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The commercial Dungeness crab (Metacarcinus magister) fishery in Oregon and Washington (USA) is one of the most valuable fisheries in the region, but it experiences high interannual variability. These fluctuations have been attributed to environmental drivers on seasonal and annual timescales. In this study, researchers and state and tribal fisheries managers develop a statistical model for Dungeness crab catch per unit effort (CPUE) to help inform dynamic management decisions in Oregon and Washington. Fishing observations were matched to seasonally forecast and lagged ocean conditions from J-SCOPE, a regional forecast system (http://www.nanoos.org/products/j-scope/). Inclusion of dynamic and lagged ocean conditions improved model skill compared to simpler models, and the best model captured intraseasonal trends and interannual variability in catch rates, and spatial catch patterns. We also found that model skill relied on fishing behaviour, which varies interannually, highlighting the need for advanced fishing behaviour modelling to reduce uncertainty. The relationships between catch rates and ocean conditions may help elucidate environmental influences of catch variability. Forecast products were co-designed with managers to meet their needs for key decision points. Our results illustrate a seasonal forecasting approach for management of other highly productive, but also dynamic, invertebrates that increasingly contribute to global fisheries yield.

Multispecies models have existed in a fisheries context since at least the 1970s, but despite much exploration, advancement, and consideration of multispecies models, there remain limited examples of their operational use in fishery management. Given that species and fleet interactions are inherently multispecies problems and the push towards ecosystem-based fisheries management, the lack of more regular operational use is both surprising and compelling. We identify impediments hampering the regular operational use of multispecies models and provide recommendations to address those impediments. These recommendations are: (1) engage stakeholders and managers early and often; (2) improve messaging and communication about the various uses of multispecies models; (3) move forward with multispecies management under current authorities while exploring more inclusive governance structures and flexible decision-making frameworks for handling tradeoffs; (4) evaluate when a multispecies modelling approach may be more appropriate; (5) tailor the multispecies model to a clearly defined purpose; (6) develop interdisciplinary solutions to promoting multispecies model applications; (7) make guidelines available for multispecies model review and application; and (8) ensure code and models are well documented and reproducible. These recommendations draw from a global assemblage of subject matter experts who participated in a workshop entitled “Multispecies Modeling Applications in Fisheries Management”.

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, use of Earth system models 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 provides a brief overview of some of the most prominent differences among the most recent generation of Earth system models 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.

Marine ecosystem management is increasingly expected to take into account a wide range of ecological and socio‐economic factors. Decision‐making is helped by end‐to‐end ecosystem models that allow exploration of alternative management scenarios given a complex range of interacting factors. We present Atlantis – a spatially structured largely deterministic end‐to‐end marine ecosystem model written in C, available for all major operating systems, based on dynamically interacting physics, biology, fisheries, management, assessment and economics submodels. A detailed installation guide and example application files are also provided. One of the main features of Atlantis is its modularity. At the simplest level Atlantis can have uniform forcing of oceanographic processes, a single primary producer and a consumer. At the most complex level, Atlantis can be used with a range of environmentally driven ecological responses, complex and habitat‐dependent food web, dynamic assessment, management and fishing effort driven by market forces and human behaviour. The combination chosen should be guided by the available data and the questions to be answered. Atlantis provides a large and customizable list of output files and summary statistics that can be analysed and plotted using a number of dedicated r packages. When applying the Atlantis package, the users should be aware of the caveats associated with complex models, such as parameter and structural model uncertainty and challenges interpreting interactions of multiple processes.

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.

Many marine mammal predators, particularly pinnipeds, have increased in abundance in recent decades, generating new challenges for balancing human uses with recovery goals via ecosystem-based management. We used a spatio-temporal bioenergetics model of the Northeast Pacific Ocean to quantify how predation by three species of pinnipeds and killer whales (Orcinus orca) on Chinook salmon (Oncorhynchus tshawytscha) has changed since the 1970s along the west coast of North America, and compare these estimates to salmon fisheries. We find that from 1975 to 2015, biomass of Chinook salmon consumed by pinnipeds and killer whales increased from 6,100 to 15,200 metric tons (from 5 to 31.5 million individual salmon). Though there is variation across the regions in our model, overall, killer whales consume the largest biomass of Chinook salmon, but harbor seals (Phoca vitulina) consume the largest number of individuals. The decrease in adult Chinook salmon harvest from 1975–2015 was 16,400 to 9,600 metric tons. Thus, Chinook salmon removals (harvest + consumption) increased in the past 40 years despite catch reductions by fisheries, due to consumption by recovering pinnipeds and endangered killer whales. Long-term management strategies for Chinook salmon will need to consider potential conflicts between rebounding predators or endangered predators and prey.

Populations of sardine, anchovy, and other forage species can fluctuate to low levels due to climate variability and fishing, leading to indirect effects on marine food webs. In the context of recent declines of sardine ( Sardinops sagax) and anchovy ( Engraulis mordax) in the California Current, we apply an end-to-end Atlantis ecosystem model that is spatially explicit, includes trophic interactions, and allows high and low recruitment regimes (production of juveniles). Our simulations suggest that depleted sardine populations, whether caused by fishing or natural cycles, may lead to declines in predator groups such as dolphins and large piscivorous flatfish (e.g. California halibut Paralichthys californicus ). Birds exhibited more moderate declines, and California sea lions ( Zalophus californianus ) exhibited relatively weak declines. The Atlantis ecosystem model also predicted indirect positive effects of sardine depletion, primarily for prey species such as zooplankton. Overall our model predicted moderate declines in most predators during simulated severe declines in sardine and anchovy, illustrating the important buffering role provided by forage species other than sardine and anchovy. This ‘buffered response’ is weaker than what would be suggested by another ecosystem model (Ecosim), as predicted by diet information and a global synthesis of Ecosim models (the PREP equation). One limitation of the Atlantis model is that it did not include processes that might give rise to localized depletion of sardine at scales relevant to central place foragers, such as birds and pinnipeds. This analysis will contribute to a collaborative multi-model approach that evaluates the role of sardine in the California Current.

Conflicts can arise when the recovery of one protected species limits the recovery of another through competition or predation. The recovery of many marine mammal populations on the west coast of the United States has been viewed as a success; however, within Puget Sound in Washington State, the increased abundance of three protected pinniped species may be adversely affecting the recovery of threatened Chinook salmon (Oncorhynchus tshawytscha) and endangered killer whales (Orcinus orca) within the region. Between 1970 and 2015, we estimate that the annual biomass of Chinook salmon consumed by pinnipeds has increased from 68 to 625 metric tons. Converting juvenile Chinook salmon into adult equivalents, we found that by 2015, pinnipeds consumed double that of resident killer whales and six times greater than the combined commercial and recreational catches. We demonstrate the importance of interspecific interactions when evaluating species recovery. As more protected species respond positively to recovery efforts, managers should attempt to evaluate tradeoffs between these recovery efforts and the unintended ecosystem consequences of predation and competition on other protected species.

Ecosystem-based fisheries management (EBFM) and ecosystem restoration are gaining momentum worldwide, including in U.S. waters of the Gulf of Mexico (GOM). Ecosystem models are valuable tools for informing EBFM and restoration activities. In this paper, we provide guidance and a roadmap for ecosystem modeling in the GOM region, with an emphasis on model development and use of model products to inform EBFM and the increasing investments in restoration. We propose eight “best practices” for ecosystem modeling efforts, including (1) identification of priority management questions, (2) scenarios as simulation experiments, (3) calibration and validation needs, (4) sensitivity and uncertainty analyses, (5) ensuring transparency, (6) improving communication between ecosystem modelers and the various stakeholders, (7) documentation of modeling efforts, and (8) maintaining the ecosystem models and codes. Fisheries management in the USA adheres to a prescriptive set of calculations. Therefore, the use of ec...

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.

An ecosystem approach to forage fish management is required because forage fish support large fisheries, are prey for many valued species in marine food webs, and provide important social and cultural benefits to humans. Complex ecosystem models are often used to evaluate potential ecosystem consequences of forage fish fisheries, but there is seldom sufficient data to parameterize them, and full consideration of uncertainty is impossible. Models of Intermediate Complexity for Ecosystem assessment (MICE) provide a link between full ecosystem models and tactical (usually single-species) models typically used in fisheries management. MICE are ideal tools to form the basis for management strategy evaluations that compare the ability of candidate strategies to achieve goals related to target fisheries and broader ecosystem protection objectives. A MICE model is developed for the California Current Ecosystem (CCE) that focuses on the fishery for the northern subpopulation of Pacific sardine ( Sardinops sajax ) and the indirect impacts of the fishery on place-based predators, in particular brown pelicans ( Pelecanus occidentalis ) and California sea lions ( Zalophus californianus ), in the Southern California Bight. The model includes three forage species (sardine, northern anchovy Engraulis mordax , and ‘other forage’), an ‘other prey’ category, and two predator species (brown pelican and California sea lion) and evaluates the impacts of variable forage availability on adult predator reproductive success and survival. Parameterization of the model is based on available monitoring data and assessment outputs. The model is used to assess the ecosystem and fishery consequences of the current sardine management systems for Mexico, the USA, and Canada, with a focus on identifying which among a long list of sources of uncertainty in the system are most consequential for predictions of fishery impacts on predators. Key sources of uncertainty to consider in ecosystem assessments for the CCE are how prey abundance and availability impact predator demography and the extent to which the dynamics of prey populations are driven by environmental factors. Data are available for some of these sources of uncertainty for CCE sardine management, but much uncertainty remains, necessitating exploration of sensitivity to alternative model formulations and parameter values when providing advice on management strategies to decision makers.

Ecosystem models can be used to understand the cumulative impacts of human pressures and environmental drivers on ecosystem structure and dynamics. Predictive modeling can show how management can influence those dynamics and structures and the ecosystem services these systems provide. Many nations and intergovernmental organizations are advocating for ecosystem-based management, often with a specific emphasis to evaluate various future management strategies. Atlantis is an end-to-end ecosystem model that is well suited for this task and has so far been developed for more than 30 diverse marine ecosystems worldwide. To provide a better understanding of the current modeling work, elicit wider interest, and foster collaboration within the Atlantis community, the first international Atlantis Summit was convened in December 2015. The main outcomes from this workshop included a clearer framework and infrastructure for model development and collaboration; the opportunity to perform common scenarios with a range of Atlantis models to analyze ecosystem responses to environmental and management-based perturbations; and the use of Atlantis as a test case for exploring the performance of single species, multispecies, and trophic food web models at an international level.

Understanding the role of forage fish in marine food webs is an important part of ecosystem-based fisheries management. Food web models are a common tool used to account for important characteristics of forage fish and their trophodynamics. One primary limitation of many existing food web models is that the taxonomic resolution of forage fish and their predators is overly simplified. Here, we developed a food web model with high taxonomic resolution of forage fish and their predators in the California Current to more comprehensively describe trophic linkages involving forage fish and examine the ecological role of forage fish in this system. We parameterized a mass-balanced food web model (Ecopath) with 92 living functional groups, and used this to quantify diet dependency on forage fish, determine the main predators of forage fish, identify the topological position of forage fish in the food web, and calculate an index that identifies forage species or species aggregations that have key ecological roles (Supportive Role to Fishery ecosystem, SURF). Throughout, we characterized parameter uncertainty using a Monte Carlo approach. Though diets revealed some predators had high diet dependencies on individual forage fish species, most predators consumed multiple forage fish and also had notable diet overlap with forage fish. Consequently, no single forage fish appeared to act as a vital nexus species that is characteristic of “wasp-waisted” food webs in other upwelling regions. Additionally, no single forage fish was identified as “key” by the SURF index, but if predators and fisheries view certain pairs of forage fish as functionally equivalent, some plausible pairs would be identified as key assemblages. Specifically, sardine & anchovy ( Sardinops sagax & Engraulis mordax ) and herring & anchovy ( Clupea pallasii & E. mordax ) are key when predator populations depend on the aggregate availability of these species. This food web model can be used to support generalized equilibrium trade-off analysis or dynamic modeling to identify specific predators that would be of conservation concern under conditions of future forage fish depletion.

As many marine mammal populations have increased following bans on their harvest, there has been a growing need to understand potential impacts of these population changes on coastal marine ecosystems. Quantifying consumption of prey species, such as fish, is particularly important when those same prey are also targeted by commercial fisheries. Estimating the impact of marine mammal predators on prey fish depends upon knowledge of marine mammal diet composition; scientific advances over the last century have improved understanding of diets but have also led to inconsistent methods that challenge attempts at synthesis and comparison. Meta-analysis techniques offer the opportunity to overcome such challenges, yet have not been widely applied to synthesize marine mammal diets over space and time. As a case study, we focus on synthesizing diet studies of Chinook (king) salmon (Oncorhynchus tshawytscha) by four species of marine mammal predators in the Northeast Pacific Ocean: Steller sea lions (Eumetopias jubatus), California sea lions (Zalophus californianus), harbor seals (Phoca vitulina), and killer whales (Orcinus orca). We also highlight several simple meta-analyses for which these types of diet databases may be employed. Our assembled database consists of > 330 records, spanning more than 100 years. Results indicate that the frequency of occurrence of Chinook salmon in killer whale studies is high (63%) relative to pinniped studies (

We review the state of knowledge of the individual and community responses of euthecosome (shelled) pteropods in the context of global environmental change. In particular, we focus on their responses to ocean acidification, in combination with ocean warming and ocean deoxygenation, as inferred from a growing body of empirical literature, and their relatively nascent place in ecosystem-scale models. Our objectives are: (1) to summarize the threats that these stressors pose to pteropod populations; (2) to demonstrate that pteropods are strong candidate indicators for cumulative effects of OA, warming, and deoxygenation in marine ecosystems; and (3) to provide insight on incorporating pteropods into population and ecosystem models, which will help inform ecosystem-based management of marine resources under future environmental regimes.

A shift towards ecosystem-based management in recent decades has led to new analytical tools such as end-to-end marine ecosystem models. End-to-end models are complex and typically simulate full ecosystems from oceanography to foodwebs and fisheries, operate on a spatial framework, and link to physical oceanographic models. Most end-to-end approaches allow multiple ways to implement human behaviours involving fishery catch, fleet movement, or other impacts such as nutrient loading or climate change effects. Though end-to-end ecosystem models were designed specifically for marine management, their novelty makes them unfamiliar to most decision makers. Before such models can be applied within the context of marine management decisions, additional levels of vetting will be required, and a dialogue with decision makers must be initiated. Here we summarize a review of an Atlantis end-to-end model, which involved a multi-day, expert review panel with local and international experts, convened to challenge models and data used in the management context. We propose nine credibility and quality control standards for end-to-end models intended to inform management, and suggest two best practice guidelines for any end-to-end modelling application. We offer our perspectives (as recent test subjects or “guinea pigs”) on how a review could be motivated and structured and on the evaluation criteria that should be used, in the most specific terms possible.

Despite the significant advances in making monthly or seasonal forecasts of weather, ocean hypoxia, harmful algal blooms and marine pathogens, few such forecasting efforts have extended to the ecology of upper trophic level marine species. Here, we test our ability to use short-term (up to 9 months) predictions of ocean conditions to create a novel forecast of the spatial distribution of Pacific sardine, Sardinops sagax. Predictions of ocean conditions are derived using the output from the Climate Forecast System (CFS) model downscaled through the Regional Ocean Modeling System (ROMS). Using generalized additive models (GAMs), we estimated significant relationships between sardine presence in a test year (2009) and salinity and temperature. The model, fitted to 2009 data, had a moderate skill [area under the curve (AUC) = 0.67] in predicting 2009 sardine distributions, 5–8 months in advance. Preliminary tests indicate that the model also had the skill to predict sardine presence in August 2013 (AUC = 0.85) and August 2014 (AUC = 0.96), 4–5 months in advance. The approach could be used to provide fishery managers with an early warning of distributional shifts of this species, which migrates from the U.S.–Mexico border to as far north as British Columbia, Canada, in summers with warm water and other favorable ocean conditions. We expect seasonal and monthly forecasts of ocean conditions to be broadly useful for predicting spatial distributions of other pelagic and midwater species.

Recent developments in global dynamical climate prediction systems have allowed for skillful predictions of climate variables relevant to living marine resources (LMRs) at a scale useful to understanding and managing LMRs. Such predictions present opportunities for improved LMR management and industry operations, as well as new research avenues in fisheries science. LMRs respond to climate variability via changes in physiology and behavior. For species and systems where climate-fisheries links are well established, forecasted LMR responses can lead to anticipatory and more effective decisions, benefitting both managers and stakeholders. Here, we provide an overview of climate prediction systems and advances in seasonal to decadal prediction of marine-resource relevant environmental variables. We then describe a range of climate-sensitive LMR decisions that can be taken at lead-times of months to decades, before highlighting a range of pioneering case studies using climate predictions to inform LMR decisions. The success of these case studies suggests that many additional applications are possible. Progress, however, is limited by observational and modeling challenges. Priority developments include strengthening of the mechanistic linkages between climate and marine resource responses, development of LMR models able to explicitly represent such responses, integration of climate driven LMR dynamics in the multi-driver context within which marine resources exist, and improved prediction of ecosystem-relevant variables at the fine regional scales at which most marine resource decisions are made. While there are fundamental limits to predictability, continued advances in these areas have considerable potential to make LMR managers and industry decision more resilient to climate variability and help sustain valuable resources. Concerted dialog between scientists, LMR managers and industry is essential to realizing this potential.

Growing human populations put increasing demands on marine ecosystems. Studies have demonstrated the importance of large biomass forage groups in model food webs, but small biomass contributors are often overlooked. Here, we predict the ecosystem effects of three potential future fisheries targeting functional groups that make up only a small proportion of total ecosystem biomass using the California Current Atlantis Model: deep demersal fish such as grenadier ( Albatrossia pectoralis and Coryphaenoides acrolepis ), nearshore fish such as white croaker ( Genyonemus lineatus ), and shortbelly rockfish ( Sebastes jordani ). Using a spatially explicit ecosystem model, we explored individual fishing scenarios for these groups that resulted in abundance levels of 75, 40, 25, and 0 percent of the status quo fishing scenario and a combined fishing scenario simultaneously targeting all three groups. We evaluated the effects on coast-wide biomass and describe variation in affected groups by region. Results indicate that developing fisheries on the proposed targets would have small coast-wide effects on other species. However, effects varied significantly within the ecosystem, with higher impacts concentrated in the central California region of the model. Effects of fishing all three groups simultaneously were additive in some cases coastwide, but were not additive at the regional scale. This work provides a framework for evaluating effects of new fisheries and suggests that regional effects should be evaluated within a larger management context.

The advent of an ecosystem-based approach dramatically expanded the scope of fisheries management, creating a critical need for new kinds of data and quantitative approaches that could be integrated into the management system. Ecosystem models are needed to codify the relationships among drivers, pressures and resulting states, and to quantify the trade-offs between conflicting objectives. Incorporating ecosystem considerations requires moving from the single-species models used in stock assessments, to more complex models that include species interactions, environmental drivers and human consequences. With this increasing model complexity, model fit can improve, but parameter uncertainty increases. At intermediate levels of complexity, there is a ‘sweet spot’ at which the uncertainty in policy indicators is at a minimum. Finding the sweet spot in models requires compromises: for example, to include additional component species, the models of each species have in some cases been simplified from age-structured to logistic or bioenergetic models. In this paper, we illuminate the characteristics, capabilities and short-comings of the various modelling approaches being proposed for ecosystem-based fisheries management. We identify key ecosystem needs in fisheries management and indicate which types of models can meet these needs. Ecosystem models have been playing strategic roles by providing an ecosystem context for single-species management decisions. However, conventional stock assessments are being increasingly challenged by changing natural mortality rates and environmentally driven changes in productivity that are observed in many fish stocks. Thus, there is a need for more tactical ecosystem models that can respond dynamically to changing ecological and environmental conditions.

Isaac C. Kaplan, Daniel S. Holland, and Elizabeth A. Fulton. 2014. Finding the accelerator and brake in an individual quota fishery: linking ecology, economics, and fleet dynamics of US West Coast trawl fisheries. – ICES Journal of Marine Science, 71: 308–319. In 2011, the Pacific Fisheries Management Council implemented an individual transferrable quota (ITQ) system for the US West Coast groundfish trawl fleet. Under the ITQ system, each vessel now receives transferrable annual allocations of quota for 29 groundfish species, including target and bycatch species. Here we develop an ecosystem and fleet dynamics model to identify which components of an ITQ system are likely to drive responses in effort, target species catch, bycatch, and overall profitability. In the absence of penalties for discarding over-quota fish, ITQs lead to large increases in fishing effort and bycatch. The penalties fishermen expect for exceeding quota have the largest effect on fleet behaviour, capping effort and total bycatch. Quota prices for target or bycatch species have lesser impacts on fishing dynamics, even up to bycatch quota prices of $50 kg−1. Ports that overlap less with bycatch species can increase effort under individual quotas, while other ports decrease effort. Relative to a prior management system, ITQs with penalties for exceeding quotas lead to increased target species landings and lower bycatch, but with strong variation among species. The model illustrates how alternative fishery management policies affect profitability, sustainability and the ecosystem.

SUMMARYHuman demands for food and fish meal are often in direct competition with forage needs of marine mammals, birds and piscivorous harvested fish. Here, two well-developed ecosystem models for the California Current on the West Coast of the USA were used to test the impacts on other parts of the ecosystem of harvesting euphausiids, forage fish, mackerel and mesopelagic fish such as myctophids. Depleting individual forage groups to levels that led to maximum sustainable yield of those groups may have both positive and negative effects on other species in the California Current. The most common impacts were on predators of forage groups, some of which showed declines of >20% under the scenarios that involved depletion of forage groups to 40% of unfished levels. Depletion of euphausiids and forage fish, which each comprise >10% of system biomass, had the largest impact on other species. Depleting euphausiids to 40% of unfished levels altered the abundance of 13–30% of the other functional groups by >20%; while depleting forage fish to 40% altered the abundance of 20–50% of the other functional groups by >20%. There are clear trade-offs between the harvest of forage groups and the ability of the California Current to sustain other trophic levels. Though higher trophic level species, such as groundfish, are often managed on the basis of reference points that can reduce biomass to below half of unfished levels, this level of forage species removal is likely to impact the abundance of other target species, protected species and the structure of the ecosystem.

Resource managers at the state, federal, and tribal levels make decisions on a weekly to quarterly basis, and fishers operate on a similar timeframe. To determine the potential of a support tool for these efforts, a seasonal forecast system is experimented with here. JISAO’s Seasonal Coastal Ocean Prediction of the Ecosystem (J-SCOPE) features dynamical downscaling of regional ocean conditions in Washington and Oregon waters using a combination of a high-resolution regional model with biogeochemistry and forecasts from NOAA’s Climate Forecast System (CFS). Model performance and predictability were examined for sea surface temperature (SST), bottom temperature, bottom oxygen, pH, and aragonite saturation state through model hindcasts, reforecast, and forecast comparisons with observations. Results indicate J-SCOPE forecasts have measurable skill on seasonal timescales. Experiments suggest that seasonal forecasting of ocean conditions important for fisheries is possible with the right combination of components. Those components include regional predictability on seasonal timescales of the physical environment from a large-scale model, a high-resolution regional model with biogeochemistry that simulates seasonal conditions in hindcasts, a relationship with local stakeholders, and a real-time observational network. Multiple efforts and approaches in different regions would advance knowledge to provide additional tools to fishers and other stakeholders.

There is a need to better understand the linkages between marine ecosystems and the human communities and economies that depend on these systems. Here those linkages are drawn for the California Current on the US West Coast, by combining a fishery ecosystem model (Atlantis) with an economic model (IO-PAC) that traces how changes in seafood landings impact the broader economy. The potential effects of broad fisheries management options are explored, including status quo management, switching effort from trawl to other gears, and spatial management scenarios. Relative to Status Quo, the other scenarios here involved short-term ex-vessel revenue losses, primarily to the bottom trawl fleet. Other fleets, particularly the fixed gear fleet that uses pots and demersal longlines, gained revenue in some scenarios, though spatial closures of Rockfish Conservation Areas reduced revenue to fixed gear fleets. Processor and wholesaler revenue tracked trends in the bottom trawl fleet, which accounted for 58% of total landings by value. Income impacts (employee compensation and earnings of business owners) on the broader economy mirrored the revenue trends. The long-term forecast (15 years) from the Atlantis ecosystem model predicted substantial stock rebuilding and increases in fleet catch. The 15 year projection of Status Quo suggested an additional ∼$27 million in revenue for the fisheries sectors, and an additional $23 million in income and 385 jobs in the broader economy, roughly a 25% increase. Linking the ecological and economic models here has allowed evaluation of fishery management policies using multiple criteria, and comparison of potential economic and conservation trade-offs that stem from management actions.

End-to-end marine ecosystem models link climate and oceanography to the food web and human activities. These models can be used as forecasting tools, to strategically evaluate management options and to support ecosystem-based management. Here we report the results of such forecasts in the California Current, using an Atlantis end-to-end model. We worked collaboratively with fishery managers at NOAA’s regional offices and staff at the National Marine Sanctuaries (NMS) to explore the impact of fishery policies on management objectives at different spatial scales, from single Marine Sanctuaries to the entire Northern California Current. In addition to examining Status Quo management, we explored the consequences of several gear switching and spatial management scenarios. Of the scenarios that involved large scale management changes, no single scenario maximized all performance metrics. Any policy choice would involve trade-offs between stakeholder groups and policy goals. For example, a coast-wide 25% gear shift from trawl to pot or longline appeared to be one possible compromise between an increase in spatial management (which sacrificed revenue) and scenarios such as the one consolidating bottom impacts to deeper areas (which did not perform substantially differently from Status Quo). Judged on a coast-wide scale, most of the scenarios that involved minor or local management changes (e.g. within Monterey Bay NMS only) yielded results similar to Status Quo. When impacts did occur in these cases, they often involved local interactions that were difficult to predict a priori based solely on fishing patterns. However, judged on the local scale, deviation from Status Quo did emerge, particularly for metrics related to stationary species or variables (i.e. habitat and local metrics of landed value or bycatch). We also found that isolated management actions within Monterey Bay NMS would cause local fishers to pay a cost for conservation, in terms of reductions in landed value. However, this cost was minimal when local conservation actions were part of a concerted coast-wide plan. The simulations demonstrate the utility of using the Atlantis end-to-end ecosystem model within NOAA’s Integrated Ecosystem Assessment, by illustrating an end-to-end modeling tool that allows consideration of multiple management alternatives that are relevant to numerous state, federal and private interests.

Ecosystem-based fisheries management calls for the consideration of the indirect and cumulative effects of fishing, in addition to estimating direct fishing mortality. Here, we quantify such effects of fishing fleets, and their interactions, using a spatially explicit Atlantis simulation model of the food web and fisheries in the California Current. Simulations testing the effects of single fleets suggested that bottom trawl, fixed gear, and hake (Merluccius productus) trawl primarily have direct impacts on their target and bycatch species. Few indirect effects from these three fleets extended through predator–prey links to other parts of the food web. In contrast, effects of the purse seine fleet extended beyond the three groups it harvested, strongly altering the abundance of predators, planktonic prey, and benthos. In terms of nine ecosystem attributes, our experiments involving single fleets identified six fleets that caused the bulk of negative impacts. Specific fleets impacted different aspects of the ecosystem, for instance with groundfish gears causing reductions in piscivore abundance, and hake trawl and purse seine increasing krill through reducing abundance of planktivores. In terms of interactions among fleets' effects, the vast majority of effects were simply additive – the combined effect of two fleets was simply the sum of the individual fleets' effects. The analyses offer one way to sharpen the focus of ecosystem-based fisheries management in the California Current, emphasizing impacts and interactions of particular stressors.

Summary 1. The Northern Gulf of California is an ecologically important marine area with a high degree of biodiversity, endemism and productivity. Mounting conservation concerns have prompted researchers to propose new management regulations, restricting fishing and protecting sensitive species. Compliance with existing regulations is poor. Rules that are currently in place, if followed, may go a long way towards achieving the ecological goals of management. 2. We conduct a review of existing fisheries regulations in this area. Then, using a spatially explicit marine ecosystem model (Atlantis), we estimate the benefits of compliance with existing fisheries regulations. 3. Under a full compliance scenario, we find large increases in protected species biomass within 25 years and a slowed rate of ecosystem degradation because of fishing. However, full compliance costs the fishing industry about 30% of its annual revenue. 4. We parse out the benefits offered by management instruments (including spatial management protections, seasonal fishery closures, gear restrictions, cessation of illegal fishing and vessel buy-out programmes) and conclude that a suite of measures is needed to address major conservation objectives. 5. Synthesis and applications. This exercise quantifies the benefits of improved fisheries enforcement and provides a benchmark by which the value of future regulatory amendments can be assessed. Where compliance with existing regulations is poor, conservation goals may be better served by strengthening enforcement than by enacting new rules and legislation.

Low-trophic level species account for more than 30% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low-trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield (MSY) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80% of MSY.

Models are key tools for integrating a wide range of system information in a common framework. Attempts to model exploited marine ecosystems can increase understanding of system dynamics; identify major processes, drivers and responses; highlight major gaps in knowledge; and provide a mechanism to ‘road test’ management strategies before implementing them in reality. The Atlantis modelling framework has been used in these roles for a decade and is regularly being modified and applied to new questions (e.g. it is being coupled to climate, biophysical and economic models to help consider climate change impacts, monitoring schemes and multiple use management). This study describes some common lessons learned from its implementation, particularly in regard to when these tools are most effective and the likely form of best practices for ecosystem-based management (EBM). Most importantly, it highlighted that no single management lever is sufficient to address the many trade-offs associated with EBM and that the mix of measures needed to successfully implement EBM will differ between systems and will change through time. Although it is doubtful that any single management action will be based solely on Atlantis, this modelling approach continues to provide important insights for managers when making natural resource management decisions.