@article{sadchatheeswaran_novel_2021,

title = {A novel approach to explicitly model the spatiotemporal impacts of structural complexity created by alien ecosystem engineers in a marine benthic environment},

author = {S. Sadchatheeswaran and G. M. Branch and L. J. Shannon and M. Coll and J. Steenbeek},

url = {https://www.sciencedirect.com/science/article/pii/S0304380021002830},

doi = {10.1016/j.ecolmodel.2021.109731},

issn = {0304-3800},

year  = {2021},

date = {2021-11-01},

urldate = {2021-11-01},

journal = {Ecological Modelling},

volume = {459},

pages = {109731},

keywords = {Ecoengineer, Ecopath with Ecosim, Ecospace, Ecosystem engineer, Intertidal, Invasive},

pubstate = {published},

tppubtype = {article}

}

@article{sadchatheeswaranNovelApproachExplicitly2021,

title = {A Novel Approach to Explicitly Model the Spatiotemporal Impacts of Structural Complexity Created by Alien Ecosystem Engineers in a Marine Benthic Environment},

author = {Saachi Sadchatheeswaran and George M. Branch and Lynne J. Shannon and Marta Coll and Jeroen Steenbeek},

doi = {10.1016/j.ecolmodel.2021.109731},

issn = {0304-3800},

year  = {2021},

date = {2021-11-01},

urldate = {2021-09-22},

journal = {Ecological Modelling},

volume = {459},

pages = {109731},

abstract = {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 \textendash the first indirectly via mediation, and the second via a novel plug-in `Ecoengineer' \textendash 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.},

keywords = {Ecoengineer, Ecopath with Ecosim, Ecospace, Ecosystem engineer, Intertidal, Invasive},

pubstate = {published},

tppubtype = {article}

}

@article{horn_food_2021,

title = {Food web models reveal potential ecosystem effects of seagrass recovery in the northern Wadden Sea},

author = {S. Horn and M. Coll and H. Asmus and T. Dolch},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/rec.13328},

doi = {10.1111/rec.13328},

issn = {1526-100X},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Restoration Ecology},

volume = {29},

number = {S2},

pages = {e13328},

note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/rec.13328},

keywords = {Ecopath with Ecosim, ecosystem services, food webs, seagrass recovery, Wadden Sea, Zostera},

pubstate = {published},

tppubtype = {article}

}

@article{hornFoodWebModels2021,

title = {Food Web Models Reveal Potential Ecosystem Effects of Seagrass Recovery in the Northern Wadden Sea},

author = {Sabine Horn and Marta Coll and Harald Asmus and Tobias Dolch},

doi = {10.1111/rec.13328},

issn = {1526-100X},

year  = {2021},

date = {2021-01-01},

urldate = {2021-08-19},

journal = {Restoration Ecology},

volume = {29},

number = {S2},

pages = {e13328},

abstract = {In contrast to the global trend, seagrass beds have recovered in size and density in the northern part of the European Wadden Sea, but ecosystem effects of seagrass recovery and the impacts to ecosystem services are largely unknown. We used temporal-dynamic food web modeling Ecopath with Ecosim to assess potential ecosystem effects of seagrass recovery in the semi-enclosed Sylt-R\om\o Bight at the German-Danish border. In addition to changes in the system's structure and functioning over time, the model predicted changes in biomass of seagrass-associated species. For seagrass consumers, we projected an increase in biomass as a result of an increase in food supply. Likewise, the model predicted an increase in biomass of seagrass meadow inhabitants from decreased predation pressure. Correspondingly, the main predators of these inhabitants decreased in biomass according to model results. Proxies representing ecosystem services predicted an increase of tourism appeal of the site with increasing seagrass meadows. Indirect mediation effects of seagrass severely influenced the model output and are thus crucial to forecast potential effects of the recovery of habitat-forming species. Our study illustrates that holistic approaches such as food web models could provide a suitable basis for predicting ecosystem effects of changes in the biomass of habitat-forming species such as seagrasses.},

keywords = {Ecopath with Ecosim, ecosystem services, food webs, seagrass recovery, Wadden Sea, Zostera},

pubstate = {published},

tppubtype = {article}

}

@article{serpettiModelingSmallScale2021,

title = {Modeling Small Scale Impacts of Multi-Purpose Platforms: An Ecosystem Approach},

author = {Natalia Serpetti and Steven Benjamins and Stevie Brain and Maurizio Collu and Bethany J. Harvey and Johanna J. Heymans and Adam D. Hughes and Denise Risch and Sophia Rosinski and James J. Waggitt and Ben Wilson},

doi = {10.3389/fmars.2021.694013},

issn = {2296-7745},

year  = {2021},

date = {2021-01-01},

urldate = {2021-07-25},

journal = {Frontiers in Marine Science},

volume = {0},

publisher = {Frontiers},

abstract = {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 Multi-Purpose 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 (harbour 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 to each of these impacts and the cumulative effects on the ecosystem, discuss the capabilities and limitations of the Ecospace modelling 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.},

keywords = {aquaculture, Ecopath with Ecosim, Ecospace, Marine renewable energy, Marine Strategy Framework Directive, Maritime spatial planning, Multi purpose platform, Offshore wind, West coast of Scotland},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeekUsingGamingTechnology2021,

title = {Using Gaming Technology to Explore and Visualize Management Impacts on Marine Ecosystems},

author = {Jeroen Steenbeek and Dalai Felinto and Mike Pan and Joe Buszowski and Villy Christensen},

doi = {10.3389/fmars.2021.619541},

issn = {2296-7745},

year  = {2021},

date = {2021-01-01},

urldate = {2021-03-04},

journal = {Frontiers in Marine Science},

volume = {8},

publisher = {Frontiers},

abstract = {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 modelling community and beyond.},

keywords = {3D visualizations, Ecopath with Ecosim, Environmental decision support systems, Immersive Visualizations, Information overload, serious gaming},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeek_using_2021,

title = {Using Gaming Technology to Explore and Visualize Management Impacts on Marine Ecosystems},

author = {Jeroen Steenbeek and Dalai Felinto and Mike Pan and Joe Buszowski and Villy Christensen},

url = {https://www.frontiersin.org/articles/10.3389/fmars.2021.619541/full},

doi = {10.3389/fmars.2021.619541},

issn = {2296-7745},

year  = {2021},

date = {2021-01-01},

urldate = {2021-03-04},

journal = {Frontiers in Marine Science},

volume = {8},

abstract = {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 modelling community and beyond.},

note = {Publisher: Frontiers},

keywords = {3D visualizations, Ecopath with Ecosim, Environmental decision support systems, Immersive Visualizations, Information overload, OceanViz, serious gaming},

pubstate = {published},

tppubtype = {article}

}

@article{puts_insights_2020b,

title = {Insights on integrating habitat preferences in process-oriented ecological models \textendash a case study of the southern North Sea},

author = {M. P\"{u}ts and M. Taylor and I. N\'{u}\~{n}ez-Riboni and J. Steenbeek and M. St\"{a}bler and C. M\"{o}llmann and A. Kempf},

url = {http://www.sciencedirect.com/science/article/pii/S030438002030260X},

doi = {10.1016/j.ecolmodel.2020.109189},

issn = {0304-3800},

year  = {2020},

date = {2020-09-01},

urldate = {2020-09-01},

journal = {Ecological Modelling},

volume = {431},

pages = {109189},

keywords = {Ecopath with Ecosim, Ecospace, Food web model, Habitat capacity, Spatial-temporal framework, species distribution model},

pubstate = {published},

tppubtype = {article}

}

@article{putsInsightsIntegratingHabitat2020,

title = {Insights on Integrating Habitat Preferences in Process-Oriented Ecological Models \textendash a Case Study of the Southern North Sea},

author = {Miriam P\"{u}ts and Marc Taylor and Ismael N\'{u}\~{n}ez-Riboni and Jeroen Steenbeek and Moritz St\"{a}bler and Christian M\"{o}llmann and Alexander Kempf},

doi = {10.1016/j.ecolmodel.2020.109189},

issn = {0304-3800},

year  = {2020},

date = {2020-09-01},

urldate = {2020-06-30},

journal = {Ecological Modelling},

volume = {431},

pages = {109189},

abstract = {One of the most applied tools to create ecosystem models to support management decisions in the light of ecosystem-based fisheries management is Ecopath with Ecosim (EwE). Recently, its spatial routine Ecospace has evolved due to the addition of the Habitat Foraging Capacity Model (HFCM), a spatial-temporal dynamic niche model to drive the foraging capacity to distribute biomass over model grid cells. The HFCM allows for continuous implementation of externally derived habitat preference maps based on single species distribution models. So far, guidelines are lacking on how to best define habitat preferences for inclusion in process-oriented trophic modeling studies. As one of the first studies, we applied the newest Ecospace development to an existing EwE model of the southern North Sea with the aim to identify which definition of habitat preference leads to the best model fit. Another key aim of our study was to test for the sensitivity of implementing externally derived habitat preference maps within Ecospace to different time-scales (seasonal, yearly, multi-year, and static). For this purpose, generalized additive models (GAM) were fit to scientific survey data using either presence/absence or abundance as differing criteria of habitat preference. Our results show that Ecospace runs using habitat preference maps based on presence/absence data compared best to empirical data. The optimal time-scale for habitat updating differed for biomass and catch, but implementing variable habitats was generally superior to a static habitat representation. Our study hence highlights the importance of a sigmoidal representation of habitat (e.g. presence/absence) and variable habitat preferences (e.g. multi-year) when combining species distribution models with an ecosystem model. It demonstrates that the interpretation of habitat preference can have a major influence on the model fit and outcome.},

keywords = {Ecopath with Ecosim, Ecospace, Food web model, Habitat capacity, Spatial-temporal framework, species distribution model},

pubstate = {published},

tppubtype = {article}

}

@article{vilas_effects_2020,

title = {The effects of marine protected areas on ecosystem recovery and fisheries using a comparative modelling approach},

author = {D. Vilas and M. Coll and X. Corrales and J. Steenbeek and C. Piroddi and A. Cal\`{o} and A. Di Franco and T. Font and P. Guidetti and A. Ligas and J. Lloret and G. Prato and R. Sahyoun and P. Sartor and J. Claudet},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aqc.3368},

doi = {10.1002/aqc.3368},

issn = {1099-0755},

year  = {2020},

date = {2020-08-14},

journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},

abstract = {The overexploitation of many marine resources and ecosystems calls for the development and implementation of measures to support their recovery and conservation. The potential contributions to support fisheries and ecosystem recovery were assessed at the local level of the three multiple-use marine protected areas (MPAs) of Cerb\`{e}re-Banyuls, Medes Islands, and Cap de Creus, located in the north-western Mediterranean Sea. For each MPA, a food-web model accounting for each protection level (PL) was developed: the fully protected area (FPA), the partially protected area (PPA) and the unprotected area (UPA) surrounding the MPA. Using the resulting nine food-web models, the ecosystem structure and functioning of each PL were compared and characterized, differences and similarities within and among the three MPAs were assessed, and ecosystem response to full protection was evaluated for the three MPAs. Differences in terms of ecosystem structure and functioning were found among PLs. Overall, FPAs presented the most positive effect of protection in terms of ecosystem structure and functioning, followed by PPAs. However, the effects of protection on neighbouring UPAs were hardly noticeable. Similarities between Cerb\`{e}re-Banyuls and Medes Islands MPAs were observed, while Cap de Creus MPA showed the least benefits from protection overall. These results are likely to be due to similarities in the configuration of the protected areas, the levels of enforcement and compliance, and the impact of recreational and small-scale fisheries allowed in the PPAs and UPAs. This study illustrates that well-enforced Mediterranean MPAs, even when small, can yield local positive impacts on the structure and functioning of marine ecosystems that can contribute to support local fisheries.},

keywords = {Ecopath with Ecosim, local study, Marine protected areas (MPA), NW Mediterranean},

pubstate = {published},

tppubtype = {article}

}

@article{puts_insights_2020,

title = {Insights on integrating habitat preferences in process-oriented ecological models \textendash a case study of the southern North Sea},

author = {M. P\"{u}ts and M. Taylor and I. N\'{u}\~{n}ez-Riboni and J. Steenbeek and M. St\"{a}bler and C. M\"{o}llmann and A. Kempf},

url = {http://www.sciencedirect.com/science/article/pii/S030438002030260X},

doi = {10.1016/j.ecolmodel.2020.109189},

issn = {0304-3800},

year  = {2020},

date = {2020-01-01},

urldate = {2020-06-30},

journal = {Ecological Modelling},

volume = {431},

pages = {109189},

abstract = {One of the most applied tools to create ecosystem models to support management decisions in the light of ecosystem-based fisheries management is Ecopath with Ecosim (EwE). Recently, its spatial routine Ecospace has evolved due to the addition of the Habitat Foraging Capacity Model (HFCM), a spatial-temporal dynamic niche model to drive the foraging capacity to distribute biomass over model grid cells. The HFCM allows for continuous implementation of externally derived habitat preference maps based on single species distribution models. So far, guidelines are lacking on how to best define habitat preferences for inclusion in process-oriented trophic modeling studies. As one of the first studies, we applied the newest Ecospace development to an existing EwE model of the southern North Sea with the aim to identify which definition of habitat preference leads to the best model fit. Another key aim of our study was to test for the sensitivity of implementing externally derived habitat preference maps within Ecospace to different time-scales (seasonal, yearly, multi-year, and static). For this purpose, generalized additive models (GAM) were fit to scientific survey data using either presence/absence or abundance as differing criteria of habitat preference. Our results show that Ecospace runs using habitat preference maps based on presence/absence data compared best to empirical data. The optimal time-scale for habitat updating differed for biomass and catch, but implementing variable habitats was generally superior to a static habitat representation. Our study hence highlights the importance of a sigmoidal representation of habitat (e.g. presence/absence) and variable habitat preferences (e.g. multi-year) when combining species distribution models with an ecosystem model. It demonstrates that the interpretation of habitat preference can have a major influence on the model fit and outcome.},

keywords = {Ecopath with Ecosim, Ecospace, food web, GIS, local study, niches, North Sea, species distributions},

pubstate = {published},

tppubtype = {article}

}

@article{vilas_effects_2020b,

title = {The effects of marine protected areas on ecosystem recovery and fisheries using a comparative modelling approach},

author = {D. Vilas and M. Coll and X. Corrales and J. Steenbeek and C. Piroddi and A. Cal\`{o} and A. Di Franco and T. Font and P. Guidetti and A. Ligas and J. Lloret and G. Prato and R. Sahyoun and P. Sartor and J. Claudet},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aqc.3368},

doi = {10.1002/aqc.3368},

issn = {1099-0755},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},

volume = {30},

number = {10},

pages = {1885--1901},

note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/aqc.3368},

keywords = {Ecopath with Ecosim, fully protected areas, Management units, north-west Mediterranean Sea, partially protected areas, protection levels},

pubstate = {published},

tppubtype = {article}

}

@article{shannon_exploring_2020,

title = {Exploring temporal variability in the Southern Benguela ecosystem over the past four decades using a time-dynamic ecosystem model},

author = {L. J. Shannon and K. Ortega-Cisneros and T. Lamont and H. Winker and R. Crawford and A. Jarre and M. Coll},

doi = {10.3389/fmars.2020.00540},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

note = {Publisher: Frontiers Media},

keywords = {Ecopath with Ecosim, Southern benguela},

pubstate = {published},

tppubtype = {article}

}

@article{vilasEffectsMarineProtected2020,

title = {The Effects of Marine Protected Areas on Ecosystem Recovery and Fisheries Using a Comparative Modelling Approach},

author = {Daniel Vilas and Marta Coll and Xavier Corrales and Jeroen Steenbeek and Chiara Piroddi and Antonio Cal\`{o} and Antonio Di Franco and Toni Font and Paolo Guidetti and Alessandro Ligas and Josep Lloret and Giulia Prato and Rita Sahyoun and Paolo Sartor and Joachim Claudet},

doi = {10.1002/aqc.3368},

issn = {1099-0755},

year  = {2020},

date = {2020-01-01},

urldate = {2020-10-07},

journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},

volume = {30},

number = {10},

pages = {1885\textendash1901},

abstract = {The overexploitation of many marine resources and ecosystems calls for the development and implementation of measures to support their recovery and conservation. The potential contributions to support fisheries and ecosystem recovery were assessed at the local level of the three multiple-use marine protected areas (MPAs) of Cerb\`{e}re-Banyuls, Medes Islands, and Cap de Creus, located in the north-western Mediterranean Sea. For each MPA, a food-web model accounting for each protection level (PL) was developed: the fully protected area (FPA), the partially protected area (PPA) and the unprotected area (UPA) surrounding the MPA. Using the resulting nine food-web models, the ecosystem structure and functioning of each PL were compared and characterized, differences and similarities within and among the three MPAs were assessed, and ecosystem response to full protection was evaluated for the three MPAs. Differences in terms of ecosystem structure and functioning were found among PLs. Overall, FPAs presented the most positive effect of protection in terms of ecosystem structure and functioning, followed by PPAs. However, the effects of protection on neighbouring UPAs were hardly noticeable. Similarities between Cerb\`{e}re-Banyuls and Medes Islands MPAs were observed, while Cap de Creus MPA showed the least benefits from protection overall. These results are likely to be due to similarities in the configuration of the protected areas, the levels of enforcement and compliance, and the impact of recreational and small-scale fisheries allowed in the PPAs and UPAs. This study illustrates that well-enforced Mediterranean MPAs, even when small, can yield local positive impacts on the structure and functioning of marine ecosystems that can contribute to support local fisheries.},

keywords = {Ecopath with Ecosim, fully protected areas, Management units, north-west Mediterranean Sea, partially protected areas, protection levels},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeek_ecosampler:_2018,

title = {Ecosampler: A new approach to assessing parameter uncertainty in Ecopath with Ecosim},

author = {J. Steenbeek and X. Corrales and M. Platts and M. Coll},

url = {http://www.sciencedirect.com/science/article/pii/S2352711018300803},

doi = {10.1016/j.softx.2018.06.004},

issn = {2352-7110},

year  = {2018},

date = {2018-01-01},

urldate = {2018-07-13},

journal = {SoftwareX},

volume = {7},

number = {C},

pages = {198--204},

abstract = {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 \textendash alternate mass-balanced parameter sets for a food web model \textendash 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\textendashtemporal module Ecospace, and plug-ins such as Ecological Network Analysis, Value Chain, and Ecological Indicators.},

keywords = {Ecopath with Ecosim, Ecosampler, input parameter sensitivity},

pubstate = {published},

tppubtype = {article}

}

@article{tierney_modelling_2018,

title = {Modelling marine trophic transfer of radiocarbon (14C) from a nuclear facility},

author = {K. M. Tierney and J. J. Heymans and G. K. P. Muir and G. T. Cook and J. Buszowski and J. Steenbeek and W. J. Walters and V. Christensen and G. MacKinnon and A. J. A. Howe and S. Xu},

url = {https://www.sciencedirect.com/science/article/pii/S1364815217306163},

doi = {10.1016/j.envsoft.2018.01.013},

issn = {1364-8152},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Environmental Modelling \& Software},

volume = {102},

pages = {138--154},

abstract = {Sellafield marine discharges of 14C are the largest contributor to the global collective dose from the nuclear fuel industry. As such, it is important to understand the fate of these discharges beyond the limitations and scope of empirical analytical investigations for this highly mobile radioactive contaminant. Ecopath with Ecosim (EwE) is widely used to model anthropogenic impacts on ecosystems, such as fishing, although very few EwE studies have modelled the fate of bioavailable contaminants. This work presents, for the first time, a spatial-temporal 14C model utilising recent developments in EwE software to predict the ecological fate of anthropogenic 14C in the marine environment. The model predicted observed trends in 14C activities between different species and through time. It also provided evidence for the integration of Sellafield 14C in species at higher trophic levels through time.},

keywords = {Ecopath with Ecosim, Ecotracer, local study, Radioactive discharges, Radiocarbon (14C), Sellafield},

pubstate = {published},

tppubtype = {article}

}

@article{bornatowski_ecological_2018b,

title = {Ecological role and historical trends of large pelagic predators in a subtropical marine ecosystem of the South Atlantic},

author = {H. Bornatowski and R. Angelini and M. Coll and R. P. Barreto and A. F. Amorim},

doi = {DOI 10.1007/s11160-017-9492-z},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Reviews in Fish Biology and Fisheries},

volume = {28},

pages = {241--259},

keywords = {Ecopath with Ecosim, large pelagic predators, South Atlantic},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeekEcosamplerNewApproach2018,

title = {Ecosampler: A New Approach to Assessing Parameter Uncertainty in Ecopath with Ecosim},

author = {Jeroen Steenbeek and Xavier Corrales and Mark Platts and Marta Coll},

doi = {10.1016/j.softx.2018.06.004},

issn = {2352-7110},

year  = {2018},

date = {2018-01-01},

urldate = {2018-07-13},

journal = {SoftwareX},

volume = {7},

number = {C},

pages = {198\textendash204},

abstract = {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 \textendash~alternate mass-balanced parameter sets for a food web model \textendash~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\textendashtemporal module Ecospace, and plug-ins such as Ecological Network Analysis, Value Chain, and Ecological Indicators.},

keywords = {ecological modelling, Ecopath with Ecosim, Ecosampler, input parameter sensitivity},

pubstate = {published},

tppubtype = {article}

}

@article{coll_standardized_2017b,

title = {Standardized ecological indicators to assess aquatic food webs: The ECOIND software plug-in for Ecopath with Ecosim models},

author = {M. Coll and J. Steenbeek},

url = {http://www.sciencedirect.com/science/article/pii/S1364815216311173},

doi = {10.1016/j.envsoft.2016.12.004},

issn = {1364-8152},

year  = {2017},

date = {2017-03-01},

urldate = {2017-01-03},

journal = {Environmental Modelling \& Software},

volume = {89},

pages = {120--130},

keywords = {Ecological standardized indicators, Ecopath with Ecosim, Ecospace, Environmental status, Food web models, Software plug-in},

pubstate = {published},

tppubtype = {article}

}

@article{coll_standardized_2017,

title = {Standardized ecological indicators to assess aquatic food webs: The ECOIND software plug-in for Ecopath with Ecosim models},

author = {M. Coll and J. Steenbeek},

url = {http://www.sciencedirect.com/science/article/pii/S1364815216311173},

doi = {10.1016/j.envsoft.2016.12.004},

issn = {1364-8152},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-03},

journal = {Environmental Modelling \& Software},

volume = {89},

pages = {120--130},

abstract = {Ecological indicators are useful tools to analyse and communicate historical changes in ecosystems and plausible future scenarios while evaluating environmental status. Here we introduce a new plug-in to the Ecopath with Ecosim (EwE) food web modelling approach, which is widely used to quantitatively describe aquatic ecosystems. The plug-in (ECOIND) calculates standardized ecological indicators. We describe the primary functionality of ECOIND and provide an example of its application in both static and temporal-spatial dynamic modelling, while we highlight several related features including a new taxonomy input database (species traits) and the ability to analyse input uncertainty on output results. ECOIND adds new capabilities to the widely used EwE food web modelling approach and enables broadening its applications into biodiversity and conservation-based frameworks to contribute to integrated ecosystem analyses.},

keywords = {Ecopath with Ecosim, food web, software development, standardized ecological indicators},

pubstate = {published},

tppubtype = {article}

}

@article{collStandardizedEcologicalIndicators2017,

title = {Standardized Ecological Indicators to Assess Aquatic Food Webs: The ECOIND Software Plug-in for Ecopath with Ecosim Models},

author = {M Coll and J Steenbeek},

year  = {2017},

date = {2017-01-01},

journal = {Environmental Modelling and Software},

volume = {89},

pages = {120\textendash130},

keywords = {Ecological standardized indicators, Ecopath with Ecosim, Ecospace, Environmental status, Food web models, Software plug-in},

pubstate = {published},

tppubtype = {article}

}

@article{heymans_best_2016,

title = {Best practice in Ecopath with Ecosim food-web models for ecosystem-based management},

author = {J. J. Heymans and M. Coll and J. S. Link and S. Mackinson and J. Steenbeek and C. J. Walters and V. Christensen},

doi = {10.1016/j.ecolmodel.2015.12.007},

year  = {2016},

date = {2016-07-10},

urldate = {2016-07-10},

journal = {Ecological Modelling},

volume = {331},

pages = {173 -184},

abstract = {Ecopath with Ecosim (EwE) models are easier to construct and use compared to most other ecosystem modelling techniques and are therefore more widely used by more scientists and managers. This, however, creates a problem with quality assurance; to address this we provide an overview of best practices for creating Ecopath models. We describe the diagnostics that can be used to check for thermodynamic and ecological principles, and highlight principles that should be used for balancing a model. We then highlight the pitfalls when comparing Ecopath models using Ecological Network Analysis indices. For dynamic simulations in Ecosim we show the state of the art in calibrating the model by fitting it to time series using a formal fitting procedure and statistical goodness of fit. Finally, we show how Monte Carlo simulations can be used to address uncertainty in input parameters, and we discuss the use of models in a management context, specifically using the concept of ‘key runs’ for ecosystem-based management. This novel list of best practices for EwE models will enable ecosystem managers to evaluate the goodness of fit of the given EwE model to the ecosystem management question.},

keywords = {best practices, EBM, Ecopath with Ecosim},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeek_ecopath_2016,

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

author = {J. Steenbeek and J. Buszowski and V. Christensen and E. Akoglu and K. Aydin and N. Ellis and D. Felinto and J. Guitton and S. Lucey and K. Kearney and S. Mackinson and M. Pan and M. Platts and C. J. Walters},

url = {http://www.sciencedirect.com/science/article/pii/S030438001500280X},

doi = {doi:10.1016/j.ecolmodel.2015.06.031},

issn = {0304-3800},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Ecological Modelling},

volume = {319},

pages = {178--189},

abstract = {Ecopath with Ecosim (EwE) is a widely applied food web model that is mostly known as desktop software for the Microsoft Windows platform. The freely available Microsoft .NET source code of EwE, however, provides a range of possibilities to use the model in different ways, to customize and extend the model, and to execute the model on different operating systems. We provide an overview of the EwE source code, its philosophy, and its technical capabilities, targeted to model builders and advanced users of the EwE software. We showcase novel scientific applications of the EwE model that have been facilitated because of the modular approach of the system. We also present three additional versions of EwE that have been written in different computer languages for dedicated purposes. Lastly, we provide an entry point for users for obtaining and using the source code for custom purposes.},

keywords = {Ecopath with Ecosim, ecosystem, fisheries, food web, model interoperability, software development},

pubstate = {published},

tppubtype = {article}

}

@article{scott_stepwise_2016,

title = {A Stepwise Fitting Procedure for automated fitting of Ecopath with Ecosim models},

author = {E. Scott and N. Serpetti and J. Steenbeek and J. J. Heymans},

url = {http://www.sciencedirect.com/science/article/pii/S2352711016000054},

doi = {10.1016/j.softx.2016.02.002},

issn = {2352-7110},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {SoftwareX},

volume = {5},

pages = {25--30},

abstract = {The Stepwise Fitting Procedure automates testing of alternative hypotheses used for fitting Ecopath with Ecosim (EwE) models to observation reference data (Mackinson et al. 2009). The calibration of EwE model predictions to observed data is important to evaluate any model that will be used for ecosystem based management. Thus far, the model fitting procedure in EwE has been carried out manually: a repetitive task involving setting \> 1000 specific individual searches to find the statistically ‘best fit’ model. The novel fitting procedure automates the manual procedure therefore producing accurate results and lets the modeller concentrate on investigating the ‘best fit’ model for ecological accuracy.},

keywords = {Ecopath with Ecosim, model fitting, software development},

pubstate = {published},

tppubtype = {article}

}

@article{villasante_modelling_2016,

title = {Modelling marine ecosystems using the Ecopath with Ecosim food web approach: New insights to address complex dynamics after 30 years of developments},

author = {S. Villasante and F. Arregu\'{i}n-S\'{a}nchez and J. J. Heymans and S. Libralato and C. Piroddi and V. Christensen and M. Coll},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Ecological Modelling},

volume = {331},

pages = {1--4},

keywords = {Ecopath with Ecosim},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeek_ecopath_2016b,

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

author = {J. Steenbeek and J. Buszowski and V. Christensen and E. Akoglu and K. Aydin and N. Ellis and D. Felinto and J. Guitton and S. Lucey and K. Kearney and S. Mackinson and M. Pan and M. Platts and C. J. Walters},

url = {http://www.sciencedirect.com/science/article/pii/S030438001500280X},

doi = {10.1016/j.ecolmodel.2015.06.031},

issn = {0304-3800},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Ecological Modelling},

volume = {319},

pages = {178--189},

keywords = {Ecopath with Ecosim, ecosystem, fisheries, Food web model, model interoperability, Open source software},

pubstate = {published},

tppubtype = {article}

}

@article{scottStepwiseFittingProcedure2016,

title = {A Stepwise Fitting Procedure for Automated Fitting of Ecopath with Ecosim Models},

author = {Erin Scott and Natalia Serpetti and Jeroen Steenbeek and Johanna Jacomina Heymans},

doi = {10.1016/j.softx.2016.02.002},

issn = {2352-7110},

year  = {2016},

date = {2016-01-01},

journal = {SoftwareX},

volume = {5},

pages = {25\textendash30},

abstract = {The Stepwise Fitting Procedure automates testing of alternative hypotheses used for fitting Ecopath with Ecosim (EwE) models to observation reference data (Mackinson et~al. 2009). The calibration of EwE model predictions to observed data is important to evaluate any model that will be used for ecosystem based management. Thus far, the model fitting procedure in EwE has been carried out manually: a repetitive task involving setting \> 1000 specific individual searches to find the statistically `best fit' model. The novel fitting procedure automates the manual procedure therefore producing accurate results and lets the modeller concentrate on investigating the `best fit' model for ecological accuracy.},

keywords = {ecological modelling, Ecopath with Ecosim, model fitting, Stepwise model fitting procedure},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeekEcopathEcosimModelbuilding2016,

title = {Ecopath with Ecosim as a Model-Building Toolbox: Source Code Capabilities, Extensions, and Variations},

author = {Jeroen Steenbeek and Joe Buszowski and Villy Christensen and Ekin Akoglu and Kerim Aydin and Nick Ellis and Dalai Felinto and Jerome Guitton and Sean Lucey and Kelly Kearney and Steven Mackinson and Mike Pan and Mark Platts and Carl Walters},

doi = {10.1016/j.ecolmodel.2015.06.031},

issn = {0304-3800},

year  = {2016},

date = {2016-01-01},

urldate = {2015-09-09},

journal = {Ecological Modelling},

volume = {319},

pages = {178\textendash189},

abstract = {Ecopath with Ecosim (EwE) is a widely applied food web model that is mostly known as desktop software for the Microsoft Windows platform. The freely available Microsoft .NET source code of EwE, however, provides a range of possibilities to use the model in different ways, to customize and extend the model, and to execute the model on different operating systems. We provide an overview of the EwE source code, its philosophy, and its technical capabilities, targeted to model builders and advanced users of the EwE software. We showcase novel scientific applications of the EwE model that have been facilitated because of the modular approach of the system. We also present three additional versions of EwE that have been written in different computer languages for dedicated purposes. Lastly, we provide an entry point for users for obtaining and using the source code for custom purposes.},

keywords = {Ecopath with Ecosim, ecosystem, fisheries, Food web model, model interoperability, Open source software},

pubstate = {published},

tppubtype = {article}

}

@article{fouzai_fishing_2012,

title = {Fishing management scenarios to rebuild exploited resources and ecosystems of the Northern-Central Adriatic (Mediterranean Sea)},

author = {N. Fouzai and M. Coll and I. Palomera and A. Santojanni and E. Arneri and V. Christensen},

url = {http://www.sciencedirect.com/science/article/pii/S0924796312001169},

doi = {10.1016/j.jmarsys.2012.05.003},

issn = {0924-7963},

year  = {2012},

date = {2012-01-01},

urldate = {2012-06-03},

journal = {Journal of Marine Systems},

volume = {102-104},

pages = {39--51},

abstract = {We examined various fishing management options to recover exploited marine resources and ecosystems of the Northern-Central Adriatic Sea. Dynamic simulations were based on a spatial ecological model previously calibrated with time series of data. Scenarios regarding spatial management were evaluated with the establishment of two marine protected areas, respectively, in the Pomo pit and the northern region. In addition, three temporal simulations of temporary closures and overall reduction of fishing effort of demersal and pelagic fleets (bottom, mid-water trawls and purse seines) were also considered. Simulations were run for 45\ years (1975\textendash2020), including the calibration period (1975\textendash2002), and changes in biomass and catch of marine resources were analyzed. Our results confirm that current fishing management in the Adriatic Sea does not have clear beneficial impacts for the recovery of exploited resources, which will remain depleted in 2020 if “business as usual” continues. Simulations of alternative management suggest that both protected areas could be beneficial for fish population recovery predicting an increase in the biomass of commercial fish and predatory organisms. Simulations of temporary closures and overall reduction of fishing effort also show significant benefits for several commercial resources. We argue that both management measures may be effective tools to recover exploited ecosystems of the Northern-Central Adriatic Sea and halt the decline of marine resources.},

keywords = {Adriatic Sea, Ecopath with Ecosim, Ecospace, fisheries management, Marine protected areas (MPA), trophic ecology},

pubstate = {published},

tppubtype = {article}

}

@article{fouzaiFishingManagementScenarios2012,

title = {Fishing Management Scenarios to Rebuild Exploited Resources and Ecosystems of the Northern-Central Adriatic (Mediterranean Sea)},

author = {N. Fouzai and M. Coll and I. Palomera and A. Santojanni and E. Arneri and V. Christensen},

doi = {10.1016/j.jmarsys.2012.05.003},

issn = {0924-7963},

year  = {2012},

date = {2012-01-01},

urldate = {2012-06-03},

journal = {Journal of Marine Systems},

volume = {102\textendash104},

pages = {39\textendash51},

abstract = {We examined various fishing management options to recover exploited marine resources and ecosystems of the Northern-Central Adriatic Sea. Dynamic simulations were based on a spatial ecological model previously calibrated with time series of data. Scenarios regarding spatial management were evaluated with the establishment of two marine protected areas, respectively, in the Pomo pit and the northern region. In addition, three temporal simulations of temporary closures and overall reduction of fishing effort of demersal and pelagic fleets (bottom, mid-water trawls and purse seines) were also considered. Simulations were run for 45\ years (1975\textendash2020), including the calibration period (1975\textendash2002), and changes in biomass and catch of marine resources were analyzed. Our results confirm that current fishing management in the Adriatic Sea does not have clear beneficial impacts for the recovery of exploited resources, which will remain depleted in 2020 if ``business as usual'' continues. Simulations of alternative management suggest that both protected areas could be beneficial for fish population recovery predicting an increase in the biomass of commercial fish and predatory organisms. Simulations of temporary closures and overall reduction of fishing effort also show significant benefits for several commercial resources. We argue that both management measures may be effective tools to recover exploited ecosystems of the Northern-Central Adriatic Sea and halt the decline of marine resources.},

keywords = {Ecopath with Ecosim, Ecospace, fisheries management, Marine protected areas (MPA), Northern-Central Adriatic Sea, Trophic models},

pubstate = {published},

tppubtype = {article}

}