide a method for predicting pelagic megalopae occurrence. This work is a step toward developing a forecast product to support management of the fishery.

Worldwide fisheries management has been undergoing a paradigm shift from a single-species approach to ecosystem approaches. In the United States, NOAA has adopted a policy statement and Road Map to guide the development and implementation of ecosystem-based fisheries management (EBFM). NOAA’s EBFM policy supports addressing the ecosystem interconnections to help maintain resilient and productive ecosystems, even as they respond to climate, habitat, ecological, and social and economic changes. Managing natural marine resources while taking into account their interactions with their environment and our human interactions with our resources and environment requires the support of ecosystem science, modeling, and analysis. Implementing EBFM will require using existing mandates and approaches that fit regional management structures and cultures. The primary mandate for managing marine fisheries in the United States is the Magnuson-Stevens Fishery Conservation and Management Act. Many tenets of the Act align well with the EBFM policy, however, incorporating ecosystem analysis and models into fisheries management processes has faced procedural challenges in many jurisdictions. In this paper, we review example cases where scientists have had success in using ecosystem analysis and modeling to inform management priorities, and identify practices that help bring new ecosystem science information into existing policy processes. A key to these successes is regular communication and collaborative discourse among modelers, stakeholders, and resource managers to tailor models and ensure they addressed the management needs as directly as possible.

The sustainable use of global marine resources depends upon science-based decision processes and systems. Informing decisions with science is challenging for many reasons, including the nature of science and science-based institutions. The complexity of ecosystem-based management often requires the use of models, and model-based advice can be especially difficult to convert into policies or decisions. Here, we suggest five characteristics of model-based information and advice for successfully informing ocean management decision-making, based on the Ocean Modeling Forum framework. Illustrated by examples from two fisheries case studies, Pacific sardines 'Sardinops sagax' and Pacific herring 'Clupea pallasii', we argue that actionable model-based output should be aspirational, applicable, parsimonious, co-produced, and amplifying.

Ecosystem-based management (EBM) of the ocean considers all impacts on and uses of marine and coastal systems. In recent years, there has been a heightened interest in EBM tools that allow testing of alternative management options and help identify tradeoffs among human uses. End-to-end ecosystem modeling frameworks that consider a wide range of management options are a means to provide integrated solutions to the complex ocean management problems encountered in EBM. Here, we leverage the global advances in ecosystem modeling to explore common opportunities and challenges for ecosystem-based management, including changes in ocean acidification, spatial management, and fishing pressure across eight Atlantis (atlantis.cmar.csiro.au) end-to-end ecosystem models. These models represent marine ecosystems from the tropics to the arctic, varying in size, ecology, and management regimes, using a three-dimensional, spatially-explicit structure parametrized for each system. Results suggest stronger impacts from ocean acidification and marine protected areas than from altering fishing pressure, both in terms of guild-level (i.e., aggregations of similar species or groups) biomass and in terms of indicators of ecological and fishery structure. Effects of ocean acidification were typically negative (reducing biomass), while marine protected areas led to both “winners” and “losers” at the level of particular species (or functional groups). Changing fishing pressure (doubling or halving) had smaller effects on the species guilds or ecosystem indicators than either ocean acidification or marine protected areas. Compensatory effects within guilds led to weaker average effects at the guild level than the species or group level. The impacts and tradeoffs implied by these future scenarios are highly relevant as ocean governance shifts focus from single-sector objectives (e.g., sustainable levels of individual fished stocks) to taking into account competing industrial sectors' objectives (e.g., simultaneous spatial management of energy, shipping, and fishing) while at the same time grappling with compounded impacts of global climate change (e.g., ocean acidification and warming).

We use food-web models to develop visualizations to compare and evaluate the interactions of tuna fisheries with their supporting food webs in the eastern tropical Pacific (ETP) and the central north Pacific (CNP) Oceans. In the ETP and CNP models, individual fisheries use slightly different food webs that are defined by the assemblage of targeted tuna species. Distinct energy pathways are required to support different tuna species and, consequently, the specific fisheries that target different tuna assemblages. These simulations suggest that catches of tunas, sharks, and billfishes have lowered the biomass of the upper trophic levels in both systems, whereas increases in intermediate and lower trophic level animals have accompanied the decline of top predators. Trade-offs between fishing and predation mortality rates that occur when multiple fisheries interact with their respective food webs may lead to smaller changes in biomass than if only the effect of a single fishery is considered. Historical simulations and hypothetical management scenarios further demonstrate that the effects of longline and purse seine fisheries have been strongest in upper trophic levels, but that lower trophic levels may respond more strongly to purse-seine fisheries. The apex predator guild has responded most strongly to longlining. Simulations of alternative management strategies that attempt to rebuild shark and billfish populations in each ecosystem reveal that (1) changes in longlining more effectively recover top predator populations than do changes in purse seining and (2) restrictions on both shallow-set longline gear and shark finning may do more to recover top predators than do simple reductions in fishing effort.

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.

Species are experiencing a suite of novel stressors from anthropogenic activities that have impacts at multiple scales. Vulnerability assessment is one tool to evaluate the likely impacts that these stressors pose to species so that high-vulnerability cases can be identified and prioritized for monitoring, protection, or mitigation. Commonly used semi-quantitative methods lack a framework to explicitly account for differences in exposure to stressors and organism responses across life stages. Here we propose a modification to commonly used spatial vulnerability assessment methods that includes such an approach, using ocean acidification in the California Current as an illustrative case study. Life stage considerations were included by assessing vulnerability of each life stage to ocean acidification and were used to estimate population vulnerability in two ways. We set population vulnerability equal to: (1) the maximum stage vulnerability and (2) a weighted mean across all stages, with weights calculated using Lefkovitch matrix models. Vulnerability was found to vary across life stages for the six species explored in this case study: two krill-Euphausia pacifica and Thysanoessa spinifera, pteropod-Limacina helicina, pink shrimp-Pandalus jordani, Dungeness crab-Metacarcinus magister and Pacific hake-Merluccius productus. The maximum vulnerability estimates ranged from larval to subadult and adult stages with no consistent stage having maximum vulnerability across species. Similarly, integrated vulnerability metrics varied greatly across species. A comparison showed that some species had vulnerabilities that were similar between the two metrics, while other species' vulnerabilities varied substantially between the two metrics. These differences primarily resulted from cases where the most vulnerable stage had a low relative weight. We compare these methods and explore circumstances where each method may be appropriate.

Millions of people rely on the ecosystem services provided by coral reefs, but sustaining these benefits requires an understanding of how reefs and their biotic communities are affected by local human-induced disturbances and global climate change. Ecosystem-based management that explicitly considers the indirect and cumulative effects of multiple disturbances has been recommended and adopted in policies in many places around the globe. Ecosystem models give insight into complex reef dynamics and their responses to multiple disturbances and are useful tools to support planning and implementation of ecosystem-based management. We adapted the Atlantis Ecosystem Model to incorporate key dynamics for a coral reef ecosystem around Guam in the tropical western Pacific. We used this model to quantify the effects of predicted climate and ocean changes and current levels of current land-based sources of pollution (LBSP) and fishing. We used the following six ecosystem metrics as indicators of ecosystem state, resilience and harvest potential: 1) ratio of calcifying to non-calcifying benthic groups, 2) trophic level of the community, 3) biomass of apex predators, 4) biomass of herbivorous fishes, 5) total biomass of living groups and 6) the end-to-start ratio of exploited fish groups. Simulation tests of the effects of each of the three drivers separately suggest that by mid-century climate change will have the largest overall effect on this suite of ecosystem metrics due to substantial negative effects on coral cover. The effects of fishing were also important, negatively influencing five out of the six metrics. Moreover, LBSP exacerbates this effect for all metrics but not quite as badly as would be expected under additive assumptions, although the magnitude of the effects of LBSP are sensitive to uncertainty associated with primary productivity. Over longer time spans (i.e., 65 year simulations), climate change impacts have a slight positive interaction with other drivers, generally meaning that declines in ecosystem metrics are not as steep as the sum of individual effects of the drivers. These analyses offer one way to quantify impacts and interactions of particular stressors in an ecosystem context and so provide guidance to managers. For example, the model showed that improving water quality, rather than prohibiting fishing, extended the timescales over which corals can maintain high abundance by at least 5-8 years. This result, in turn, provides more scope for corals to adapt or for resilient species to become established and for local and global management efforts to reduce or reverse stressors.

High bycatch of non-target species and species of conservation concern often drives the implementation of fisheries policies. However, species- or fishery-specific policies may lead to indirect consequences, positive or negative, for other species or fisheries. We use an Atlantis ecosystem model of the Northern Gulf of California to evaluate the effects of fisheries policies directed at reducing bycatch of vaquita (Phocoena sinus) on other species of conservation concern, priority target species, and metrics of ecosystem function and structure. Vaquita, a Critically Endangered porpoise endemic to the Upper Gulf of California, are frequently entangled by finfish gillnets and shrimp driftnets. We tested five fishery management scenarios, projected over 30 years (2008 to 2038), directed at vaquita conservation. The scenarios consider progressively larger spatial restrictions for finfish gillnets and shrimp driftnets. The most restrictive scenario resulted in the highest biomass of species of conservation concern; the scenario without any conservation measures in place resulted in the lowest. Vaquita experienced the largest population increase of any functional group; their biomass increased 2.7 times relative to initial (2008) levels under the most restrictive spatial closure scenario. Bycatch of sea lions, sea turtles, and totoaba decreased > 80% in shrimp driftnets and at least 20% in finfish gillnet fleets under spatial management. We found indirect effects on species and ecosystem function and structure as a result of vaquita management actions. Biomass and catch of forage fish declined, which could affect lower-trophic level fisheries, while other species such as skates, rays, and sharks increased in both biomass and catch. When comparing across performance metrics, we found that scenarios that increased ecosystem function and structure resulted in lower economic performance indicators, underscoring the need for management actions that consider ecological and economic tradeoffs as part of the integrated management of the Upper Gulf of California.

BACKGROUND: Minimizing fishery bycatch threats might involve trade-offs between maintaining viable populations and economic benefits. Understanding these trade-offs can help managers reconcile conflicting goals. An example is a set of bycatch reduction measures for the Critically Endangered vaquita porpoise (Phocoena sinus), in the Northern Gulf of California, Mexico. The vaquita is an endemic species threatened with extinction by artisanal net bycatch within its limited range; in this area fisheries are the chief source of economic productivity. METHODOLOGY/PRINCIPAL FINDINGS: We analyze trade-offs between conservation of the vaquita and fisheries, using an end-to-end Atlantis ecosystem model for the Northern Gulf of California. Atlantis is a spatially-explicit model intended as a strategic tool to test alternative management strategies. We simulated increasingly restrictive fisheries regulations contained in the vaquita conservation plan: implementing progressively larger spatial management areas that exclude gillnets, shrimp driftnets and introduce a fishing gear that has no vaquita bycatch. We found that only the most extensive spatial management scenarios recovered the vaquita population above the threshold necessary to downlist the species from Critically Endangered. The scenario that excludes existing net gear from the 2008 area of vaquita distribution led to moderate decrease in net present value (US$ 42 million) relative to the best-performing scenario and a two-fold increase in the abundance of adult vaquita over the course of 30 years. CONCLUSIONS/SIGNIFICANCE: Extended spatial management resulted in the highest recovery of the vaquita population. The economic cost of proposed management actions was unequally divided between fishing fleets; the loss of value from finfish gillnet fisheries was never recovered. Our analysis shows that managers will have to confront difficult trade-offs between management scenarios for vaquita conservation.