@article{vilasEvaluatingRedTide2023,

title = {Evaluating Red Tide Effects on the West Florida Shelf Using a Spatiotemporal Ecosystem Modeling Framework},

author = {Daniel Vilas and Joe Buszowski and Skyler Sagarese and Jeroen Steenbeek and Zach Siders and David Chagaris},

year  = {2023},

date = {2023-01-01},

urldate = {2024-01-18},

journal = {Scientific Reports},

volume = {13},

number = {1},

pages = {2541},

publisher = {Nature Publishing Group UK London},

keywords = {Community ecology, ecological modelling, Ecosystem ecology, ecosystem services, Environmental impact, Marine biology, Population dynamics},

pubstate = {published},

tppubtype = {article}

}

@article{piroddi_modelling_2022,

title = {Modelling the Mediterranean Sea ecosystem at high spatial resolution to inform the ecosystem-based management in the region},

author = {Chiara Piroddi and Marta Coll and Diego Macias and Jeroen Steenbeek and Elisa Garcia-Gorriz and Alessandro Mannini and Daniel Vilas and Villy Christensen},

url = {https://www.nature.com/articles/s41598-022-18017-x},

doi = {10.1038/s41598-022-18017-x},

issn = {2045-2322},

year  = {2022},

date = {2022-11-01},

urldate = {2022-11-19},

journal = {Scientific Reports},

volume = {12},

number = {1},

pages = {19680},

abstract = {Cumulative pressures are rapidly expanding in the Mediterranean Sea with consequences for marine biodiversity and marine resources, and the services they provide. Policy makers urge for a marine ecosystem assessment of the region in space and time. This study evaluates how the whole Mediterranean food web may have responded to historical changes in the climate, environment and fisheries, through the use of an ecosystem modelling over a long time span (decades) at high spatial resolution (8 × 8 km), to inform regional and sub-regional management. Results indicate coastal and shelf areas to be the sites with highest marine biodiversity and marine resources biomass, which decrease towards the south-eastern regions. High levels of total catches and discards are predicted to be concentrated in the Western sub-basin and the Adriatic Sea. Mean spatial\textendashtemporal changes of total and commercial biomass show increases in offshore waters of the region, while biodiversity indicators show marginal changes. Total catches and discards increase greatly in offshore waters of the Western and Eastern sub-basins. Spatial patterns and temporal mean changes of marine biodiversity, community biomasses and trophic indices, assessed in this study, aim at identifying areas and food web components that show signs of deterioration with the overall goal of assisting policy makers in designing and implementing spatial management actions for the region.},

note = {Number: 1 

Publisher: Nature Publishing Group},

keywords = {Climate sciences, ecological modelling, Ecology, Environmental impact, Ocean sciences, Zoology},

pubstate = {published},

tppubtype = {article}

}

@article{piroddiModellingMediterraneanSea2022,

title = {Modelling the Mediterranean Sea Ecosystem at High Spatial Resolution to Inform the Ecosystem-Based Management in the Region},

author = {Chiara Piroddi and Marta Coll and Diego Macias and Jeroen Steenbeek and Elisa Garcia-Gorriz and Alessandro Mannini and Daniel Vilas and Villy Christensen},

doi = {10.1038/s41598-022-18017-x},

issn = {2045-2322},

year  = {2022},

date = {2022-11-01},

urldate = {2024-01-18},

journal = {Scientific Reports},

volume = {12},

number = {1},

pages = {19680},

publisher = {Nature Publishing Group},

abstract = {Cumulative pressures are rapidly expanding in the Mediterranean Sea with consequences for marine biodiversity and marine resources, and the services they provide. Policy makers urge for a marine ecosystem assessment of the region in space and time. This study evaluates how the whole Mediterranean food web may have responded to historical changes in the climate, environment and fisheries, through the use of an ecosystem modelling over a long time span (decades) at high spatial resolution (8,×,8~km), to inform regional and sub-regional management. Results indicate coastal and shelf areas to be the sites with highest marine biodiversity and marine resources biomass, which decrease towards the south-eastern regions. High levels of total catches and discards are predicted to be concentrated in the Western sub-basin and the Adriatic Sea. Mean spatial\textendashtemporal changes of total and commercial biomass show increases in offshore waters of the region, while biodiversity indicators show marginal changes. Total catches and discards increase greatly in offshore waters of the Western and Eastern sub-basins. Spatial patterns and temporal mean changes of marine biodiversity, community biomasses and trophic indices, assessed in this study, aim at identifying areas and food web components that show signs of deterioration with the overall goal of assisting policy makers in designing and implementing spatial management actions for the region.},

keywords = {Climate sciences, ecological modelling, Ecology, Environmental impact, Ocean sciences, Zoology},

pubstate = {published},

tppubtype = {article}

}

@article{tittensor_next-generation_2021,

title = {Next-generation ensemble projections reveal higher climate risks for marine ecosystems},

author = {D. P. Tittensor and C. Novaglio and C. S. Harrison and R. F. Heneghan and N. Barrier and D. Bianchi and L. Bopp and A. Bryndum-Buchholz and G. L. Britten and M. B\"{u}chner and W. W. L. Cheung and V. Christensen and M. Coll and J. P. Dunne and T. D. Eddy and J. D. Everett and J. A. Fernandes-Salvador and E. A. Fulton and E. D. Galbraith and D. Gascuel and J. Guiet and J. G. John and J. S. Link and H. K. Lotze and O. Maury and K. Ortega-Cisneros and J. Palacios-Abrantes and C. Petrik and H. Pontavice and J. Rault and A. J. Richardson and L. J. Shannon and Y-J Shin and J. Steenbeek and C. A. Stock and J. L. Blanchard},

url = {https://www.nature.com/articles/s41558-021-01173-9},

doi = {10.1038/s41558-021-01173-9},

issn = {1758-6798},

year  = {2021},

date = {2021-10-01},

urldate = {2021-10-01},

journal = {Nature Climate Change},

pages = {1--9},

note = {Bandiera_abtest: a Cc_license_type: cc_by Cg_type: Nature Research Journals Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Climate-change ecology;Ecological modelling;Marine biology Subject_term_id: climate-change-ecology;ecological-modelling;marine-biology},

keywords = {Climate-change ecology, ecological modelling, EcoOcean, Marine biology},

pubstate = {published},

tppubtype = {article}

}

@article{tittensorNextgenerationEnsembleProjections2021,

title = {Next-Generation Ensemble Projections Reveal Higher Climate Risks for Marine Ecosystems},

author = {Derek P. Tittensor and Camilla Novaglio and Cheryl S. Harrison and Ryan F. Heneghan and Nicolas Barrier and Daniele Bianchi and Laurent Bopp and Andrea Bryndum-Buchholz and Gregory L. Britten and Matthias B\"{u}chner and William W. L. Cheung and Villy Christensen and Marta Coll and John P. Dunne and Tyler D. Eddy and Jason D. Everett and Jose A. Fernandes-Salvador and Elizabeth A. Fulton and Eric D. Galbraith and Didier Gascuel and Jerome Guiet and Jasmin G. John and Jason S. Link and Heike K. Lotze and Olivier Maury and Kelly Ortega-Cisneros and Juliano Palacios-Abrantes and Colleen M. Petrik and Hubert Pontavice and Jonathan Rault and Anthony J. Richardson and Lynne Shannon and Yunne-Jai Shin and Jeroen Steenbeek and Charles A. Stock and Julia L. Blanchard},

doi = {10.1038/s41558-021-01173-9},

issn = {1758-6798},

year  = {2021},

date = {2021-10-01},

urldate = {2021-10-26},

journal = {Nature Climate Change},

pages = {1\textendash9},

publisher = {Nature Publishing Group},

abstract = {Projections of climate change impacts on marine ecosystems have revealed long-term declines in global marine animal biomass and unevenly distributed impacts on fisheries. Here we apply an enhanced suite of global marine ecosystem models from the Fisheries and Marine Ecosystem Model Intercomparison Project (Fish-MIP), forced by new-generation Earth system model outputs from Phase 6 of the Coupled Model Intercomparison Project (CMIP6), to provide insights into how projected climate change will affect future ocean ecosystems. Compared with the previous generation CMIP5-forced Fish-MIP ensemble, the new ensemble ecosystem simulations show a greater decline in mean global ocean animal biomass under both strong-mitigation and high-emissions scenarios due to elevated warming, despite greater uncertainty in net primary production in the high-emissions scenario. Regional shifts in the direction of biomass changes highlight the continued and urgent need to reduce uncertainty in the projected responses of marine ecosystems to climate change to help support adaptation planning.},

keywords = {Climate-change ecology, ecological modelling, Marine biology},

pubstate = {published},

tppubtype = {article}

}

@article{piroddi_effects_2021,

title = {Effects of Nutrient Management Scenarios on Marine Food Webs: A Pan-European Assessment in Support of the Marine Strategy Framework Directive},

author = {C. Piroddi and E. Akoglu and E. Andonegi and J. W. Bentley and I. Celi\'{c} and M. Coll and D. Dimarchopoulou and R. Friedland and K. de Mutsert and R. Girardin and E. Garcia-Gorriz and B. Grizzetti and P. -Y. Hernvann and J. J. Heymans and B. M\"{u}ller-Karulis and S. Libralato and C. P. Lynam and D. Macias and S. Miladinova and F. Moullec and A. Palialexis and O. Parn and N. Serpetti and C. Solidoro and J. Steenbeek and A. Stips and M. Tomczak and M. Travers-Trolet and A. C. Tsikliras},

url = {https://www.frontiersin.org/articles/10.3389/fmars.2021.596797/full},

doi = {10.3389/fmars.2021.596797},

issn = {2296-7745},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Frontiers in Marine Science},

volume = {8},

note = {Publisher: Frontiers},

keywords = {criteria, Ecological Indicators, ecological modelling, higher trophic level modelling, Hydrodynamic and biogeochemical modelling, hydrological modelling, policy support},

pubstate = {published},

tppubtype = {article}

}

@article{piroddiEffectsNutrientManagement2021,

title = {Effects of Nutrient Management Scenarios on Marine Food Webs: A Pan-European Assessment in Support of the Marine Strategy Framework Directive},

author = {Chiara Piroddi and Ekin Akoglu and Eider Andonegi and Jacob W. Bentley and Igor Celi\'{c} and Marta Coll and Donna Dimarchopoulou and Ren\'{e} Friedland and Kim Mutsert and Raphael Girardin and Elisa Garcia-Gorriz and Bruna Grizzetti and P. -Y. Hernvann and Johanna J. Heymans and B\"{a}rbel M\"{u}ller-Karulis and Simone Libralato and Christopher P. Lynam and Diego Macias and Svetla Miladinova and Fabien Moullec and Andreas Palialexis and Ove Parn and Natalia Serpetti and Cosimo Solidoro and Jeroen Steenbeek and Adolf Stips and Maciej T. Tomczak and Morgane Travers-Trolet and Athanassios C. Tsikliras},

doi = {10.3389/fmars.2021.596797},

issn = {2296-7745},

year  = {2021},

date = {2021-01-01},

urldate = {2021-06-11},

journal = {Frontiers in Marine Science},

volume = {8},

publisher = {Frontiers},

abstract = {Eutrophication is one of the most important anthropogenic pressures impacting our seas. In Europe, several legislations and management measures have been implemented to halt nutrient overloading in marine ecosystems. This study evaluates the impact of freshwater nutrient control measures on higher trophic levels (HTL) in European marine ecosystems following descriptors and criteria as defined by the Marine Strategy Framework Directive (MSFD). We used a novel pan-European marine modeling ensemble of fourteen HTL models, covering almost all the EU seas. Results from our projections suggest that nutrient reduction measures would not have a significant impact on the structure and function of European marine ecosystems. Among the assessed criteria, the spawning stock biomass of commercially important fish stocks and the biomass of small pelagic fishes would be the most impacted, albeit with values lower than 2.5%. For the other criteria/indicators, such as species diversity and trophic level indicators, the impact was even lower. The Black Sea and the North-East Atlantic were the most negatively impacted regions, while the Baltic Sea was the only region showing signs of improvement. Coastal and shelf areas were more sensitive to environmental changes than large regional and sub-regional ecosystems that also include open seas. This is the first pan-European multi-model comparison study used to assess the impacts of land-based measures on marine and coastal European ecosystems through a set of selected ecological indicators. Since anthropogenic pressures are expanding apace in the marine environment and since policy makers need to use rapid and effective policy measures for fast-changing environments, this modeling framework is an essential asset in supporting and guiding EU policy needs and decisions.},

keywords = {criteria, Ecological Indicators, ecological modelling, higher trophic level modelling, Hydrodynamic and biogeochemical modelling, hydrological modelling, policy support},

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{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}

}