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Ecopath with Ecosim as a model-building toolbox: Source code capabilities, extensions, and variations

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... Ecopath with Ecosim (EwE), a freely available, widely used software for describing the structure of ecosystems, provides outputs at the ecosystem level, reflecting food-web linkages, energy cycling, and changes in biomass of the ecological functional groups defined in the model (Christensen et al. 2005). EwE is composed of three routines: Ecopath, a static mass-balance trophic model (Polovina 1984;Christensen and Pauly 1992;1993), Ecosim, time-dynamic model simulations built upon the initial Ecopath model (Walters et al. 1997;Walters 2000;Christensen and Walters 2004), and Ecospace, a spatial-temporal component of the temporal (Ecosim) model (Walters et al. 1999;Steenbeek et al. 2016). Plug-ins such as ecological indicators (EcoIND) and ecological network analysis (ENA) allow for additional analyses on the environ-mental response of modeled ecosystems to climate change (Steenbeek et al. 2016). ...
... EwE is composed of three routines: Ecopath, a static mass-balance trophic model (Polovina 1984;Christensen and Pauly 1992;1993), Ecosim, time-dynamic model simulations built upon the initial Ecopath model (Walters et al. 1997;Walters 2000;Christensen and Walters 2004), and Ecospace, a spatial-temporal component of the temporal (Ecosim) model (Walters et al. 1999;Steenbeek et al. 2016). Plug-ins such as ecological indicators (EcoIND) and ecological network analysis (ENA) allow for additional analyses on the environ-mental response of modeled ecosystems to climate change (Steenbeek et al. 2016). ...
... The Ecopath Model from the Ecosim plug-in is a feature that allows the user to create an Ecopath model from any point in the Ecosim time series (Steenbeek et al. 2016). Individual Ecopath models for the five start (BSS s = 1970(BSS s = -1974 and five end years (BSS e = 2008-2012) were extracted using the plug-in to derive, average, and compare ecological network indices over time. ...
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Arctic ecosystems are at risk to climate impacts, challenging existing conservation measures such as protected areas. This study aims to describe the ecological dynamics of the Canadian Beaufort Sea Shelf (BSS) ecosystem and the Tarium Niryutait Marine Protected Area (TNMPA) under historical changes in sea surface temperature and sea ice extent. Using Ecopath with Ecosim, we compared the status of the BSS between two time periods, 1970-1974 and 2008-2012, and against four ecosystem models (Eastern Chukchi Sea, Barents Sea, Eastern Bering Sea, Gulf of Alaska) to inform the relative long-term health and status of Arctic marine ecosystems. We find that relative to the comparable ecosystems, the BSS had a greater proportion of biomass from pelagic primary and secondary producers, and limited production from higher trophic levels. Estimates of trophic structure indices for the BSS indicate temporal ecosystem stability, and no loss in diversity. While beluga whales are a focus of the TNMPA management plan, they are not considered a key component of the modeled food web. Rather, Arctic and polar cods (main beluga prey group), arthropods, large copepods, micro-zooplankton, and herring and smelt, were identified as keystone species and warrant attention as proxies for both beluga whales and ecosystem health.
... The EwE approach consists of a three computational modules: Ecopath, a mass-balance energy accounting model to capture relevant components, their interactions, and their exploitation in a food web; Ecosim, which applies the Ecopath assumptions across time; and Ecospace, which adds a spatial dimension to the temporal dynamics [1,2]. In addition, the EwE approach contains a range of analytical modules, and features a powerful plug-in system that allows third-part analytical tools to seamlessly integrate into the flow of EwE and its computational models [3]. ...
... EcoRanger, which provided a Monte Carlo-like approach to find the best fitting Ecopath parameter set to a series of user-defined criteria [9], received criticism for making it too easy to 'fix' faulty models and was discontinued with the release of EwE version 6.0 [10]. Two distinct management strategy evaluation tools include Ecopath input parameter uncertainty when evaluating the impact of alternative fishing policies [3,11]. The stepwise fitting routine automates the process of testing ranges of hypotheses to find the best statistical fit to time series [12]. ...
... The EwE source code is free and open source, which means that anyone can use and extend the code within code license terms [10]. The code is modular, which allows programmers to replace or omit EwE building blocks, or to integrate EwE food web modelling logic into their own code, for addressing specific research questions [3]. The source code is highly extensible through the plug-in system, which allows programmers to connect any logic into the EwE execution flow without having to alter the EwE source code [3,10]. ...
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The widely used Ecopath with Ecosim (EwE) food web modelling approach has been extended with a new module to measure the impact of input parameter sensitivity on its results. Ecosampler records samples-alternate mass-balanced parameter sets for a food web model-from the built-in Monte Carlo routine, and replays these samples through all of EwE modules and any loaded plug-in. Via Ecosampler, output variation due to base input parameter sensitivity can be captured, of any computational component including the temporal module Ecosim, the spatial-temporal module Ecospace, and plug-ins such as Ecological Network Analysis, Value Chain, and Ecological Indicators.
... Ecopath with Ecosim (EwE) is a comprehensive modelling framework initially developed in the early 1980s, based on the theoretical approach by Polovina (1984aPolovina ( , 1984b, and since then, continuously improved with various extensions and specific functionalities (Christensen et al., 2005;Steenbeek et al., 2016). It has three major parts: Ecopath (static, mass-balanced system); Ecosim (time-dynamic simulation); and Ecospace (spatial and temporal simulation) (Christensen et al., 2005). ...
... Recently, an extension to R open-source framework was developed (Naimi & Voinov, 2012). (1) Christensen et al., 2005; (2) Steenbeek et al., 2016; (3) Heymans et al., 2014;(4) Colléter et al., 2013;(5) Richmond, 1985;(6) Naimi & Voinov, 2012;(7) Fath et al., 2007;(8) isee Exchange, 2021; (9) R Development Core Team, 2020; (10) Levins, 1974;(11) Novak et al., 2011;(12) Ortiz & Wolff, 2008;(13) ...
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Freshwater ecosystems are under multiple stressors and it is crucial to find methods to better describe, manage, and sustain aquatic ecosystems. Ecosystem modelling has become an important tool in integrating trophic relationships into food webs, assessing important nodes using network analysis, and making predictions via simulations. Fortunately, several modelling techniques exist, but the question is which approach is relevant and applicable when? In this study, we compare three modelling frameworks (Ecopath, Loop Analysis in R, STELLA software) using a case study of a small aquatic network (8 nodes). The choice of framework depends on the research question and data availability. We approach this topic from a methodological aspect by describing the data requirements and by comparing the applicability and limitations of each modelling approach. Each modelling framework has its specific focus, but some functionalities and outcomes can be compared. The predictions of Loop Analysis as compared to Ecopath’s Mixed Trophic Impact plot are in good agreement at the top and bottom trophic levels, but the middle trophic levels are less similar. This suggests that further comparisons are needed of networks of varying resolution and size. Generally, when data are limiting, Loop Analysis can provide qualitative predictions, while the other two methods provide quantitative results, yet rely on more data.
... 2014; Coll et al., 2020;Steenbeek et al., 2016). Climate models quantify IIV uncertainty by starting models at different times with different realizations (e.g., Nadiga et al., 2019), which is hard to achieve for marine ecosystem models that have much more complex starting states to represent the living components in the system (e.g., Skogen et al., 2021). ...
... MEMs are mostly slowly developing emergent products of a research team's progressive work on addressing specific research questions. With some notable exceptions Purves et al., 2013;Steenbeek et al., 2016), the choice of analytical framework, programming language, operating system and other implementation decisions tend to be dictated by the experiences within a research group. Consequently, MEMs are still rarely developed according to modern software engineering practices. ...
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Marine Ecosystem Models (MEMs) provide a deeper understanding of marine ecosystem dynamics. The United Nations Decade of Ocean Science for Sustainable Development has highlighted the need to deploy these complex mechanistic spatial-temporal models to engage policy makers and society into dialogues towards sustainably managed oceans. From our shared perspective, MEMs remain underutilized because they still lack formal validation, calibration, and uncertainty quantifications that undermines their credibility and uptake in policy arenas. We explore why these shortcomings exist and how to enable the global modelling community to increase MEMs’ usefulness. We identify a clear gap between proposed solutions to assess model skills, uncertainty, and confidence and their actual systematic deployment. We attribute this gap to an underlying factor that the ecosystem modelling literature largely ignores: technical issues. We conclude by proposing a conceptual solution that is cost-effective, scalable and simple, because complex spatial-temporal marine ecosystem modelling is already complicated enough.
... RL agents typically develop strategies by interacting with simulators, a practice that should not be unsettling to ecologists since learning from simulators is common across ecology. Rich, processes-based simulations such as the SORTIE model in forest management (Pacala et al. 1996), Ecopath with Ecosim in fisheries management (Steenbeek et al. 2016), or climate change policy models (Nordhaus 1992) are already used to explore scenarios and inform ecosystem management. Decision-theoretic approaches based on optimal control techniques can only find the best strategy in the simplest of ecological models; the so called "curse of dimensionality" makes problems with a large number of states or actions intractable by conventional methods (Wilson et al. 2006;Marescot et al. 2013;Ferrer-Mestres et al. 2021). ...
... In contrast, the process of training an RL algorithm on a more complex problem is no different than training on a simple one: we only need access to a simulation which can generate plausible future states in response to possible actions. This flexibility of RL could allow us to attain better decision-making insight for our most realistic ecological models such as the individual-based models used in the management of forests and wildfire (Pacala et al. 1996;Moritz et al. 2014), disease (Dobson et al. 2020), marine ecosystems (Steenbeek et al. 2016), or global climate change (Nordhaus 1992). ...
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Can machine learning help us make better decisions about a changing planet? In this paper, we illustrate and discuss the potential of a promising corner of machine learning known as _reinforcement learning_ (RL) to help tackle the most challenging conservation decision problems. RL is uniquely well suited to conservation and global change challenges for three reasons: (1) RL explicitly focuses on designing an agent who _interacts_ with an environment which is dynamic and uncertain, (2) RL approaches do not require massive amounts of data, (3) RL approaches would utilize rather than replace existing models, simulations, and the knowledge they contain. We provide a conceptual and technical introduction to RL and its relevance to ecological and conservation challenges, including examples of a problem in setting fisheries quotas and in managing ecological tipping points. Four appendices with annotated code provide a tangible introduction to researchers looking to adopt, evaluate, or extend these approaches.
... is the most widely used food web modelling approach in marine ecosystems (Christensen & Walters, 2004;Colléter et al., 2015;Pauly et al., 2000;Polovina, 1984;Steenbeek et al., 2016;Walters et al., 1997). Ecospace is a spatial representation of EwE that allows for the movement of represented groups (Steenbeek et al., 2021;Walters et al., 1999). ...
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The implementation of ecosystem management requires ecosystem modelling within the context of a natural resource management process. Ecopath with Ecosim (EwE) is the most widely used modelling platform for investigating the dynamics of marine ecosystems, but has played a limited role in fisheries management and in multi‐sector resource decision‐making. We review 10 case studies that demonstrate the use of EwE to support operational resource management. EwE models are being used to inform tactical decision‐making in fisheries and other ocean use sectors, as well as to identify key trade‐offs, develop appropriate policy objectives, and reconcile conflicting legislative mandates in a variety of ecosystems. We suggest the following criteria to enhance the use of EwE and other ecosystem models in operational resource management: (1) a clear management objective that can be addressed through modelling; (2) an important trade‐off and a receptive policy context amenable to trade‐off evaluation; (3) an accessible and well‐documented model that follows best practices; (4) early and iterative engagement among scientists, stakeholders, and managers; (5) integration within a collaborative management process; (6) a multi‐model approach; and (7) a rigorous review process. Our review suggests that existing management frameworks are as much or more of a limitation to the operational use of EwE than technical issues related to data availability and model uncertainty. Ecosystem models are increasingly needed to facilitate more effective and transparent decision‐making. We assert that the requisite conditions currently exist for enhanced strategic and tactical use of EwE to support fisheries and natural resource management.
... To that end, ecosystem modelling software, such as Ecopath with Ecosim (EwE) (Christensen et al. 2005;Buszowski et al. 2007) can approximate food-web structure using both locally relevant and inferred data, and can facilitate comparisons within and among ecosystems (Walters et al. 1997;Plaganyi 2007;Colléter et al. 2015;Steenbeek et al. 2015). EwE approaches use mass-balances (Plaganyi 2007) to estimate key food-web parameters that can describe structure and function of an ecosystem, and can include food-web members ranging from primary producers to top predators (Walters et al. 1997;Christensen et al. 2007). ...
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Climate-driven impacts on marine trophic pathways worldwide are compounded by sea-ice loss at northern latitudes. For the Arctic, current information describing food web linkages is fragmented, and there is a need for tools that can describe overarching trophic structure despite limited species-specific data. Here, we tested the ability of a mass-balanced ecosystem model (Ecopath with Ecosim, EwE) to reconstruct the trophic hierarchy of 31 groups, from primary producers to polar bears, in the Canadian Beaufort Sea continental shelf. Trophic level (TL) estimates from EwE were compared with those derived from two nitrogen stable isotope (SI) modelling approaches (SI linear and scaled) to assess EwE accuracy, using a dataset of 642 δ15N observations across 282 taxa. TLs from EwE were strongly, positively related to those from both SI models (R2 > 0.80). EwE performed well (within 0.2 TL) for groups with relatively well-known diets or for taxa characterized by fewer trophic connections (e.g., primary consumers). Performance was worse (> 0.5 TL) for species groups aggregated at coarse taxonomic levels, those with poorly documented diets, and for anadromous fishes. Comparisons with SI models suggested that the scaled approach can overestimate the TL of top predators if ecosystem-specific information is not considered.
... logiciel, Ecopath with EcosimWalters et al. (1997);Pauly et al. (2000);Steenbeek et al. (2016) permet de simuler une activité de pêche facilement et est une référence dans le domaine. Sa fonction principale est la modélisation basée sur l'équilibre des masses mais il a été utilisé dans de nombreux projets avec différents objectifs comme le repeuplement d'espèces en difficultéFouzai et al. (2012), l'amélioration des gains et des stocks Christensen andWalters (2004b), les performances économiques des pêcheries sur le court et long terme LeFloc'h et al. (2008). ...
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In this document, we detail 15 years of activities; first as a PhD student (2005-2008), then as an assistant professor (2008-2011) and finally as a lecturer (since 2011) at the University of Corsica. We describe our contributions, our research projects, our administrative and teaching activities. The main aim of our thesis work (Bisgambiglia (2008)) was to take into account imprecise data in a modeling and simulation process. They led to a proposal for the integration of the Fuzzy-Set theory, in- troduced by Zadeh (1975), in a Discrete EVent system Specification formalism (DEVS Zeigler (1976)). They continued with the goal of integrating into the modeling and simulation processes other methods of considering the uncertainties (Dubois and Prade (1988b)). Thereafter, we work to the representation of systems from the multi-agent paradigm (Ferber (1995b)) and proposed a formalization of a multi-agent systems from the formalisms PDEVS (parallel version of DEVS allowing to manage simultaneous events Chow and Zeigler (1994)) and DSDE (dynamic version of PDEVS to change structure dynamically Barros (1995)). The aim was to introduce more scientific rigor in multi-agent simulations and to allow their numerical reproducibility (c.f. Dynamic Parallel Discrete Event Multi-Agent Specification : DPDEMAS Franceschini et al. (2017)). Currently, we are working on optimization and machine learning methods to provide agents with the means to check the impact of their actions on the environment (Poiron-Guidoni et al. (2020b)). We wish to propose a complete approach to describe decision processes, from data to the formalization of simulation models adapted to the study domain.
... Alternately, a TMDL may have to be developed for ecological objectives that require an understanding of the biology of a single species or an entire food web or ecosystem. In such cases, agentbased (Sridharan et al. 2018a) or individual-based models (Railsback et al. 2013) for the former or ecosystem models such as Ecopath with Ecosim (EwE) (Steenbeek 2016) for the latter may be selected. ...
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Computer models and simpler methods must be used to reliably determine total maximum daily loads (TMDLs) for impaired waters of the US. Models are also useful to develop implementation plans that allocate load reductions to meet water quality standards. During model selection, practical considerations sometimes override the fundamental requirements of parsimony and defensibility. For the first time, we present a rationale for efficiently selecting reliable models for TMDL determinations in this open access paper, based on deliberations of the TMDL Analysis and Modeling Task Committee of the Environmental and Water Resources Institute of ASCE. This protocol is based on technical criteria (waterbody, water quality, and data requirements) and management constraints (state plans and priorities, stakeholder and expert engagement, and state authority to manage pollution sources and state allocation priorities). Uncertainties due to changes in economic 15 activity, population, land use, climate, sea level, and policies are also included. To reduce wasteful trial-and-error iterations during model selection, an optimal conceptual modeling framework is identified and subsequently refined in a flowchart based on practical considerations. The proposed protocol holistically defines the state of the science in model selection and is anticipated to soon define the state of the practice for TMDL determination.
... Food web modeling frameworks for the marine ecosystem are diverse in structure and complexity. To identify the modeling frameworks capable of explicitly representing biological interactions, the ecosystem model reviews presented by Plag anyi (2007) Christensen and Walters 2004;Steenbeek et al. 2016) and Comprehensive Aquatic System Models (CASM) (DeAngelis et al. 1989;Bartell et al. 1999). Biogeochemical-based endto-end models (category 5) simulate nutrients and planktonic organisms in addition to fish and other top predators-allowing both bottom-up and topdown interactions. ...
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Management Strategy Evaluation (MSE) is a framework to explore the tradeoffs amongst fishing strategies and assess the consequences for achieving management goals provided sources of uncertainty by means of simulation models (referred to as operating models). Single-species stock assessment often implements simulations for MSE, but the operating models often omit the dynamics of key biological interactions. This could be a disadvantage for the evaluation of tradeoffs as species interactions could have an impact on the performance of harvesting strategies. Tools for conducting ecosystem-based fisheries management (EBFM), such as integrated ecosystem assessments, include executing MSEs with ecosystem models, many of which explicitly include biological interactions. Although the support for EBFM has grown over the years, the amount of information provided by MSEs based on ecosystem models appears to be limited. A clear summary of such efforts would provide beneficial information for future efforts for EBFM. Herein, an inventory of applications simulating MSEs with ecosystem models that explicitly include biological interactions was developed based on findings from a literature review. First, the methodologies and foci across all identified applications are analyzed. Next, summaries of each application are provided. Lastly, general observations are provided along with recommendations for future applications.
... The EwE approach is widely used to address ecological questions, evaluate ecosystem effects of fishing, explore management policy options, analyze impact, and placement of marine protected areas, model the combined effect of environmental changes, and combinations of the above Colléter et al., 2015). EwE is most known as a desktop software for the Windows platform, but it is in fact an ecosystem model-building toolkit written in .NET and can be extended through plugins (Steenbeek et al., 2016). Additionally, EwE is an open-source approach built and supported through a global scientific community. ...
Article
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We have developed an approach that connects a complex and widely used scientific ecosystem modeling approach with a game engine for real-time communication and visualization of scientific results. The approach, OceanViz, focuses on communicating scientific data to non-scientific audiences to foster dialogue, offering experimental, immersive approaches to visualizing complex ecosystems whilst avoiding information overload. Within the context of ecosystem-based fisheries management, OceanViz can engage decision makers into the implicit operation of scientific software as an aid during the decision process, and it can be of direct use for public communication through appealing and informative visualizations. Beside a server-client architecture to centralize decision making around an ecosystem model, OceanViz includes an extensive visualization toolkit capable of accurately reflecting marine ecosystem changes through a simulated three-dimensional (3D) underwater environment. Here we outline the ideas and concepts that went into OceanViz, its implementation and its related challenges. We reflect on challenges to scientific visualization and communication as food-for-thought for the marine ecosystem modeling community and beyond.
... Os projetos abertos possuem acesso universal e podem ser redistribuídos ou subsequentemente melhorados de acordo com o interesse dos usuários (STEENBEEK et al., 2015), apesar de ainda não serem amplamente conhecidos, estão conquistando mais espaço no mercado. Iniciativas como a RepRap e o Github são cada vez mais conhecidas e consequentemente fomentam a inovação e ampliam o acesso à diversas novas ideias. ...
... However, the absence of time series data for a large number of groups (e.g., catches, biomass and fishing effort) is considered as our primary weakness. Alternatively, to minimize the limitations cited above, we performed a sensitivity analysis (Monte Carlo routine) to evaluate the uncertainty around model parameters and to assess, in our case, the biomass and ecological indicators (Christensen and Walters, 2004;Niiranen et al., 2012;Steenbeek et al., 2016). In addition, although we recognize the importance of incorporating specific periods of the closing season within scenarios, some major data, as for example the spawning parameters (egg production, egg-laying timing etc.), are lacking, hampering this analysis within the model. ...
Article
Global shrimp catches are reported primarily in association with large industrial trawling, but they also occur through small-scale fishing, which plays a substantial role in traditional communities. We developed an Ecopath model in north-eastern Brazil, and applied a temporally dynamic model (Ecosim) to evaluate the potential effects of different fishing effort control policies and environmental changes on marine resources and ecosystem between 2015 to 2030 with a case study for small-scale shrimp fishing, novelty for tropical region. These scenarios included different management options related to fishing controls (changing effort and closed season) and environmental changes (primary production changes). Our findings indicate that it is possible to maintain the same level of landings with a controlled reduction of bottom trawlers activities, for example, close to 10 %, without compromising the ecosystem structure. This scenario provided better results than 3–4 months of closing the fishing season, which led to significant losses in catches of high market-value target species (white shrimp, Penaeus schmitti and pink shrimp, Penaeus subtilis). However, intense negative effects on biomass, catch and biodiversity indicators were reported in scenarios with decreasing primary production, from 2 %, reinforcing the need to simulate and project the possible impacts caused by environmental change. However, the control of bottom trawling activity may help to reduce, even at low levels, the highly adverse effects due to primary production reduction. The impacts of climate change in a near future on organisms and ecosystems is an imminent reality, and therefore the search for measures for mitigating and even minimizing these impacts is crucial.
... The supply and use tables provide the foundation for input-output tables that show how sectors in the economy are interconnected. These tables have a similar structure to ecosystem models such as Atlantis and EcoPath/ EcoSim [22][23][24] , which can facilitate integrated assessment of environmental and economic change. Ocean production, such as shipping, and ocean capital investment, such as port expansion, are also within the scope of national accounts. ...
Article
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Sustainable development of the ocean economy requires a system for measuring progress. The standard system of national accounting provides a solid foundation for doing so, though the scope requires expansion to adequately cover household-produced services; for example, ocean-based leisure, and the role of natural capital in the ocean economy. The accounts summary needs indicators beyond gross domestic product that enable users to choose what is included. New technologies make digital dashboards of indicators easy to produce. Such dashboards facilitate rapid comparison of indicators that cannot be aggregated into a single metric, which enables national ocean accounts to coherently present physical and monetary data.
... The EwE model has been modified multiple times by many different authors for a range of purposes. Some of these modifications have been integrated back into the main release in the form of plugins (Steenbeek et al., 2016). The model also has been translated into a range of different programming languages. ...
Thesis
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Cold-water corals are found globally but little is known about energy flows associated with these habitats. The degree to which the benthic ecosystems containing cold-water corals are linked to the overlying pelagic ecosystems is also poorly understood. Observational studies have indicated that fish abundance is greater in the waters surrounding cold-water coral reefs compared to nearby waters over barren seafloor, implying enhanced productivity in the cold-water coral ecosystems. Support for this hypothesis is tested in this study using a customised Ecopath with Ecosim model. The model is applied to Childs Bank, a region on the west coast of South Africa located in the southern Benguela eastern boundary ecosystem. A previously constructed Ecopath model of the southern Benguela was modified to represent the main groups of organisms found on Childs Bank and additional groups were added to better represent the main groups associated with cold-water coral. In total, including the additional compartments, the model ecosystem consisted of 34 living compartments and three non-living compartments. Three novel living compartments were considered in the model: Cold-water corals, Sponges and Tube-worms. Two additional non-living compartments comprised Coral skeleton and Coral mucus. The Ecopath model was balanced by assuming that the three additional living groups had the same production to biomass ratios as the Macrobenthos group. The production to consumption ratio of Sponges and Cold-water corals were sourced from literature. An unconstrained non-linear minimisation function was used to solve for the biomass of the Sponge and Cold-water coral groups as their production was needed for the Ecopath model to balance; thus a biomass estimate was required for both these groups. The balanced Ecopath model was used in an Ecosim model, which was applied to three scenarios designed to investigate whether trophic links in the cold-water coral ecosystems could account for increased fish abundance: scenario 1, the removal of both cold-water coral and cold-water coral skeleton; scenario 2, changes in fishing pressure on small pelagic fish; scenario 3, the removal of cold-water coral skeleton without damage to the living coral. Scenario 3 is an artificial scenario designed to isolate the effects of cold-water coral skeleton loss from the trophic interactions from the living cold-water corals. None of the scenarios produced results with notable changes in biomasses of groups in the wider ecosystem. It is thus hypothesised that enhanced fish production results from cold-water corals changing the local oceanographic conditions through their physical structure rather than primarily by their trophic interactions.
... Similarly, changing of primary productivity can cascade through the food-web by means of bottom-up controls [144,145] as well as environmental drivers [144,171]. The use of Ecospace to assess cumulative impacts of these effects have been exponentially increased since the later development of this software [172,169,144,173], with new capabilities of coupling the spatial model with external spatial data (e.g. spatial habitats and hydrodynamic drivers). ...
Article
“Blue Growth” and “Blue Economy” is defined by the World Bank as: “the sustainable use of ocean resources for economic growth, improved livelihoods and jobs, while preserving the health of ocean ecosystem”. Multi-purpose platforms (MPPs) can be defined as offshore platforms serving the needs of multiple offshore industries (energy and aquaculture), aim at exploiting the synergies and managing the tensions arising when closely co-locating systems from these industries. Despite a number of previous projects aimed at assessing, from a multidisciplinary point of view, the feasibility of multipurpose platforms, it is here shown that the state-of-the-art has focused mainly on single-purpose devices, and adopting a single discipline (either economic, or social, or technological, or environmental) approaches. Therefore, the aim of the present study is to provide a multidisciplinary state of the art review on, whenever possible, multi-purpose platforms, complementing it with single-purpose and/or single discipline literature reviews when not possible. Synoptic tables are provided, giving an overview of the multi-purpose platform concepts investigated, the numerical approaches adopted, and a comprehensive snapshot classifying the references discussed by industry (offshore renewables, aquaculture, both) and by aspect (technological, environmental, socio-economic). The majority of the multi-purpose platform concepts proposed are integrating only multiple offshore renewable energy devices (e.g. hybrid wind-wave), with only few integrating also aquaculture systems. MPPs have significant potential in economizing CAPEX and operational costs for the offshore energy and aquaculture industry by means of concerted spatial planning and sharing of infrastructure.
... There are numerous methods that can be used to assess end-to-end model skill, but most commonly, model parameters are adjusted to plausible levels (changes made within confidence limits of observed monitoring or assessment data) or are matched to estimates from time series data. This is frequently an iterative process that is unique to each model type, but general guidelines and best practices are documented in the literature (Shin and Cury, 2001;Link et al., 2011;Heymans et al., 2016;Steenbeek et al., 2016). Indicators act as a pathway to assess model skill by additionally including emergent properties that reflect the interactions between model components. ...
Article
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Ecological and socio-economic indicators are used as proxies for attributes of ecosystems and human communities, respectively. End-to-end models are used to predict how ecosystems will respond to alternative management actions and changing environmental conditions. Despite the importance of these two tools for Ecosystem-Based Management (EBM), there has been limited integration of ecological indicators directly into end-to-end models; the former are typically calculated post hoc with output from the latter. Here we explore how ecological indicators can be better incorporated into end-to-end models and examine the importance of this union with regards to cumulative impacts and indirect effects, setting management objectives, practical indicator selection, and applications to management. We conclude that the inclusion of ecological indicators in end-to-end models is not only feasible, but provides needed guidance on describing ecosystem status relative to strategic as well as tactical ecosystem-level management goals, and will escalate the implementation of EBM.
... Simulations were carried out for all possible combinations of Fs within the F MSY ranges tested, resulting in 180,000 scenarios being explored in addition to the F status quo and F MSY scenarios. These simu- lations were performed using the Multisim plugin from the EwE soft- ware ( Steenbeek et al., 2016). Table 1 Fishing mortalities for the main west of Scotland commercial species used in the model simulations with corresponding references. ...
Article
The latest reform of the Common Fisheries Policy (CFP) which regulates the exploitation of fish stocks in European waters entails a move from the traditional single stock management towards Ecosystem Based Fisheries Management (EBFM). Meanwhile the Marine Strategy Framework Directive dictates that Good Environmental Status (GES) should be achieved in European waters by 2020. Here we apply an EBFM approach to the west of Scotland demersal fisheries which are currently facing several management issues: depleted stocks of cod (Gadus morhua) and whiting (Merlangius merlangus), increased predation from grey seals (Halichoerus grypus), and large bycatch of juvenile whiting by crustacean fisheries. A food web ecosystem model was em- ployed to simulate the outcomes of applying the traditional single stock fishing mortalities (F), and management scenarios which explored F ranges in accordance with the CFP. Ecosystem indicators were calculated to assess the performance of these scenarios towards achieving GES. Our results highlight the importance of considering prey-predator interactions, in particular the impact of the top predators, cod and saithe (Pollachius virens), on juvenile cod and whiting. The traditional single stock approach would likely recover cod, but not whiting. Exploring the F ranges revealed that a drastic reduction of juvenile whiting bycatch is necessary for the whiting stock to recover. Predation from grey seals had little impact overall, but did affect the timing of cod and whiting recovery. With the exception of whiting, little difference was observed between the single stock scenario, and the best scenario identified towards achieving GES. The findings advocate for the use of ecosystem modelling alongside the traditional singl ecision making in order to better inform fisheries management.
... It has been applied in many hundreds of ecosystems over the last 30 years and to a diverse set of topics to do with the functioning, perturbation and management of aquatic ecosystemsfor example: climate change (Alva-Basurto and Arias- Gonzalez, 2014;Christensen et al., 2015;Cornwall and Eddy ,2015;Serpetti et al., 2017;Suprenand and Ainsworth, 2017) ; regime shifts (Heymans and Tomczak, 2016;Ofir et al., 2016); hypoxia (de Mutsert et al., 2016); fishing impacts (Coll et al., 2009a;Coll et al., 2009b;Heymans et al., 2009;Piroddi et al., 2010b;Christensen et al., 2014a;Coll et al., 2016;Geers et al., 2016;Eddy et al., 2017b); single and multi-species fisheries management (Cornwall and Eddy, 2015;Eddy et al., 2017a); ecosystem-based management (Lercari and Arreguin-Sanchez ,2009;Jiang et al., 2017); ecosystem-based fisheries management Alva-Basurto and Arias-Gonzalez, 2014;Bourdaud et al., 2016;Jacobsen et al., 2016;Musinguzi et al., 2017;Sagarese et al., 2017), invasive species (Corrales et al., 2017;Haak et al., 2017;McGill et al., 2017); marine protected areas (Abdou et al., 2016); environmental impact assessment (Port MetroVancouver, 2015;Fretzer, 2016); cumulative impact assessment ; ecological indicator monitoring (Gonzalez et al., 2016;Coll and Steenbeek, 2017); primary productivity (Chaalali et al., 2015;Maldonado et al., 2016); impacts of decommissioning of power plants (Vasslides et al., 2017); oil spill restoration (Okey et al., 1999;Okey and Wright, 2004;Sagarese et al., 2017) and contaminant tracing (Larsen et al., 2016). The spatial expansion of EwE, Ecospace, has several relatively new features that allow for representation of spatial processessuch as influencing the distribution of ecological components based on habitat (environmental) preferencesand linking to external environmental forcing data, such as hydrodynamic transports or temperature and salinity patterns (Steenbeek et al., 2013;Christensen et al., 2014b;Steenbeek et al., 2016). Unfortunately, limited project resources meant we could not make use of these Ecospace features and our EwE implementation was constrained to the temporally dynamic module Ecosim. ...
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... Such a wealth of information allowed us to generate reliable products in bulk for assisting EBFM efforts in the Gulf of Mexico. During the past 15 years, many valuable tools have been developed and enhanced for advancing EBFM worldwide, including different ecosystem modeling approaches, conservation planning software packages, and risk assessment frameworks (e.g., Smith et al. 2007;Möllmann et al. 2013;Steenbeek et al. 2016). It is now time to focus efforts on designing and using methodologies for improving the inputs used in EBFM studies, as we did in the present study (Gr€ uss et al. 2016a). ...
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Statistical habitat models, such as generalized additive models (GAMs), are key tools for assisting ecosystem-based fisheries management (EBFM) efforts. Predictions from GAMs can be used, for example, to produce preference functions for the ecosystem-modeling platform Ecospace; preference functions permit a flexible representation of spatial distribution patterns in Ecospace by defining the preferences of marine organisms for certain environmental parameter values. Generalized additive model predictions can also be used to map species distributions for assisting marine protected area (MPA) planning. In this study, we applied a recently proposed methodology to produce preference functions for the fish and invertebrates represented in an Ecospace model of the West Florida Shelf (WFS) and to map the hotspots of juveniles and adults of three economically important species for informing future MPA planning in the WFS region. This proposed methodology consists of (1) compiling a comprehensive survey database blending all of the encounter and nonencounter data of the study ecosystem collected by the fisheries-independent and fisheries-dependent surveys that employ random sampling schemes, (2) developing a large environmental database to store all of the environmental parameters influencing the spatial distribution patterns of the marine organisms of the study ecosystem, (3) using the comprehensive survey database and the large environmental database to fit binomial GAMs that integrate the confounding effects of survey and year, and (4) making predictions with fitted GAMs to Subject editor: Donald Noakes,
... Such a wealth of information allowed us to generate reliable products in bulk for assisting EBFM efforts in the Gulf of Mexico. During the past 15 years, many valuable tools have been developed and enhanced for advancing EBFM worldwide, including different ecosystem modeling approaches, conservation planning software packages, and risk assessment frameworks (e.g., Smith et al. 2007;Möllmann et al. 2013;Steenbeek et al. 2016). It is now time to focus efforts on designing and using methodologies for improving the inputs used in EBFM studies, as we did in the present study (Gr€ uss et al. 2016a). ...
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Statistical habitat models, such as generalized additive models (GAMs), are key tools for assisting ecosystem-based fisheries management (EBFM) efforts. Predictions from GAMs can be used, for example, to produce preference functions for the ecosystem-modeling platform Ecospace; preference functions permit a flexible representation of spatial distribution patterns in Ecospace by defining the preferences of marine organisms for certain environmental parameter values. Generalized additive model predictions can also be used to map species distributions for assisting marine protected area (MPA) planning. In this study, we applied a recently proposed methodology to produce preference functions for the fish and invertebrates represented in an Ecospace model of the West Florida Shelf (WFS) and to map the hotspots of juveniles and adults of three economically important species for informing future MPA planning in the WFS region. This proposed methodology consists of (1) compiling a comprehensive survey database blending all of the encounter and nonencounter data of the study ecosystem collected by the fisheries-independent and fisheries-dependent surveys that employ random sampling schemes, (2) developing a large environmental database to store all of the environmental parameters influencing the spatial distribution patterns of the marine organisms of the study ecosystem, (3) using the comprehensive survey database and the large environmental database to fit binomial GAMs that integrate the confounding effects of survey and year, and (4) making predictions with fitted GAMs to Subject editor: Donald Noakes,
... Spatially-explicit ecosystem models, especially highly sophisticated models such as applications of the Atlantis modeling platforms, rely on numerous data inputs, many of which can have a significant impact on ecosystem model predictions (Fulton et al., 2007;Shin et al., 2010;Walters et al., 2010;Steele et al., 2013). Many spatially-explicit ecosystem models have been designed worldwide (Fulton, 2010;Espinoza-Tenorio et al., 2012;Steele et al., 2013), and significant attention has been devoted to enhance the structure and assumptions of ecosystem modeling platforms (e.g., Shin et al., 2010;Steenbeek et al., 2013Steenbeek et al., , 2016Travers-Trolet et al., 2014;Grüss et al., 2016b,c). Therefore, it is now high time to develop and employ methodologies such as ours for ensuring that the spatially-explicit ecosystem models available around the world are provided with reliable inputs generated using the best available data and information. ...
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To be able to simulate spatial patterns of predator-prey interactions, many spatially-explicit ecosystem modeling platforms, including Atlantis, need to be provided with distribution maps defining the annual or seasonal spatial distributions of functional groups and life stages. We developed a methodology combining extrapolation and interpolation of the predictions made by statistical habitat models to produce distribution maps for the fish and invertebrates represented in the Atlantis model of the Gulf of Mexico (GOM) Large Marine Ecosystem (LME) (“Atlantis-GOM”). This methodology consists of: (1) compiling a large monitoring database, gathering all the fisheries-independent and fisheries-dependent data collected in the northern (U.S.) GOM since 2000; (2) compiling a large environmental database, storing all the environmental parameters known to influence the spatial distribution patterns of fish and invertebrates of the GOM; (3) fitting binomial generalized additive models (GAMs) to the large monitoring and environmental databases, and geostatistical binomial generalized linear mixed models (GLMMs) to the large monitoring database; and (4) employing GAM predictions to infer spatial distributions in the southern GOM, and GLMM predictions to infer spatial distributions in the U.S. GOM. Thus, our methodology allows for reasonable extrapolation in the southern GOM based on a large amount of monitoring and environmental data, and for interpolation in the U.S. GOM accurately reflecting the probability of encountering fish and invertebrates in that region. We used an iterative cross-validation procedure to validate GAMs. When a GAM did not pass the validation test, we employed a GAM for a related functional group/life stage to generate distribution maps for the southern GOM. In addition, no geostatistical GLMMs were fit for the functional groups and life stages whose depth, longitudinal and latitudinal ranges within the U.S. GOM are not entirely covered by the data from the large monitoring database; for those, only GAM predictions were employed to obtain distribution maps for Atlantis-GOM. Pearson residuals were computed to validate geostatistical binomial GLMMs. Ultimately, 53 annual maps and 64 seasonal maps (for 32 different functional groups/life stages) were produced for Atlantis-GOM. Our methodology could serve other world's regions characterized by a large surface area, particularly LMEs bordered by several countries.
... Consideration of these multiple objectives classifies the evaluation as taking a postmodern view of sustainability [7], aiming to contribute to the progress in developing more comprehensive evaluations of management plans (Sensu Trenkel et al. [8]). We used a bespoke routine developed inside the ecosystem modelling framework Ecopath with Ecosim (EwE) [9,10,11], specifically designed to assess the robustness of management strategies to the uncertainties in model predictions arising from model error, observation error, and implementation error [12]. Core to the routine is the Management Strategy Evaluation (MSE) methodology [13,14,15], which addresses the need to provide decision makers with the risks and uncertainties associated with alternative strategies, and thus identify where trade-offs may lie. ...
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The possible impacts of the European Commission’s proposed North Sea Multi-Annual Plan are evaluated in terms of its likely outcomes to achieve management objectives for fishing pressure, species’ biomass, fishery yield, the landed value of key species and ecosystem objectives. The method applies management strategy evaluation procedures that employ an ecosystem model of the North Sea and its fisheries as the operating model. Taking five key dimensions of the proposed plan, it identifies those areas that are key to its successful performance. Overwhelmingly, choices in the options for the implementation of regulatory measures on discarding practices outweigh the effects of options related to fishing within ranges associated with ‘pretty good yield’, the way that biomass conservation safeguard mechanisms are applied and the timeframe for achieving fishing mortality targets. The impact of safeguard options and ranges in fishing mortality become important only when stock biomass is close to its reference points. The fifth dimension–taking into account wider conservation and ecosystem objectives—reveals that discard policy has a big impact on conservation species, but also that the type of harvest control rule can play an important role in limiting risks to stocks by ‘applying the brakes’ early. The consequences to fisheries however is heightened risk to their viability, thus exposing the sustainability trade-offs faced with balancing societal pressures for blue growth and enhanced conservation. It also reveals the wider ecosystem impacts that emphasise the connectivity between the demersal and pelagic realms, and thus, the importance of not treating the demersal NSMAP in isolation from other management plans. When stocks are below their biomass reference points, low F strategies lead to better long term economic performance, but for stocks consistently above biomass reference points, high F strategies lead to higher long term value. Nephrops and whiting often show contradictory responses to the strategies because changes in their predators abundance affects their abundance and success of their fisheries.
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The West Florida Shelf (WFS), located in the eastern Gulf of Mexico, fosters high species richness and supports highly valuable fisheries. However, red tide events occur regularly that can impact fisheries resources as well as ecosystem state, functioning, and derived services. Therefore, it is important to evaluate and quantify the spatiotemporal impacts of red tides to improve population assessments, mitigate potential negative effects through management, and better understand disturbances to support an ecosystem-based management framework. To model red tide effects on the marine community, we used Ecospace, the spatiotemporal module of the ecosystem modeling framework Ecopath with Ecosim. The inclusion of both lethal and sublethal response functions to red tide and a comprehensive calibration procedure allowed to systematically evaluate red tide effects and increased the robustness of the model and management applicability. Our results suggest severe red tide impacts have occurred on the WFS at the ecosystem, community, and population levels in terms of biomass, catch, and productivity. Sublethal and indirect food-web effects of red tide triggered compensatory responses such as avoidance behavior and release from predation and/or competition.. This study represents a step forward to operationalize spatiotemporal ecosystem models for management purposes that may increase the ability of fisheries managers to respond more effectively and be more proactive to episodic mortality events, such as those caused by red tides.
Thesis
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Marine species and ecosystems are increasingly impacted by episodic environmental events that may affect mortality and behavior. Spatiotemporal models are important tools to explore ecosystem dynamics, but the unpredictable and localized nature of episodic environmental events represents an important challenge for the successful management of marine resources. For instance, red tides on the West Florida Shelf impact marine ecosystems and represent an increasing concern for fisheries management. Therefore, it is important to account for these ecosystem processes using spatiotemporal models and critically assess parametrization to help efficiently implement adaptative management. To accomplish such objectives, I developed a set of ecological niche models (regression and machine learning), a spatiotemporal ecosystem model (Ecopath with Ecosim and Ecospace), and single-species stock assessment models (statistical catch-at-age) with emphasis on the West Florida Shelf ecosystem and red tide events. Intrinsic population aspects, sampling effort, environment, and red tides influenced the interpretation of fish environmental niche dynamics. Red tides caused negative effects at the ecosystem, ecosystem service, and population levels in terms of biomass, and the year 2005 was the most severely impacted. The inclusion of sub-lethal and indirect red tide effects in the Ecospace model revealed compensatory responses on behavior, trophic interactions, and recruitment. When informing stock assessment models, the absence or missparametrization of time-varying natural mortality caused by red tides can bias fishing mortality and spawning stock biomass which may prevent the successful management of fish stocks. This research represents an example of how to evaluate episodic environmental mortality events that require a spatiotemporal framework and produce a robust ecosystem index for use in stock assessment and fisheries management. Uncertainty assessment, stability, validation, and calibration processes for Ecospace model development greatly improved the model robustness and represented a step forward to operationalize spatiotemporal ecosystem models. Spatiotemporal operating models can be useful to assess future red tide scenarios, simulate data, evaluate model parametrization, and inform single-species stock assessment models to support ecosystem-based fisheries management. Increasing the operationalization of ecosystem models may help to achieve a more adaptative and proactive management approach to future red tide events that could be crucial for fisheries management and red tide impact mitigation.
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Successful management of lake ecosystems and the ecosystem services they provide necessitates ecosystem‐based management. The application of ecosystem‐based management can assist in achieving sustainable management of the ecosystem to ensure continued and sustainable supply of ecosystem services such as fisheries. One concept for defining sustainable fishing is the Safe Operating Space (SOS). In our study, we apply the Ecopath with Ecosim suite of models to predict the SOS required for the management of a commercial fishery. We use the Lake Kinneret (Israel) ecosystem as a case study to illustrate the approach by developing an Ecospace model of the lake and incorporating the spatio‐temporal framework and varying environmental conditions. We test, and demonstrate, the methodology for developing a SOS for a commercial fish population that can be implemented by lake managers elsewhere and illustrate it's use by defining example target values of biomass (e.g., 200 and 250 tons) and catch (e.g., 125 tons/year). Our results show that the SOS for a given target can be defined by a range of fishing efforts and vegetation cover in the lake as a function of lake level. The complexity in defining the actual values highlight the benefit of the approach we present here.
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Technical Report
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Utah Lake continues to be a highly abused ecosystem ever since Americans of European decent settled along its shores over 150 years ago. The lake has lost its ecological integrity and is in poor health by most qualitative and bioassessment based standards. Its resilience to future perturbation and resistance to improvement (restoration) appears to be compromised. There is much concern as to the future of Utah Lake and what can be done to improve its condition (i.e., health, integrity), including the reduction of algal blooms and restoration of its native biota. However, there has been little to no effort expended to examine or understand the importance of the lake’s food web and how top-down, trophic cascades effect and respond to current conditions or how biomanipulation may help restore its ecosystem health despite decades of research documenting their importance worldwide. Restoring the lake cannot proceed without this understanding. Consequently, a representative food web model was urgently needed. This report presents the first ever proof-of-concept, trophic- level, mass- balanced foodweb model of Utah Lake that will allow researchers and managers to understand and better manage this important ecosystem. The model chosen and developed was the widely used and freely available EcoPath with EcoSim (EwE) model. Biomasses, diets, and production/biomass ratios of eighty- one taxonomic groups were modeled as inputs including taxa from phytoplankton, zooplankton, benthic invertebrates, fishes, benthic algae, and detritus based on lengthy synthesis of extremely limited data augmented with literature values. Carp removal program fisheries ‘catch’, and chironomid export estimates were also modeled. The EwE model produced dozens of ecosystem metrics and indices, most of which supported the premise that Utah Lake ecosystem is impaired and dominated by only a handful of taxa including invasive Common Carp, other invasive fishes, and pollution tolerant chironomids, and that the lake energy sources are co-dominated by water column primary production and strongly respiring detritus mostly in the form of detrital snow. Model results also showed that the lake has low robustness (e.g., resistance), is well below optimal trophic functioning, and is in an ‘immature’ early succession stage primarily because of chronic wave action that consistently disturb unconsolidated sediments and reset the food web thus preventing maturation of the system. The carp reduction program had both negative and positive mixed level trophic impacts on several groups. These results support continued and increased carp reduction efforts. EwE clearly demonstrated that increased monitoring and research are essential to best manage the lake. Additional model inputs, forcing functions, scenarios, and incorporation with models being developed by others are required to ensure that the EwE model is the most useful tool for scientifically managing Utah Lake and is the go-to model. This proof-of-concept draft Utah Lake EwE model is available to all interested researchers and managers. Collaboration, refinement, and utilization by others is strongly encouraged
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Freshwater ecosystems are under multiple stressors and it is crucial to find methods to better describe, manage, and sustain aquatic ecosystems. Ecosystem modelling has become an important tool in integrating trophic relationships into food webs, assessing important nodes using network analysis, and making predictions via simulations. Fortunately, several modelling techniques exist, but the question is which approach is relevant and applicable when? In this study, we compare three modelling frameworks (Ecopath, Loop Analysis in R, STELLA software) using a case study of a small aquatic network (8 nodes). The choice of framework depends on the research question and data availability. We approach this topic from a methodological aspect by describing the data requirements and by comparing the applicability and limitations of each modelling approach. Each modelling framework has its specific focus, but some functionalities and outcomes can be compared. Predictions of Ecopath’s Mixed Trophic Impact plot and the Loop Analysis models are in agreement for groups at higher trophic levels, but not for lower trophic levels. This suggests that further comparisons are needed of networks of varying resolution and size. Generally, when data are limiting, loop analysis can provide qualitative predictions, while the other two methods provide quantitative results, yet rely on more data.
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Introductions or alien species invasions will induce changes in aquatic ecosystems but are rarely reported in Chinese highland lakes. The Japanese smelt (Hypomesus nipponensis) invaded and has become a dominant fish species in Lake Erhai, a highland lake in southwestern China, since 2016. Here, we engineered Ecopath models for two different periods, 2008–2009 (preinvasion) and 2016–2018 (postinvasion), in Lake Erhai to model ecosystem impacts from the Japanese smelt invasion. In the dynamic Ecosim model based on the 2016–2018 Ecopath model, we ran three 50-year scenarios to simulate the potential effects of Japanese smelts on the system. Our results showed competition between invasive and native species as well as changes in trophic structures, highlighting the impacts of the invasive species over time. The lake ecosystem additionally experienced significant degradation after invasion, mainly reflected in several related indicators, such as total biomass/total system throughput (TB/TST), total primary production/total biomass (TPP/TB), total primary production/total respiration (TPP/TR), Finn's mean path length (FML), Finn's cycling index (FCI) and the Connectance Index (CI). The simulation results indicated that the relative biomass of icefish (Neosalanx taihuensis), bighead carp (Hypophthalmichthys nobilis), sharpbelly (Hemiculter leucisculus), and zooplankton were significantly affected by increasing the strength of the top-down control of the Japanese smelt on its prey. It is also important to do ecological regulation of planktivorous fishes in the studied Lake Erhai, especially the Japanese smelt.
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Globally important services are supported by Southern Ocean ecosystems, underpinned by the structure, function, and dynamics of complex interconnected and regionally distinctive food webs. These food webs vary in response to a combination of physical and chemical processes that alter productivity, species composition and the relative abundance and dynamics of organisms. Combined with regional and seasonal variability, climate-induced changes and human activities have and are expected to continue to drive important structural and functional changes to Southern Ocean food webs. However, our current understanding of food web structure, function, status, and trends is patchy in space and time, and methods for systematically assessing and comparing community-level responses to change within and across regional and temporal scales are not well developed. Insights gained from food web modelling studies-ranging from theoretical analyses of ecosystem resilience and adaptation, to qualitative and quantitative descriptions of the system-can assist in resolving patterns of energy flow and the ecological mechanisms that drive food web structure, function, and responses to drivers (such as fishing and climate change). This understanding is required to inform robust management strategies to conserve Southern Ocean food webs and the ecosystem services they underpin in the face of change. This paper synthesises the current state of knowledge regarding Southern Ocean pelagic food webs, highlighting the distinct regional food web characteristics, including key drivers of energy flow, dominant species, and network properties that may indicate Frontiers in Ecology and Evolution | www.frontiersin.org 1 October 2021 | Volume 9 | Article 624763 McCormack et al. Southern Ocean Food Web Modelling GRAPHICAL ABSTRACT | Graphical summary of multiple aspects of Southern Ocean food web structure and function including alternative energy pathways through pelagic food webs, climate change and fisheries impacts and the importance of microbial networks and benthic systems. system resilience. In particular, the insights, gaps, and potential integration of existing knowledge and Southern Ocean food web models are evaluated as a basis for developing integrated food web assessments that can be used to test the efficacy of alternative management and policy options. We discuss key limitations of existing models for assessing change resulting from various drivers, summarise priorities for model development and identify that significant progress could be made to support policy by advancing the development of food web models coupled to projected biogeochemical models, such as in Earth System models.
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In a prequel to this paper, we used non-spatial temporal modelling to investigate the impact of non-native ecosystem engineers on a small-scale, intertidal rocky shore in Saldanha Bay, on the west coast of South Africa, where invasive species have changed the physical environment between 1980 and 2015. However, we considered this approach incomplete without the direct inclusion of spatial modelling and zonation. To address this, we compared multiple, layered simulations employing the food-web approach of Ecospace, the spatial-temporal module of Ecopath with Ecosim (EwE). Our simulations included a control; a simulation that restricted drivers to depth and habitat preferences; two simulations to account for structural complexity as a function of the biomass of alien ecosystem engineers – the first indirectly via mediation, and the second via a novel plug-in ‘Ecoengineer’ – and lastly the inclusion of wave action to replicate its effects. Only the simulation that included the Ecoengineer routine matched empirical observations of species diversity indices and the exclusion of the native mussel Choromytilus meridionalis by the arriving alien Mytilus galloprovincialis. Inclusion of mediation did not differ from the model simulation that used only habitat preference and depth to drive the model, and the addition of wave action did not improve model fits. Our results emphasise that when analysing intertidal ecosystems, they should be modelled with an explicit representation of structural habitat complexity over time and space, and we consider that the application of our Ecoengineer plug-in is an effective and novel way of accomplishing this.
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Large sharks generally occupy the highest trophic levels and are important links in the structuring of trophic networks. However, the decline of these predators has been observed worldwide, with population reduction rates reaching over 90% for some species. Through these declines, it is believed that the effect of the loss of predators could result in the disturbances in ecosystems. Based on this, the present study aimed to test the role of elasmobranchs in a coastal ecosystem in southern Brazil. Also, we tested if the changes in fishing effort cause changes in trophic structure. For this, a trophodynamic model was performed, based on reliable data on biomass and species feeding in the region. The mass balance modeling software Ecopath with Ecosim (EwE) was used to assess the trophic position of sharks and rays, and to understand what their interactions are with other groups in the ecosystem. Among the parameters of the model, the Paraná coast showed to be an immature system, with high connectivity and medium complexity. The trophic levels of the coast varied from 1 to 4.4, with level > 4 composed of sharks, and rays belonging to the third trophic level. Sharks were strong impacted by fishing. According to changes in fishing effort simulations, we observed changes of intermediate levels due to the decline of large sharks. However, no cascade effects were observed from the simulations. The high diversity of the system, feeding overlap, and the redundancy between mesopredator and other teleosts can decrease the chances of a cascade effect occurring.
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Aquaculture and marine renewable energy are two expanding sectors of the Blue Economy in Europe. Assessing the long-term environmental impacts in terms of eutrophication and noise is a priority for both the EU Water Framework Directive and the Marine Strategy Framework Directive, and cumulative impacts will be important for the Maritime Spatial Planning under the Integrated Maritime Policy. With the constant expansion of aquaculture production, it is expected that farms might be established further offshore in more remote areas, as high-energy conditions offer an opportunity to generate more power locally using Marine Renewable Energy (MRE) devices. A proposed solution is the co-location of MRE devices and aquaculture systems using MultiPurpose Platforms (MPPs) comprising offshore wind turbines (OWTs) that will provide energy for farm operations as well as potentially shelter the farm. Disentangling the impacts, conflicts and synergies of MPP elements on the surrounding marine ecosystem is challenging. Here we created a high-resolution spatiotemporal Ecospace model of the West of Scotland, in order to assess impacts of a simple MPP configuration on the surrounding ecosystem and how these impacts can cascade through the food web. The model evaluated the following specific ecosystem responses: (i) top-down control pathways due to distribution changes among top-predators (harbor porpoise, gadoids and seabirds) driven by attraction to the farming sites and/or repulsion/killing due to OWT operations; (ii) bottom-up control pathways due to salmon farm activity providing increasing benthic enrichment predicated by a fish farm particle dispersal model, and sediment nutrient fluxes to the water column by early diagenesis of organic matter (recycled production). Weak responses of the food-web were found for top-down changes, whilst the results showed high sensitivity to increasing changes of bottom-up drivers that cascaded through the food-web from primary producers and detritus to pelagic and benthic consumers, respectively. We assessed the sensitivity of the model Frontiers in Marine Science | www.frontiersin.org 1 July 2021 | Volume 8 | Article 694013 Serpetti et al. MultiPurpose Platforms: An Ecosystem Approach to each of these impacts and the cumulative effects on the ecosystem, discuss the capabilities and limitations of the Ecospace modeling approach as a potential tool for marine spatial planning and the impact that these results could have for the Blue Economy and the EU's New Green Deal.
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Ecosystem-based modeling is rapidly becoming an established technique to investigate the health and stability of ecosystems. In the Gulf of Mexico, ecosystem models are applied to neritic systems, but less focus has been placed on the oceanic domain. Since 2011, severe declines have been observed in many micronekton groups that occupy the mesopelagic zone (200-1000 m depth). Here we present an ecosystem model for the oceanic northern Gulf of Mexico for the year 2011, simulate that model according to micronekton trends through 2018, and quantify the top-down and bottom-up impacts that each functional group has on one another. These trends were examined to determine whether interactions between the two groups have changed directionally over time. In 2011, zooplankton (trophic level =2) occupied greater than one-third of the total metazoan biomass, and also 40% of the total energy throughput ascended to higher trophic levels in the system. Of the 1849 possible functional group interactions (most of which are indirect), approximately 27% showed significant changes between 2011 and 2018, which were related to shifts in biomass and diet throughout the simulation. Direct top-down interactions changed more frequently than other types of trophic relationships. The frequency of direct changes that occurred in the simulation was not observed evenly among all functional groups, as opposed to indirect interactions. These changes between functional group interactions can be used to further examine potential shifts in the trophic structure of marine ecosystems under various forcing scenarios.
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Both trophic structure and biomass flow within marine food webs are influenced by the abiotic environment and anthropogenic stressors such as fishing. The abiotic environment has a large effect on species spatial distribution patterns and productivity and, consequently, spatial co-occurrence between predators and prey, while fishing alters species abundances and food-web structure. In order to disentangle the impacts of the abiotic environment and fishing in the Celtic Sea ecosystem, we developed a spatio-temporal trophic model, specifically an Ecopath with Ecosim with Ecospace model, for the period 1985–2016. In this model, particular attention was paid to the parameterization of the responses of all trophic levels to abiotic environmental changes. Satellite remote sensing data were employed to determine the spatial distribution and annual fluctuations of primary production (PP). Spatial and temporal changes in the habitat favorable for zooplankton were predicted with a novel ecological-niche approach using daily detection of productivity fronts from satellite ocean color. Finally, functional responses characterizing the effect of several abiotic environmental variables (including, among others, temperature, salinity and dissolved oxygen concentration, both at the surface and at the bottom) on fish species groups’ habitat suitability were produced from the predictions of statistical habitat models fitted to presence-absence data collected by multiple fisheries-independent surveys. The dynamic component of our model (Ecosim) was driven by time-series of fishing effort, PP, zooplankton habitat suitability and abiotic environmental variables, and was fitted to abundance and fisheries catch data. The spatial component of our model (Ecospace) was constructed, for specific years of the period 1985–2016 with contrasted abiotic environmental conditions, to predict the variable distribution of the biomass of all functional groups. We found that fishing was the main driver of observed ecosystem changes in the Celtic Sea over the period 1985–2016. However, the integration of the environmental variability into the model and the subsequent improvement of the fit of the dynamic Ecosim component highlighted (i) the control of the overall pelagic production by PP and (ii) the influence of temperature on the productivity of several trophic levels in the Celtic Sea, especially on trophic groups with warm and cold water affinities. In addition, Ecospace predictions indicated that the spatial distributions of commercial fish species may have substantially changed over the studied period. These spatial changes mainly appeared to be driven by temperature and may, therefore, largely impact future fisheries given the continuity of climatic changes.
Technical Report
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Anthropogenic and ecological impacts affect not only the environment, but also the livelihoods of the fishers and communities reliant on them. It is, therefore, crucial to study the entire chain of well-being for an ecosystem, from changing environmental conditions, to the impacts of humans and social processes, to the effect of high-level policies and ecosystem services. As part of the Sustainable Poverty Alleviation from Costal Ecosystem Services project (SPACES), this research addresses the important question: how can we best develop sustainable, effective fisheries decisions while preserving the livelihoods of fishers and their dependents? This volume outlines the steps taken and data sources used for the development of a representative food web model for the Nyali-Mombasa ecosystem, reproducing and quantifying main energy flows, and holistically investigating dominant food-web dynamics, and the role of fisheries on the system. Specifically, the work described herein is intended as a preliminary step towards the estimation of the broad community, ecological, and economic effects of anthropogenic impacts as well as targeted fisheries management decisions (e.g., ban of specific fishing gears) with a view to inform future policies in support of responsible and sustainable fisheries, as well as to identify gaps in the data, and guide future research programmes.
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Considerable effort is being deployed to predict the impacts of climate change and anthropogenic activities on the ocean's biophysical environment, biodiversity, and natural resources to better understand how marine ecosystems and provided services to humans are likely to change and explore alternative pathways and options. We present an updated version of EcoOcean (v2), a spatial-temporal ecosystem modeling complex of the global ocean that spans food-web dynamics from primary producers to top predators. Advancements include an enhanced ability to reproduce spatial-temporal ecosystem dynamics by linking species productivity, distributions, and trophic interactions to the impacts of climate change and worldwide fisheries. The updated modeling platform is used to simulate past and future scenarios of change, where we quantify the impacts of alternative configurations of the ecological model, responses to climate-change scenarios, and the additional impacts of fishing. Climate-change scenarios are obtained from two Earth-System Models (ESMs, GFDL-ESM2M, and IPSL-CMA5-LR) and two contrasting emission pathways (RCPs 2.6 and 8.5) for historical (1950–2005) and future (2006–2100) periods. Standardized ecological indicators and biomasses of selected species groups are used to compare simulations. Results show how future ecological trajectories are sensitive to alternative configurations of EcoOcean, and yield moderate differences when looking at ecological indicators and larger differences for biomasses of species groups. Ecological trajectories are also sensitive to environmental drivers from alternative ESM outputs and RCPs, and show spatial variability and more severe changes when IPSL and RCP 8.5 are used. Under a non-fishing configuration, larger organisms show decreasing trends, while smaller organisms show mixed or increasing results. Fishing intensifies the negative effects predicted by climate change, again stronger under IPSL and RCP 8.5, which results in stronger biomass declines for species already losing under climate change, or dampened positive impacts for those increasing. Several species groups that win under climate change become losers under combined impacts, while only a few (small benthopelagic fish and cephalopods) species are projected to show positive biomass changes under cumulative impacts. EcoOcean v2 can contribute to the quantification of cumulative impact assessments of multiple stressors and of plausible ocean-based solutions to prevent, mitigate and adapt to global change.
Presentation
Although they likely dominate the world’s total fish biomass, the roles of mesopelagic fishes in oceanic ecosystems are poorly represented in ecosystem models. Mesopelagic fishes are occasionally practiced as commercial species, but restrictions due to fishing cost and gear selectivity have stunted global production. Many mesopelagic fishes undertake a diel vertical migration where they ascend to the near-surface waters during the night to feed and descend into the depths during the day. Other mesopelagic fishes remain at depth throughout the diel cycle. Apex predators (e.g., tunas, marine mammals, sharks) make routine dives to prey on micronekton in the mesopelagic zone (200 – 1000 m depth). Here we introduce an ecosystem model of the oceanic Gulf of Mexico and emphasize the trophic impact that mesopelagic fishes have on other functional groups within the system. This model has been coupled with a biogeochemical model (ROMS-NPZD), compared to 39 time series, and validated with a Monte Carlo procedure. Mesopelagic fishes occupy a secondary consumer role in the ecosystem (trophic level 3.3 – 4.0), where feeding guilds range from zooplanktivores to micronektonivores. In total, mesopelagic fishes occupy greater than 80% of the total energy pathways that progress from primary producers to apex predators. Lanternfishes are an important prey species for juvenile tunas and dragonfishes. Based on predator and prey groups, hatchetfishes and lanternfishes both occupy a similar niche to pelagic cephalopods (another important prey group to apex predators). Mesopelagic fishes are prey to upper-trophic level organisms and consume zooplankton, potentially providing wasp-waist control in oceanic ecosystems.
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Ecosystem models are important tools for conducting ecosystem-based management. A particularly useful method of characterizing the flow of energy through an ecosystem and the subsequent direct and indirect implications of management actions is mass balance modeling. Here we outline the equations as utilized in Rpath, an R implementation of the mass balance algorithms popularized by Ecopath with Ecosim that are designed to work with fisheries data sources. We believe that common practices in R will aid in the reproducibility of conducting analysis using a mass balance model as all of the code is contained within a single script file. This includes the built-in statistical and graphical functions of R. In addition to added reproducibility, R is a coding language with which ecologists are familiar. This familiarity offers greater flexibility for practitioners to tailor the model to their needs. We have made the code available on an open software development platform which should aid in continuous community development of the tool.
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Fisher's knowledge offers a valuable source of information to run parallel to observed data and fill gaps in our scientific knowledge. In this study we demonstrate how fishers' knowledge of historical fishing effort was incorporated into an Ecopath with Ecosim (EwE) model of the Irish Sea to fill the significant gap in scientific knowledge prior to 2003. The Irish Sea model was fitted and results compared using fishing effort time-series based on: (i) scientific knowledge, (ii) fishers' knowledge, (iii) adjusted fishers' knowledge, and (iv) a combination of (i) and (iii), termed “hybrid knowledge.” The hybrid model produced the best overall statistical fit, capturing the biomass trends of commercially important stocks. Importantly, the hybrid model also replicated the increase in landings of groups such as “crabs & lobsters” and “epifauna” which were poorly simulated in scenario (i). Incorporating environmental drivers and adjusting vulnerabilities in the foraging arena further improved model fit, therefore the model shows that both fishing and the environment have historically influenced trends in finfish and shellfish stocks in the Irish Sea. The co-production of knowledge approach used here improved the accuracy of model simulations and may prove fundamental for developing ecosystem-based management advice in a global context.
Technical Report
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The effects of six common forms of fisheries support are estimated using a bioeconomic model of the global fishery. The results show that all have the potential to provoke overfishing, to lead to fish stocks being overfished, to encourage illegal, unreported or unregulated (IUU) fishing and to increase fleet capacity, but that their effects can vary significantly both in scale and how they are distributed at the fleet level. The fisheries management system can mitigate, though not entirely eliminate, these impacts. Supports based on reducing the cost of inputs purchased by fishers provoke the greatest increase in fishing effort, with associated risks of overfishing. This includes fuel subsidies, which are also shown to deliver less than 10% of their value in actual benefits to fishers in some cases, making them the least effective means of transferring income to fishers of those evaluated. Payments based on improving fishers’ business operations provided the greatest benefit to fishers and had relatively less tendency to increase fishing effort. If only USD 5 billion in fuel support was converted into support of this type, fishers would see increased income of more than USD 2 billion, while at the same time reducing effort and improving fish stocks. Such a change would also provide relatively more benefit to smaller fishers.
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Environmental decision makers are required to understand complex ecological processes and ecological computer models are designed to facilitate this understanding. A set of interviews reveals three main perceptions affecting senior environmental decision makers’ trust in ecological computer models as decision facilitation tools: an ecological computer model is perceived as (i) a ‘black box’, (ii) processing poorly documented, sparse and out-of-date input data, and (iii) whose sensitivity to model parameters enables manipulation to produce desired outcomes justifying pre-conceived decisions. This leads to lack of trust towards both ecological computer models and model-users, including other scientists and decision makers. Model acceptance appears to depend on the amount, currency and geographical origin of input data. This is at odds with modellers’ communication style, which typically places more emphasis on highlighting the ecological computer model’s features and performance, rather than on describing the input data. Developing ‘big data’ capabilities could deliver the large, real-time, local data that may enhance acceptance. However, the size and complexity of ‘big data’ requires automated pre-processing, using modelling and algorithms that are even more inscrutable than current ecological computer models. Future trust in ecological computer models will likely depend on how this dilemma is resolved, which is likely to require improved communication between modellers and decision makers.
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The opportunistic feeder Pterois volitans is a voracious invader, causing large impacts in marine food-webs. We have used a Ecopath-with-Ecosim model to hypothesize an invasion by lionfish and to predict the likely impact of this potential generalist mesopredator in a subtropical food-web model. With thirty-three functional groups, the initial Ecopath model was balanced with a low biomass of lionfish (0.07 t/km2). In Ecosim, three scenarios of different vulnerability settings for the linkages between the introduced fish and its prey were tested, representing the default setting, a top-down control, and an extreme top-down control. The scenarios were tested using different assumptions on the ability of the invasive fish to change the proportions of prey consumed according to prey availability. Our model predicted that the hypothesized lionfish invasion would have a strong impact on this subtropical marine food web: (1) by reducing prey populations and, consequently, food for native predators, and; (2) by predating on key species, causing direct impacts and possibly cascading trophic effects. Reef fish were the most affected, including some groups ecologically and economically important, like lutjanids and groupers. However, some adaptations in the fishing strategy of fishermen are expected which may affect other fish groups. Stakeholders should be warned of the potential ecological and socio-economic impacts that may arise from a lionfish invasion and various strategies and policy options should be immediately developed and applied (1) to prevent the arrival and establishment of the lionfish, and; (2) to make the ecosystem more resilient to this and other possible exotic species.
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Ecotracer is a tool in the Ecopath with Ecosim (EwE) software package used to simulate and analyze the transport of contaminants such as methylmercury or radiocesium through aquatic food webs. Ecotracer solves the contaminant dynamic equations simultaneously with the biomass dynamic equations in Ecosim/Ecospace. In this paper, we give a detailed description of the Ecotracer module and analyze the performance on two problems of differing complexity. Ecotracer was modified from previous versions to more accurately model contaminant excretion, and new numerical integration algorithms were implemented to increase accuracy and robustness. To test the mathematical robustness of the computational algorithm, Ecotracer was tested on a simple problem for which we know an analytical solution. These results demonstrated the effectiveness of the program numerics. A much more complex model, the release of the cesium radionuclide (137)Cs from the Fukushima Dai-ichi nuclear accident, was also modeled and analyzed. A comparison of the Ecotracer results to sampled (137)Cs measurements in the coastal ocean area around Fukushima show the promise of the tool but also highlight some important limitations.
Technical Report
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South East Queensland (SEQ) is the fastest growing population in Australia. With the projected population growth from nearly 3 million in 2010 to approximately 4 million in 2026, changes in land-use (e.g. from rural to urban) and construction of additional infrastructure are inevitable. More people in the region will also increase demands for water, sewage treatment plants and recreational areas in SEQ waterways. If not properly managed, these changes are expected to have profound consequences on environmental, social and economic values in the region.
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Societal and scientific challenges foster the implementation of the ecosystem approach to marine ecosystem analysis and management, which is a comprehensive means of integrating the direct and indirect effects of multiple stressors on the different components of ecosystems, from physical to chemical and biological and from viruses to fishes and marine mammals. Ecopath with Ecosim (EwE) is a widely used software package, which offers capability for a dynamic description of the multiple interactions occurring within a food web, and, potentially, a crucial component of an integrated platform supporting the ecosystem approach. However, being written for the Microsoft .NET framework, seamless integration of this code with Fortran-based physical and/or biogeochemical oceanographic models is technically not straightforward. In this work we release a re-coding of EwE in Fortran (EwE-F). We believe that the availability of a Fortran version of EwE is an important step towards setting up coupled/integrated modelling schemes utilising this widely adopted software because it (i) increases portability of the EwE models and (ii) provides additional flexibility towards integrating EwE with Fortran-based modelling schemes. Furthermore, EwE-F might help modellers using the Fortran programming language to get close to the EwE approach. In the present work, first fundamentals of EwE-F are introduced, followed by validation of EwE-F against standard EwE utilising sample models. Afterwards, an end-to-end (E2E) ecological representation of the Gulf of Trieste (northern Adriatic Sea) ecosystem is presented as an example of online two-way coupling between an EwE-F food web model and a biogeochemical model. Finally, the possibilities that having EwE-F opens up are discussed.
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Societal and scientific challenges foster the implementation of the ecosystem approach to marine ecosystem analysis and management, which is a comprehensive means of integrating the direct and indirect effects of multiple stressors on the different components of ecosystems, from physical to chemical and biological and from viruses to fishes and marine mammals. Ecopath with Ecosim (EwE) is a widely used software package, which offers great capability for a dynamic description of the multiple interactions occurring within a food web, and potentially, a crucial component of an integrated platform supporting the ecosystem approach. However, being written for the Microsoft .NET framework, seamless integration of this code with Fortran-based physical oceanographic and/or biogeochemical models is technically not straightforward. In this work we release a re-coding of EwE in Fortran (EwE-F). We believe that the availability of a Fortran version of EwE is an important step towards setting-up integrated end-to-end (E2E) modelling schemes utilising this widely adopted software because it (i) increases portability of the EwE models, (ii) provides greater flexibility towards integrating EwE with Fortran-based modelling schemes. Furthermore, EwE-F might help modellers using Fortran programming language to get close to the EwE approach. In the present work, first the fundamentals of EwE-F are introduced, followed by validation of EwE-F against standard EwE utilising sample models. Afterwards, an E2E ecological representation of the Trieste Gulf (Northern Adriatic Sea) ecosystem is presented as an example of online two-way coupling between an EwE-F food web model and a biogeochemical model. Finally, the possibilities that having EwE-F opens up for are discussed.
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Why are marine species where they are? The scientific community is faced with an urgent need to understand aquatic ecosystem dynamics in the context of global change. This requires development of scientific tools with the capability to predict how biodiversity, natural resources, and ecosystem services will change in response to stressors such as climate change and further expansion of fishing. Species distribution models and ecosystem models are two methodologies that are being developed to further this understanding. To date, these methodologies offer limited capabilities to work jointly to produce integrated assessments that take both food web dynamics and spatial-temporal environmental variability into account. We here present a new habitat capacity model as an implementation of the spatial-temporal model Ecospace of the Ecopath with Ecosim approach. The new model offers the ability to drive foraging capacity of species from the cumulative impacts of multiple physical, oceanographic, and environmental factors such as depth, bottom type, temperature, salinity, oxygen concentrations, and so on. We use a simulation modeling procedure to evaluate sampling characteristics of the new habitat capacity model. This development bridges the gap between envelope environmental models and classic ecosystem food web models, progressing toward the ability to predict changes in marine ecosystems under scenarios of global change and explicitly taking food web direct and indirect interactions into account.
Conference Paper
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Why are marine species where they are? The scientific community is faced with an urgent need to understand aquatic ecosystem dynamics in the context of global change. This requires development of scientific tools with the capability to predict how biodiversity, natural resources, and ecosystem services will change in response to stressors such as climate change and further expansion of fishing. Species distribution models and ecosystem models are two methodologies that are being developed to further this understanding. To date, these methodologies offer limited capabilities to work jointly to produce integrated assessments that take both food web dynamics and spatial-temporal environmental variability into account. We here present a new habitat capacity model as an implementation of the spatial-temporal model Ecospace of the Ecopath with Ecosim approach. The new model offers the ability to drive foraging capacity of species from the cumulative impacts of multiple physical, oceanographic, and environmental factors such as depth, bottom type, temperature, salinity, oxygen concentrations, and so on. We use a simulation modeling procedure to evaluate sampling characteristics of the new habitat capacity model. This development bridges the gap between envelope environmental models and classic ecosystem food web models, progressing toward the ability to predict changes in marine ecosystems under scenarios of global change and explicitly taking food web direct and indirect interactions into account.
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Ecosystem-orientated thinking is increasingly incorporated into fishery management. Given the complexity of ecosystem processes, there is a need to evaluate the tools used to steer this thinking critically. ECOPATH with ECOSIM (EwE), an aggregate system-modelling package, is currently the most widely employed approach to assess the ecosystem effects of fishing. The basic equations and assumptions, strengths and weaknesses, and the potential of this approach to contribute to practical fisheries management advice are reviewed. Strengths include the structured parameterization framework, the inclusion of a well-balanced level of conceptual realism, a novel representation of predator-prey interaction terms, and the inclusion of a Bayes-like approach (ECORANGER) to take account of the uncertainty associated with values for model inputs. Weaknesses in model structure include the constraining nature of the mass-balance assumption (of ECOPATH) for initiating projections, the questionable handling of life history responses such as compensatory changes in the natural mortality rates of marine mammals, overcompensatory stock-recruit relationships that result from default parameter settings, possible problems in extrapolating from the microscale to the macroscale, as well as some (not too far-reaching) mathematical inconsistencies in the underlying equations. There is a paucity of systematic and stepwise investigations into model behaviour and properties, and users are cautioned against non-critical use of the default settings. An important limitation related to the predominant use of EwE as a "black-box" modelling tool is that some users fail to consider a range of alternative interaction representations. As with all multispecies approaches, the major limitation in applying the EwE approach lies in the quality and quantity of available data. Current EwE applications generally do not adequately address uncertainty in data inputs and model structure. Prudent EwE applications that utilize good data and are based upon rigorous statistical analyses can complement the quantitative predictions of traditional single-species models. They could be particularly useful in some contexts if output in the form of probability distributions encompassing a range of likely ecosystem responses were to be coupled with attempts to extend Operational Management Procedure (OMP) approaches to fisheries management beyond the singlespecies level. In particular, such applications could serve as the operating models of the underlying dynamics that are used for computer simulation testing of OMPs.
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Recent advances in aquatic ecosystem modelling have particularly focused on trophic network analysis through trophodynamic models. We present here a R package devoted to a recently developed model, EcoTroph. This model enables the analysis of aquatic ecological networks and the related impacts of fisheries. It was available through a plug-in in the well-known Ecopath with Ecosim software or through implementations in Excel sheets. The R package we developed simplifies the access to the EcoTroph model and offers a new interfacing between two widely used software, Ecopath and R.
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Dynamic food web models are increasingly used to investigate the ecosystem effects of fishing; however, key unknown functional response parameters describing predator-prey interactions strongly influence model behavior. We explored functional response parameter uncertainty and its effect on fishing simulation results using a dynamic food web model of the Gulf of Alaska (GOA) with14 fishing fleets, 104 consumer groups, four primary producer groups, and five detritus pools. After generating millions of potential ecosystems with randomly selected functional response parameters, we assigned groups of these randomly parameterized systems to one of five increasingly intense ecosystem-wide fishing treatments. For each fishing treatment, we counted and compared resulting ecosystems with no extinctions. Surprisingly, the model GOA ecosystems were robust to a wide range of functional response parameters. However, we found an abrupt threshold effect between moderate and heavy exploitation rates, beyond which a much lower proportion of model ecosystems persisted. Beyond this fishing threshold, extinction was more likely, and system attributes differed greatly from moderately fished model ecosystems. Fishing thresholds were not found with default functional response parameters, implying that model simulations should include a wide range of parameterizations to reflect ecological uncertainty and to support sustainable ecosystem-based fishery management.
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We use a dynamic ecosystem model to evaluate the relative effects of fishing history, climate change, and predator–prey interactions in determining biomass trajectories for 12 species groups ranging from marine mammals through commercially exploited fish and invertebrates in the Gulf of Alaska (GOA). Ecosystem model fits under six alternative hypotheses relating fishing, climate, and predation were evaluated. Fishing alone explained few GOA biomass trajectories; it was necessary to both estimate specific predator–prey relationships and provide some mechanism for increased production. No single control hypothesis explained all species dynamics simultaneously, suggesting that in the GOA, there is no single main driver of the ecosystem. Furthermore, the alternative control hypotheses implied contrasting sets of predator–prey relationships (estimated functional response parameters). Therefore, a single set of “best fit” parameters for a given control hypothesis is unlikely to be useful in forecasting. Future modeling efforts supporting ecosystem-based fishery management could retain multiple working models to accommodate complex forcing (fishing, keystone species production, and environmental) differentially affecting components of the ecosystem.
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Research toward the impacts of climate change and human activities on marine ecosystems is challenged by the limitations of present-day ecosystem models to address the interrelated spatial dynamics between climate, ocean chemistry, marine food webs, and human systems. The work presented here, the spatial–temporal data framework, is part of a larger study, the NF-UBC Nereus Program, to develop a new approach to model interoperability for closing the gap between marine ecosystem modeling tools via geographic information systems (GIS) technology. The approach we present simplifies interdisciplinary model interoperability by separating technical and scientific challenges into a flexible and modular software approach. To illustrate capabilities of the new framework, we use a remote-sensing derived spatial and temporal time series to drive the primary production dynamics in an existing food web model of the North-Central Adriatic using the Ecospace module of the Ecopath with Ecosim approach. In general, the predictive capabilities of the food web model to hind-cast ecosystem dynamics are enhanced when applying the new framework by better reflecting observed species population trends and distributions. Results show that changes at the phytoplankton level due to changes in primary production are realistically reproduced and cascade up the pelagic food web. The dynamics of zooplankton and small and large pelagic fish are impacted. Highly exploited demersal species such as European hake do, however, not show clear signs of cascading. This may be due to the high fishing pressure on this species and the resulting strong historical decline in the area. In general, the development of the new framework offers ecosystem modelers with unprecedented capabilities to include spatial–temporal time series into food web analysis with a minimal set of required steps. It is a promising step toward integrating species distribution models and food web dynamics, and future implementations of interdisciplinary model interoperability.
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There has been a rapid rise in the development of end-to-end models for marine ecosystems over the past decade. Some reasons for this rise include need for predicting effects of climate change on biota and dissatisfaction with existing models. While the benefits of a well-implemented end-to-end model are straightforward, there are many challenges. In the short term, my view is that the major role of end-to-end models is to push the modelling community forward, and to identify critical data so that these data can be collected now and thus be available for the next generation of end-to-end models. I think we should emulate physicists and build theoretically-oriented models first, and then collect the data. In the long-term, end-to-end models will increase their skill, data collection will catch up, and end-to-end models will move towards site-specific applications with forecasting and management capabilities. One pathway into the future is individual efforts, over-promise, and repackaging of poorly performing component submodels ("lipstick on a pig"). The other pathway is a community-based collaborative effort, with appropriate caution and thoughtfulness, so that the needed improvements are achieved ("significant advance"). The promise of end-to-end modelling is great. We should act now to avoid missing a great opportunity.
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The Rcpp package simplifies integrating C++ code with R. It provides a consistent C++ class hierarchy that maps various types of R objects (vectors, matrices, functions, environments, . . . ) to dedicated C++ classes. Object interchange between R and C++ is managed by simple, flexible and extensible concepts which include broad support for C++ Standard Template Library idioms. C++ code can both be compiled, linked and loaded on the fly, or added via packages. Flexible error and exception code handling is provided. Rcpp substantially lowers the barrier for programmers wanting to combine C++ code with R.
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A simple model termed ECOPATH is presented which estimates mean annual biomass, production, and consumption for components of an ecosystem. To use the model, the ecosystem must be partitioned into groups of similar species and provide for these species groups, estimates of production to biomass, diet, and food consumption. The ECOPATH model is applied to an ecosystem at French Frigate Shoals in the Northwestern Hawaiian Islands. Extensive field work provides both estimates of the input parameters as well as estimates of mean annual biomass and production. Biomass and production estimates for some of the species groups modeled are used to validate the estimates generated by the model.
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Growing disillusion with the predictive capability of single species fisheries assessment methods and the realization that the management approaches they imply will always fail to protect bycatch species has led to growing interest in the potential of marine protected areas (MPAs) as a tool for protecting such species and allowing for rebuilding populations of target species and damaged habitat. Ecospace is a spatially explicit model for policy evaluation that allows for considering the impact of MPAs in an ecosystem (that is, trophic) context, and that relies on the Ecopath mass-balance approach for most of its parameterization. Additional inputs are movement rates used to compute exchanges between grid
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Three independent modeling methods—a nutrient-phytoplankton–zooplankton (NPZ) model (NEMURO), a food web model (Ecopath/Ecosim), and a bioenergetics model for pink salmon (Oncorhynchus gorbuscha)—were linked to examine the relationship between seasonal zooplankton dynamics and annual food web productive potential for Pacific salmon feeding and growing in the Alaskan subarctic gyre ecosystem. The linked approach shows the importance of seasonal and ontogenetic prey switching for zooplanktivorous pink salmon, and illustrates the critical role played by lipid-rich forage species, especially the gonatid squid Berryteuthis anonychus, in connecting zooplankton to upper trophic level production in the subarctic North Pacific. The results highlight the need to uncover natural mechanisms responsible for accelerated late winter and early spring growth of salmon, especially with respect to climate change and zooplankton bloom timing. Our results indicate that the best match between modeled and observed high-seas pink salmon growth requires the inclusion of two factors into bioenergetics models: (1) decreasing energetic foraging costs for salmon as zooplankton are concentrated by the spring shallowing of pelagic mixed-layer depth and (2) the ontogenetic switch of salmon diets from zooplankton to squid. Finally, we varied the timing and input levels of coastal salmon production to examine effects of density-dependent coastal processes on ocean feeding; coastal processes that place relatively minor limitations on salmon growth may delay the seasonal timing of ontogenetic diet shifts and thus have a magnified effect on overall salmon growth rates.
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Inspired by the work of the renowned fisheries scientist Daniel Pauly, this book provides a detailed overview of ecosystem-based management of fisheries. It explores the complex and interdisciplinary nature of the subject by bringing together contributions from some of the world's leading fisheries scientists, managers and conservationists. Combining both research reviews and opinion pieces, and reflecting the breadth of Pauly's influence within the field, the book illustrates the range of issues associated with the implementation of the ecosystem approach and the challenge of long-term sustainability. Topics covered include global biodiversity, the impact of human actions on marine life, the implications for economic and social systems and the role of science in communicating and shaping ocean policy to preserve resources for the future. This book provides a complete and essential overview for advanced researchers and those just entering the field.
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"TCP/IP sockets in C# is an excellent book for anyone interested in writing network applications using Microsoft .Net frameworks. It is a unique combination of well written concise text and rich carefully selected set of working examples. For the beginner of network programming, its a good starting book; on the other hand professionals could also take advantage of excellent handy sample code snippets and material on topics like message parsing and asynchronous programming." Adarsh Khare, SDT, .Net Frameworks Team, Microsoft Corporation. The popularity of the C# language and the .NET framework is ever rising due to its ease of use, the extensive class libraries available in the .NET Framework, and the ubiquity of the Microsoft Windows operating system, to name a few advantages. TCP/IP Sockets in C# focuses on the Sockets API, the de facto standard for writing network applications in any programming language. Starting with simple client and server programs that use TCP/IP (the Internet protocol suite), students and practitioners quickly learn the basics and move on to firsthand experience with advanced topics including non-blocking sockets, multiplexing, threads, asynchronous programming, and multicasting. Key network programming concepts such as framing, performance and deadlocks are illustrated through hands-on examples. Using a detailed yet clear, concise approach, this book includes numerous code examples and focused discussions to provide a solid understanding of programming TCP/IP sockets in C#. Features: Tutorial-based instruction in key sockets programming techniques complemented by numerous code examples throughout. Discussion moves quickly into the C# Sockets API definition and code examples, desirable for those who want to get up-to-speed quickly. Important coverage of "under the hood" details that developers will find useful when creating and using a socket or a higher level TCP class that utilizes sockets. Includes end-of-chapter exercises to facilitate learning, as well as sample code available for download at the book's companion web site.
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Inspired by the work of the renowned fisheries scientist Daniel Pauly, this book provides a detailed overview of ecosystem-based management of fisheries. It explores the complex and interdisciplinary nature of the subject by bringing together contributions from some of the world's leading fisheries scientists, managers and conservationists. Combining both research reviews and opinion pieces, and reflecting the breadth of Pauly's influence within the field, the book illustrates the range of issues associated with the implementation of the ecosystem approach and the challenge of long-term sustainability. Topics covered include global biodiversity, the impact of human actions on marine life, the implications for economic and social systems and the role of science in communicating and shaping ocean policy to preserve resources for the future. This book provides a complete and essential overview for advanced researchers and those just entering the field.
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Responsible fisheries management is of increasing interest to the scientific community, resource managers, policy makers, stakeholders and the general public. Focusing solely on managing one species of fish stock at a time has become less of a viable option in addressing the problem. Incorporating more holistic considerations into fisheries management by addressing the trade-offs among the range of issues involved, such as ecological principles, legal mandates and the interests of stakeholders, will hopefully challenge and shift the perception that doing ecosystem-based fisheries management is unfeasible. Demonstrating that EBFM is in fact feasible will have widespread impact, both in US and international waters. Using case studies, underlying philosophies and analytical approaches, this book brings together a range of interdisciplinary topics surrounding EBFM and considers these simultaneously, with an aim to provide tools for successful implementation and to further the debate on EBFM, ultimately hoping to foster enhanced living marine resource management.
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An Ecopath-Ecosim ecosystem model under development for coastal areas of the Gulf of Mexico simulates responses of 63 biomass pools to changes in fisheries and primary productivity. Ten key species are represented by detailed, multistanza population-dynamics models (31 of the biomass pools) that attempt to account explicitly for possible changes in recruitment rates due to changes in by-catch rates and trophic interactions. Over a 1950-2004 historical reference period, the model shows good simulated agreement with time-series patterns estimated from stock assessment and relative abundance index data for many of the species, and in particular it offers an explanation for apparent nonstationarity in natural mortality rates of menhaden (declining apparent M over time). It makes one highly counterintuitive policy prediction about impacts of management efforts aimed at reducing by-catch in the shrimp trawl fishery, namely that by-catch reduction may cause negative impacts on productivity of several valued species [menhaden, Brevoortia patronus Goode, 1878; red drum, Sciaenops ocellatus (Linnaeus, 1766); red snapper, Lutjanus campechanus (Poey, I860)] by allowing recovery of some benthic predators such as catfishes [Arius felis (Linnaeus, 1766), Bagre marinus (Mitchill, 1815)] that have been reduced by trawling but are also potentially important predators on juveniles of the valued species. Recognition of this policy implication would have been impossible without explicit, multistanza representation of juvenile life histories and trophic interactions, because the predicted changes in predation regimes represent only very small overall biomass fluxes. © 2008 Rosenstiel School of Marine and Atmospheric Science of the University of Miami.
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We used an end-to-end ecosystem model that incorporates physics, biogeochemistry, and predator-prey dynamics for the Eastern Subarctic Pacific ecosystem to investigate the factors controlling propagation of changes in primary production to higher trophic levels. We found that lower trophic levels respond to increased primary production in unexpected ways due to complex predatory interactions, with small phytoplankton increasing more than large phytoplankton due to relief from predation by microzooplankton, which are kept in check by the more abundant mesozooplankton. We also found that the propagation of production to upper trophic levels depends critically on how non-predatory mortality is structured in the model, with much greater propagation occurring with linear mortality and much less with quadratic mortality, both of which functional forms are in common use in eco-system models. We used an ensemble simulation approach to examine how uncertainties in model parameters affect these results. When considering the full range of potential responses to enhanced productivity, the effect of uncertainties related to the functional form of non-predatory mortality was often masked by uncertainties in the food-web parameterization. The predicted responses of several commercially important species, however, were significantly altered by non-predatory mortality assumptions.
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Experimental tests of management policy options are becoming popular to resolve uncertainties arising from ecological processes and interactions that cannot be investigated except at held management scales. Such experiments are generally quite costly, time consuming, and sometimes risky We need objective measures of these costs and risks to justify sensible experiments and to compare design alternatives that differ widely in cost and effectiveness. One possible measure of design performance is the expected net present value from the system, averaged over alternative hypotheses about response to experimental treatment. This present value can be estimated by dividing the future stream of expected net benefits into 2 components: short run values obtained during the experiment, and long run values obtained afterward. Experiments that are costly in the short run can be highly worthwhile for the long term if they substantially reduce the odds of using incorrect policies or of overlooking opportunities for increasing value through innovative policy choices, and if the results can be applied to many locations. Optimum experiments in terms of the expected value performance measure are not likely to have as much statistical power as scientists usually demand for traditional hypothesis testing, except in situations where the costs of incorrectly adopting a new management option are high relative to benefits obtained under that option.
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AimThere has been considerable effort allocated to understanding the impact of climate change on our physical environment, but comparatively little to how life on Earth and ecosystem services will be affected. Therefore, we have developed a spatial-temporal food web model of the global ocean, spanning from primary producers through to top predators and fisheries. Through this, we aim to evaluate how alternative management actions may impact the supply of seafood for future generations. LocationGlobal ocean. Methods We developed a modelling complex to initially predict the combined impact of environmental parameters and fisheries on global seafood production, and initially evaluated the model's performance through hindcasting. The modelling complex has a food web model as core, obtains environmental productivity from a biogeochemical model and assigns global fishing effort spatially. We tuned model parameters based on Markov chain random walk stock reduction analysis, fitting the model to historic catches. We evaluated the goodness-of-fit of the model to data for major functional groups, by spatial management units and globally. ResultsThis model is the most detailed ever constructed of global fisheries, and it was able to replicate broad patterns of historic fisheries catches with best agreement for the total catches and good agreement for species groups, with more variation at the regional level. Main conclusionsWe have developed a modelling complex that can be used for evaluating the combined impact of fisheries and climate change on upper-trophic level organisms in the global ocean, including invertebrates, fish and other large vertebrates. The model provides an important step that will allow global-scale evaluation of how alternative fisheries management measures can be used for mitigation of climate change.
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Spatial management is used extensively in natural resource management to address sustainability and biodiversity issues, for example through declaration of terrestrial National Parks and marine protected areas (MPAs).Spatial management is used also to optimize yields or protect key parts of the life cycle of species that are utilized (hunted, farmed or fished), for example through rotational harvesting.To evaluate the effectiveness of marine spatial closures with conflicting fisheries and conservation objectives, a series of marine fisheries closures are here analysed using an integrative modelling tool known as management strategy evaluation (MSE).This modelling framework combines a food web model of a tropical ecosystem fished by a prawn (shrimp) fishery that emulates the resource being managed, together with the present management system and risk-based tools of fishing the prawn species at maximum economic yield.A series of spatial closures are designed and tested with the aim of investigating trade-offs among biodiversity (MPA), benthic impacts, ecosystem function, key species at risk to fishing, economic and sustainability objectives.Synthesis and applications. This paper illustrates that existing tools often available in actively managed fisheries can be linked together into an effective management strategy evaluation framework. Spatial closures tended to succeed with respect to their specific design objective, but this benefit did not necessarily flow to other broad-scale objectives. This demonstrates that there is no single management tool which satisfies all objectives, and that a suite of management tools is needed.
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Global-scale planktonic ecosystem models exhibit large differences in simulated net primary production (NPP) and assessment of planktonic food web fluxes beyond primary producers has been limited, diminishing confidence in carbon flux estimates from these models. In this study, a global ocean-ice-ecosystem model was assessed against a suite of observation-based planktonic food web flux estimates, many of which were not considered in previous modeling studies. The simulation successfully captured cross-biome differences and similarities in these fluxes after calibration of a limited number of highly uncertain yet influential parameters. The resulting comprehensive carbon budgets suggested that shortened food webs, elevated growth efficiencies, and tight consumer-resource coupling enable oceanic upwelling systems to support 45% of pelagic mesozooplankton production despite accounting for only 22% of ocean area and 34% of NPP. In seasonally stratified regions (42% of ocean area and 40% of NPP), weakened consumer-resource coupling tempers mesozooplankton production to 41% and enhances export below 100 m to 48% of the global total. In oligotrophic systems (36% of ocean area and 26% of NPP), the dominance of small phytoplankton and low consumer growth efficiencies supported only 14% of mesozooplankton production and 17% of export globally. Bacterial production, in contrast, was maintained in nearly constant proportion to primary production across biomes through the compensating effects of increased partitioning of NPP to the microbial food web in oligotrophic ecosystems and increased bacterial growth efficiencies in more productive areas. Cross-biome differences in mesozooplankton trophic level were muted relative to those invoked by previous work such that significant differences in consumer growth efficiencies and the strength of consumer-resource coupling were needed to explain sharp cross-biome differences in mesozooplankton production. Lastly, simultaneous consideration of multiple flux constraints supports a highly distributed view of respiration across the planktonic food web rather than one dominated by heterotrophic bacteria. The solution herein is unlikely unique in its ability to explain observed cross-biome energy flow patterns and notable misfits remain. Resolution of existing uncertainties in observed biome-scale productivity and increasingly mechanistic phys