Search

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”.

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.

Projecting the future distributions of commercially and ecologically important species has become a critical approach for ecosystem managers to strategically anticipate change, but large uncertainties in projections limit climate adaptation planning. Although distribution projections are primarily used to understand the scope of potential change-rather than accurately predict specific outcomes-it is nonetheless essential to understand where and why projections can give implausible results and to identify which processes contribute to uncertainty. Here, we use a series of simulated species distributions, an ensemble of 252 species distribution models, and an ensemble of three regional ocean climate projections, to isolate the influences of uncertainty from earth system model spread and from ecological modeling. The simulations encompass marine species with different functional traits and ecological preferences to more broadly address resource manager and fishery stakeholder needs, and provide a simulated true state with which to evaluate projections. We present our results relative to the degree of environmental extrapolation from historical conditions, which helps facilitate interpretation by ecological modelers working in diverse systems. We found uncertainty associated with species distribution models can exceed uncertainty generated from diverging earth system models (up to 70% of total uncertainty by 2100), and that this result was consistent across species traits. Species distribution model uncertainty increased through time and was primarily related to the degree to which models extrapolated into novel environmental conditions but moderated by how well models captured the underlying dynamics driving species distributions. The predictive power of simulated species distribution models remained relatively high in the first 30 years of projections, in alignment with the time period in which stakeholders make strategic decisions based on climate information. By understanding sources of uncertainty, and how they change at different forecast horizons, we provide recommendations for projecting species distribution models under global climate change.

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.

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. 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 California Current Ecosystem 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.

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...

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.

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.

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.

Any fishery management scheme, such as individual fishing quotas (IFQs) or marine protected areas, should be designed to be robust to potential shifts in the biophysical system. Here we couple possible catch scenarios under an IFQ scheme with ocean acidification impacts on shelled benthos and plankton, using an Atlantis ecosystem model for the US West Coast. IFQ harvest scenarios alone, in most cases, did not have strong impacts on the food web, beyond the direct effects on harvested species. However, when we added the impacts of ocean acidification, the abundance of commercially important groundfish such as English sole ( Pleuronectes vetulus ), arrowtooth flounder ( Atheresthes stomias ), and yellowtail rockfish ( Sebastes flavidus ) declined up to 20%–80%, owing to the loss of shelled prey items from their diet. English sole exhibited a 10-fold decline in potential catch and economic yield when confronted with strong acidification impacts on shelled benthos. Therefore, it seems prudent to complement IFQs with careful consideration of potential global change effects such as acidification. Our analysis provides an example of how new ecosystem modeling tools that evaluate cumulative impacts can be integrated with established management reference points and decision mechanisms.

Summary 1. Resource management agencies are often charged with managing natural resources for economic and social goals, while also protecting and conserving biodiversity and ecosystem function. However, this may not always be possible. Ecosystem-based management is frequently suggested as a way to achieve multiple objectives in resource management and requires that tradeo!s among conflicting objectives be identified and an e!ective means to utilize these trade-o!s developed. 2. We examine the relationship between area and species richness in a diverse assemblage of fishes along the US West Coast and then use parameters from this relationship as input for a model that considers trade-o!s between fisheries yield and the number of species protected by di!erent management strategies. 3. The species‐area relationship (S = cA z ) for fishes along the US Pacific coast is well described

Trees that fall into lakes from riparian forest become habitat for aquatic organisms, and are potentially an important link between terrestrial and aquatic ecosystems. Coarse woody habitat (CWH) promotes the production of benthic invertebrate prey and offers refuge for prey fishes, which are in turn consumed by piscivorous fishes. We used a simulation model to explore responses of an aquatic food web to changes in CWH caused by lakeshore residential development and windstorm, as well as to harvest of adult piscivores. Residential development had a negative effect on fishes, and could lead to extirpation of benthivorous prey fish species. In contrast, pulsed addition of CWH following a windstorm had little effect on the aquatic food web. Our results suggest that CWH is more important as shelter for prey fishes than as a substrate for benthic invertebrate production. However, piscivore harvest can supersede the role of CWH as prey shelter, leading to piscivore collapse and prey persistence even when CWH levels are low enough to promote piscivore dominance. Thus, the effects of lakeshore residential development on fishes can be masked by angler harvest of top piscivores.

Blue marlin Makaira nigricans, striped marlin Tetrapturus audax, and pelagic sharks (e.g., blue shark Prionace glauca) are commonly caught as bycatch by longline fisheries in the central North Pacific Ocean. Recently, concern has increased about depletion of these species. Modifications in longline gear may offer one solution. Here, we test the use of circle hooks, rather than the conventional tuna-style hooks, on longlines using an ecosystem model of the central North Pacific Ocean. The simulations considered span a range of reasonable circle hook catchability and survival rates for released fish. The results suggest that if circle hooks have higher catchability than the currently used tuna-style hooks, switching to circle hooks depletes marlin biomass by 25–40% and shark biomass by 15–35% over 30 years. However, these depletions do not occur if circle hook catchability is equal to or lower than that of tuna-style hooks. When the effects of catch-and-release requirements for marlins and sharks w...

Leatherback turtles (Dermochelys coriacea) are critically endangered in the eastern and western Pacific Ocean. Here, I estimate the magnitude of two likely causes of their decline: (i) bycatch by longline fishing vessels and (ii) coastal sources of mortality. I calculate point estimates of longline bycatch based on turtle catch rates from the US Hawaii-based fleet and effort data for the international Pacific longline fleet. I estimate the intrinsic growth rate of the population and the magnitude of coastal mortality by fitting a simple logistic model. In the western and central Pacific, coastal sources lead to a 13% annual mortality rate, compared with a point estimate of 12% from longlining. In the eastern Pacific, coastal sources account for a 28% annual mortality rate, compared with a point estimate of only 5% from longlining. A Bayesian risk assessment reveals the importance of reducing coastal sources of mortality, as well as longline bycatch, if the populations are to avoid extinction. International efforts to protect the leatherback should expand beyond focusing solely on longline bycatch and should attempt to reduce coastal harvest of adult females and eggs, as well as reduce bycatch by inshore gears such as gillnets.

Commercial yield of tunas in the central Pacific increased severalfold between 1952 and 1998. We developed age-structured production models that incorporate information from multiple fisheries to estimate population biomass and recruitment trends of tunas (Thunnus alalunga, Thunnus albacares, Thunnus obesus, and Katsuwonus pelamis) and billfish in the central north Pacific (0°N to 40°N and 130°E to 150°W). Our results suggest that all tuna stocks remain above 40% of 1950s levels, whereas blue marlin (Makaira nigricans) declined to 21% and swordfish (Xiphias gladius) to 56%. Estimated biomasses of juvenile bigeye (T. obsesus) and yellowfin (T. albacares) tuna increased to 112 and 129%, respectively, of 1950s levels. Juvenile albacore (T. alalunga) decreased during the 1970s and 1980s but recovered to historical highs (121%) in recent years. Skipjack (K. pelamis) remained relatively stable between 1952 and 1980, declined by 35% between 1981 and 1990, and then increased to 68% of 1950s levels. These changes generally represent decreases in top predators and increases in small tunas, which make up their prey. Application of stock assessment methods set in a food web context provides an important step toward developing a method that recognizes fishery exploitation as a component of ecosystem dynamics.

Pelagic fisheries in the Pacific Ocean target both large (Thunnus spp.) and small tunas (juveniles of Thunnus spp; Katsuwonus pelamis) but also take billfishes (Xiphias gladius, Makaira spp., Tetrapturus spp., Istiophorus platypterus) and sharks (Prionace glauca, Alopias superciliosus, Isurus oxyrinchus, Carcharhinus longimanus, Galeocerdo cuvieri) as bycatch. We developed a multispecies model using the Ecopath with Ecosim software that incorporated time-series estimates of biomass, fishing mortality, and bycatch rates (1952–1998) to evaluate the relative contributions of fishing and trophic impacts on tuna dynamics in the central Pacific (0°N to 40°N and 130°E to 150°W). The Ecosim model reproduced the observed trends in abundance indices and biomass estimates for most large tunas and billfishes. A decline in predation mortality owing to depletion of large predators was greatest for small yellowfin tuna and could possibly account for apparent increases in biomass. For other tunas, however, predicted changes in predation mortality rates were small (small bigeye) or were overwhelmed by much larger increases in fishing mortality (skipjack and small albacore). Limited evidence of trophic impacts associated with declining apex predator abundance likely results from the difficulties of applying detailed trophic models to open ocean systems in which ecological and fishery data uncertainties are large.

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.

Trophic ecosystem models are one promising tool for providing ecosystem-based management advice. Diet and interaction rate parameters are critical in defining the behavior of these models, and will greatly influence any predictions made in response to management perturbations. However, most trophic ecosystem models must rely on a patchwork of data availability and must contend with knowledge gaps and poor quantification of uncertainty. Here we present a statistical method for combining diet information from field samples and literature to describe trophic relationships at the level of functional groups. In this example, original fieldwork in the northern Gulf of California, Mexico, provides gut content data for targeted and untargeted fish species. The field data are pooled with diet composition information from FishBase, an online data repository. Diet information is averaged across stomachs to represent an average predator, and then the data are bootstrapped to generate likelihood profiles. These are fit to a Dirichlet function, and from the resulting marginal distributions, maximum-likelihood estimates are generated with confidence intervals representing the likely contribution to diet for each predator-prey combination. We characterize trophic linkages into two broad feeding guilds, pelagic and demersal feeders, and explore differentiation within those guilds. We present an abbreviated food web for the northern Gulf of California based on the results of this study. This food web will form the basis of a trophic dynamic model. Compared to the common method of averaging diet compositions across predators, this statistical approach is less influenced by the presence of long tails in the distributions, which correspond to rare feeding events, and is therefore better suited to small data sets.

Moving from single-species- to ecosystem-based management requires an understanding of how community-level attributes such as diversity change with area. We used survey data from bottom trawls to examine spatial patterns of species richness in U.S. Pacific coastal fishes. Specifically, we generated and compared species–area relationships (SARs) for species classified into several groups on the basis of maximum body size, trophic level, diet, maximum depth, geographic affinity, and taxonomic order. Because SARs among groups were not parallel and z values varied significantly for several groups, groups of species were under- or overrepresented (depending on the size of the area) relative to their proportions in the entire community (i.e., entire U.S. Pacific coast). In this way, differences in SARs help demonstrate trade-offs between species representation and coastal area and suggest strategies (such as targeting the protection of habitats and locations where a particular species or groups of species are maximized) that may minimize the size of marine protected areas (MPAs) but protect diversity at the level of the community and functional group. Resumen: El traslado del manejo de una sola especie al manejo basado en ecosistemas requiere del entendimiento de los cambios en atributos de la comunidad como el cambio de diversidad con el area. Utilizamos datos de muestreo de redes de arrastre para examinar patrones espaciales de la riqueza de especies en peces costeros del Pacifico en E. U. A. Especificamente, generamos y comparamos relaciones especies–area (REAs) para especies clasificadas en varios grupos con base en la talla maxima, nivel trofico, profundidad maxima, afinidad geografica y orden taxonomico. Debido a que las REAs entre grupos no fueron paralelas y que los valores de z variaron significativamente para varios grupos, los grupos de especies estuvieron sub- o sobre- representados (dependiendo del tamano del area) en relacion con sus proporciones en toda la comunidad (i.e., toda la costa del Pacifico en E. U. A.). De esta manera, las diferencias en REAs ayudan a demostrar el balance entre la representacion de especies y el area costera y sugieren estrategias (como la proteccion de habitats y localidades donde se maximiza una especie o grupo de especies) que pueden minimizar el tamano de areas marinas protegidas pero proteger la diversidad al nivel de la comunidad y grupo funcional.

"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."