@article {4390, title = {Mussels or tunicates: That is the question. Evaluating efficient and sustainable resource use by low-trophic species in aquaculture settings}, journal = {Journal of Cleaner Production}, volume = {231}, year = {2019}, month = {Jan-09-2019}, pages = {132 - 143}, issn = {09596526}, doi = {10.1016/j.jclepro.2019.05.173}, author = {Filgueira, Ram{\'o}n and Strople, Leah C. and Strohmeier, Tore and Rastrick, Samuel and Strand, {\O}ivind} } @article {4389, title = {The effect of environmental conditions on Atlantic salmon smolts{\textquoteright} (Salmo salar) bioenergetic requirements and migration through an inland sea}, journal = {Environmental Biology of Fishes}, volume = {101}, year = {2018}, month = {Jan-10-2018}, pages = {1467 - 1482}, issn = {0378-1909}, doi = {10.1007/s10641-018-0792-5}, url = {http://link.springer.com/10.1007/s10641-018-0792-5http://link.springer.com/content/pdf/10.1007/s10641-018-0792-5.pdfhttp://link.springer.com/article/10.1007/s10641-018-0792-5/fulltext.htmlhttp://link.springer.com/content/pdf/10.1007/s10641-018-0792-5.pdf}, author = {Strople, Leah C. and Filgueira, Ram{\'o}n and Hatcher, Bruce G. and Denny, Shelley and Bordeleau, Xavier and Whoriskey, Frederick G. and Crossin, Glenn T.} } @article {4402, title = {Shifts in wind energy potential following land-use driven vegetation dynamics in complex terrain}, journal = {Science of The Total Environment}, volume = {639}, year = {2018}, month = {Jan-10-2018}, pages = {374 - 384}, abstract = {

Many mountainous regions with high wind energy potential are characterized by multi-scale variabilities of vegetation in both spatial and time dimensions, which strongly affect the spatial distribution of wind resource and its time evolution. To this end, we developed a coupled interdisciplinary modeling framework capable of assessing the shifts in wind energy potential following land-use driven vegetation dynamics in complex mountain terrain. It was applied to a case study area in the Romanian Carpathians. The results show that the overall shifts in wind energy potential following the changes of vegetation pattern due to different land-use policies can be dramatic. This suggests that the planning of wind energy project should be integrated with the land-use planning at a specific site to ensure that the expected energy production of the planned wind farm can be reached over its entire lifetime. Moreover, the changes in the spatial distribution of wind and turbulence under different scenarios of land-use are complex, and they must be taken into account in the micro-siting of wind turbines to maximize wind energy production and minimize fatigue loads (and associated maintenance costs). The proposed new modeling framework offers, for the first time, a powerful tool for assessing long-term variability in local wind energy potential that emerges from land-use change driven vegetation dynamics over complex terrain. Following a previously unexplored pathway of cause-effect relationships, it demonstrates a new linkage of agro- and forest policies in landscape development with an ultimate trade-off between renewable energy production and biodiversity targets. Moreover, it can be extended to study the potential effects of micro-climatic changes associated with wind farms on vegetation development (growth and patterning), which could in turn have a long-term feedback effect on wind resource distribution in mountainous regions.

}, issn = {00489697}, doi = {10.1016/j.scitotenv.2018.05.083}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969718317182https://api.elsevier.com/content/article/PII:S0048969718317182?httpAccept=text/xmlhttps://api.elsevier.com/content/article/PII:S0048969718317182?httpAccept=text/plain}, author = {Fang, Jiannong and Peringer, Alexander and Stupariu, Mihai-Sorin and P{\u a}tru-Stupariu, Ileana and Buttler, Alexandre and Golay, Francois and Port{\'e}-Agel, Fernando} } @mastersthesis {4388, title = {Using an individual based model to evaluate the effects of climate change on the reproductive phenology of eelgrass (Zostera marina L.) along a latitudinal gradient (master{\textquoteright}s thesis).}, volume = {Master of Science}, year = {2017}, pages = {253}, abstract = {

I explored the effects of climate change on the reproductive biology of the clonal
marine angiosperm Zostera marina L. (eelgrass) using an individual-based model.
The model captures whole plant ontogeny, morphology, and ecophysiology from seed
to reproductive adult to simulate the plasticity of eelgrass in response to
environmental variables. Using a latitudinal gradient as a proxy for climate change,
virtual seeding experiments were performed in three locations along the East coast of
the United States. I simulated the impacts of increased temperatures on Z. marina\’s
biomass, reproductive phenology, and life history. Warmer temperatures resulted in a
modeled decrease of Z. marina\’s total biomass, as well as altered reproductive timing
and strategy. These results have implications for long term predictions of Z. marina
persistence in its traditional biogeographic range, and indicate adaptation via shifts in
phenology and reproductive strategy may interact to dampen some negative
consequences of increased temperatures.

}, author = {Foley, J. L.} } @article {4342, title = {Informing Marine Spatial Planning (MSP) with numerical modelling: A case-study on shellfish aquaculture in Malpeque Bay (Eastern Canada)}, journal = {Marine Pollution Bulletin}, volume = {100}, year = {2015}, month = {11/2015}, pages = {200 - 216}, issn = {0025326X}, doi = {10.1016/j.marpolbul.2015.08.048}, author = {Ram{\'o}n Filgueira and Guyondet, Thomas and C{\'e}dric Bacher and Comeau, Luc A.} } @article {4263, title = {A fully-spatial ecosystem-DEB model of oyster (Crassostrea virginica) carrying capacity in the Richibucto Estuary, Eastern Canada}, journal = {Journal of Marine Systems}, volume = {136}, year = {2014}, month = {08/2014}, pages = {42 - 54}, abstract = {The success of shellfish aquaculture as well as its sustainability relies on adjusting the cultured biomass to local ecosystem characteristics. Oyster filter-feeding activity can control phytoplankton concentration, reaching severe depletion in extreme situations, which can threaten ecological sustainability. A better understanding of oyster{\textendash} phytoplankton interaction can be achieved by constructing ecosystem models. In this study, a fully-spatial hydro- dynamic biogeochemical model has been constructed for the Richibucto Estuary in order to explore oyster carry- ing capacity. The biogeochemical model was based on a classical nutrient{\textendash}phytoplankton{\textendash}zooplankton{\textendash}detritus (NPZD) approach with the addition of a Dynamic Energy Budget (DEB) model of Crassostrea virginica. Natural variation of chlorophyll was used as a benchmark to define a sustainability threshold based on a resilience frame- work. Scenario building was applied to explore carrying capacity of the system. However, the complex geomor- phology of the Richibucto Estuary and the associated heterogeneity in water residence time, which is integral in estuarine functioning, indicate that the carrying capacity assessment must be specific for each area of the system. The model outcomes suggest that water residence time plays a key role in carrying capacity estimations through its influence on ecological resistance.}, issn = {09247963}, doi = {10.1016/j.jmarsys.2014.03.015}, author = {R. Filgueira and Guyondet, T. and Comeau, L.A. and J. Grant} } @article {4264, title = {Implementation of marine spatial planning in shellfish aquaculture management: modeling studies in a Norwegian fjord}, journal = {Ecological Applications}, volume = {24}, year = {2014}, pages = {832{\textendash}843}, abstract = {Shellfish carrying capacity is determined by the interaction of a cultured species with its ecosystem, which is strongly influenced by hydrodynamics. Water circulation controls the exchange of matter between farms and the adjacent areas, which in turn establishes the nutrient supply that supports phytoplankton populations. The complexity of water circulation makes necessary the use of hydrodynamic models with detailed spatial resolution in carrying capacity estimations. This detailed spatial resolution also allows for the study of processes that depend on specific spatial arrangements, e.g., the most suitable location to place farms, which is crucial for marine spatial planning, and consequently for decision support systems. In the present study, a fully spatial physical-biogeochemical model has been combined with scenario building and optimization techniques as a proof of concept of the use of ecosystem modeling as an objective tool to inform marine spatial planning. The object of this exercise was to generate objective knowledge based on an ecosystem approach to establish new mussel aquaculture areas in a Norwegian fjord. Scenario building was used to determine the best location of a pump that can be used to bring nutrient-rich deep waters to the euphotic layer, increasing primary production, and consequently, carrying capacity for mussel cultivation. In addition, an optimization tool, parameter estimation (PEST), was applied to the optimal location and mussel standing stock biomass that maximize production, according to a preestablished carrying capacity criterion. Optimization tools allow us to make rational and transparent decisions to solve a well-defined question, decisions that are essential for policy makers. The outcomes of combining ecosystem models with scenario building and optimization facilitate planning based on an ecosystem approach, highlighting the capabilities of ecosystem modeling as a tool for marine spatial planning.}, doi = {10.1890/13-0479.1}, url = {http://www.esajournals.org/doi/pdf/10.1890/13-0479.1}, author = {Ram{\'o}n Filgueira and Jon Grant and {\O}ivind Strand} } @article {4262, title = {Multiscale digital Arabidopsis predicts individual organ and whole-organism growth}, journal = {Proceedings of the National Academy of Sciences}, year = {2014}, abstract = {Understanding how dynamic molecular networks affect whole-organism physiology, analogous to mapping genotype to phenotype, remains a key challenge in biology. Quantitative models that represent processes at multiple scales and link understanding from several research domains can help to tackle this problem. Such integrated models are more common in crop science and ecophysiology than in the research communities that elucidate molecular networks. Several laboratories have modeled particular aspects of growth in Arabidopsis thaliana, but it was unclear whether these existing models could productively be combined. We test this approach by constructing a multiscale model of Arabidopsis rosette growth. Four existing models were integrated with minimal parameter modification (leaf water content and one flowering parameter used measured data). The resulting framework model links genetic regulation and biochemical dynamics to events at the organ and whole-plant levels, helping to understand the combined effects of endogenous and environmental regulators on Arabidopsis growth. The framework model was validated and tested with metabolic, physiological, and biomass data from two laboratories, for five photoperiods, three accessions, and a transgenic line, highlighting the plasticity of plant growth strategies. The model was extended to include stochastic development. Model simulations gave insight into the developmental control of leaf production and provided a quantitative explanation for the pleiotropic developmental phenotype caused by overexpression of miR156, which was an open question. Modular, multiscale models, assembling knowledge from systems biology to ecophysiology, will help to understand and to engineer plant behavior from the genome to the field.}, issn = {1091-6490}, doi = {10.1073/pnas.1410238111}, url = {http://www.pnas.org/content/early/2014/08/27/1410238111.full.pdf+html?sid=66edb45d-8e99-4d84-a072-a47729a65e14}, author = {Chew, Y. H. and Wenden, B. and Flis, A. and Mengin, V. and Taylor, J. and Davey, C. L. and Tindal, C. and Thomas, H. and Ougham, H. J. and de Reffye, P. and Stitt, M. and Williams, M. and Muetzelfeldt, R. and Halliday, K. J. and Millar, A. J.} } @article {4243, title = {Physiological indices as indicators of ecosystem status in shellfish aquaculture sites}, journal = {Ecological Indicators}, volume = {39}, year = {2014}, month = {04/2014}, pages = {134 - 143}, abstract = {The filtration activity of cultured mussels may exert a strong control on phytoplankton populations. Given that phytoplankton constitutes the base of marine food webs, carrying capacity in shellfish aquaculture sites has been commonly studied in terms of phytoplankton depletion. However, spatial and temporal variability of phytoplankton concentration in coastal areas present a methodological constraint for using phytoplankton depletion as an indicator in monitoring programs, and necessitates intensive field campaigns. The main goal of this study is to explore the potential of different bivalve performance indices for use as alternatives to phytoplankton depletion as cost-effective indicators of carrying capacity. For that, a fully spatial hydrodynamic{\textendash}biogeochemical coupled model of Tracadie Bay, an intensive mussel culture embayment located in Prince of Edward Island (Canada), has been constructed and scenario building has been used to explore the relationship between phytoplankton depletion and bivalve performance. Our underlying premise is that overstocking of bivalves leads to increased competition for food resources, i.e. phytoplankton, which may ultimately have a significant effect on bivalve growth rate and performance. Following this working hypothesis, the relationships among bay-scale phytoplankton depletion and three bivalve physiological indices, one static, condition index, and two dynamic, tissue mass and shell length growth rates, have been simulated. These three metrics present methodological advantages compared to phytoplankton depletion for incorporation into monitoring programs. Although significant correlations among phytoplankton depletion and the three physiological indices have been observed, shell length growth rate is shown as the most sensitive indicator of carrying capacity, followed by tissue mass growth rate and then by condition index. These results demonstrate the potentiality of using bivalve physiological measurements in monitoring programs as indicators of ecosystem status.}, issn = {1470160X}, doi = {10.1016/j.ecolind.2013.12.006}, url = {http://www.sciencedirect.com/science/article/pii/S1470160X13004962}, author = {R. Filgueira and Guyondet, T. and Comeau, L.A. and J. Grant} } @article {4242, title = {Storm-induced changes in coastal geomorphology control estuarine secondary productivity}, journal = {Earth{\textquoteright}s Future}, year = {2014}, month = {01/2014}, pages = {n/a - n/a}, abstract = {Estuarine ecosystems are highly sensitive not only to projected effects of climate change such as ocean warming, acidification, and sea-level rise but also to the incidence of nor{\textquoteright}easter storms and hurricanes. The effects of storms and hurricanes can be extreme, with immediate impact on coastal geomorphology and water circulation, which is integral to estuarine function and consequently to provision of ecosystem services. In this article, we present the results of a natural estuarine-scale experiment on the effects of changes in coastal geomorphology on hydrodynamics and aquaculture production. A bay in Prince Edward Island, Canada, was altered when a nor{\textquoteright}easter storm eroded a second tidal inlet through a barrier island. Previous field and modeling studies allowed a comparison of prestorm and post-storm circulation, food limitation by cultured mussels, and aquaculture harvest. Dramatic increases in mussel production occurred in the year following the opening of the new inlet. Model studies showed that post-storm circulation reduced food limitation for cultured mussels, allowing greater growth. Climate change is expected to have severe effects on the delivery of marine ecosystem services to human populations by changing the underlying physical-biological coupling inherent to their functioning.}, doi = {10.1002/2013EF000145}, url = {http://onlinelibrary.wiley.com/doi/10.1002/2013EF000145/abstract;jsessionid=DBD0FB7B2443BD9C9D658F85A42F41FD.f04t04}, author = {Ram{\'o}n Filgueira and Guyondet, Thomas and Comeau, Luc A. and Jon Grant} } @article {4241, title = {Ecosystem modelling for ecosystem-based management of bivalve aquaculture sites in data-poor environment}, journal = {Aquacult Environ Interact}, volume = {4}, year = {2013}, pages = {117-133}, chapter = {117}, abstract = {Although models of carrying capacity have been around for some time, their use in aquaculture management has been limited. This is partially due to the cost involved in generating and testing the models. However, the use of more generic and flexible models could facilitate the implementation of modelling in management. We have built a generic core for coupling biogeochemical and hydrodynamic models using Simile (www.simulistics.com), a visual simulation environment software that is well-suited to accommodate fully spatial models. Specifically, Simile integrates PEST (model-independent parameter estimation, Watermark Numerical Computing, www.pesthomepage.org), an optimization tool that uses the Gauss-Marquardt-Levenberg algorithm and can be used to estimate the value of a parameter, or set of parameters, in order to minimize the discrepancies between the model results and a dataset chosen by the user. The other critical aspect of modelling exercises is the large amount of data necessary to set up, tune and groundtruth the ecosystem model. However, ecoinformatics and improvements in remote sensing procedures have facilitated acquisition of these datasets, even in data-poor environments. In this paper we describe the required datasets and stages of model development necessary to build a biogeochemical model that can be used as a decision-making tool for bivalve aquaculture management in data-poor environments.}, doi = {10.3354/aei00078}, url = {http://www.int-res.com/abstracts/aei/v4/n2/p117-133/}, author = {R. Filgueira and J. Grant and R. Stuart and M. S. Brown} } @article {4213, title = {A physical{\textendash}biogeochemical coupling scheme for modeling marine coastal ecosystems}, journal = {Ecological Informatics}, volume = {7}, year = {2012}, pages = {71-80}, doi = {http://dx.doi.org/10.1016/j.ecoinf.2011.11.007}, url = {http://www.sciencedirect.com/science/article/pii/S1574954111000975}, author = {Ram{\'o}n Filgueira and Jon Grant and C{\'e}dric Bacher and Michel Carreau} } @article {1899, title = {A Box Model for Ecosystem-Level Management of Mussel Culture Carrying Capacity in a Coastal Bay}, journal = {Ecosystems}, year = {2009}, abstract = {

The carrying capacity of shellfish aquaculture is determined by the interaction of cultured species with the ecosystem, particularly food availability to suspension feeders. A multiple box dynamic ecosystem model was constructed to examine the carrying capacity for mussel (Mytilus edulis) aquaculture in Tracadie Bay, Prince of Edward Island, Canada. Criteria for carrying capacity were based on chlorophyll concentration. The model was run in two different years (1998 and 1999) in which time series for three points inside the bay and a point outside the bay were available. This data set allows spatial validation of the ecosystem model and assessment of its sensitivity to changes in boundary conditions. The model validation process indicated that the differential equations and parameters used in the simulation provided robust prediction of the ecological dynamics within the bay. Results verified that mussel biomass exerts top-down control of phytoplankton populations.

}, doi = {10.1007/s10021-009-9289-6}, author = {Ramon Filgueira and Jon Grant} } @proceedings {1560, title = {CONCEPT MAPS FOR COMBINING HARD AND SOFT SYSTEM THINKING IN THE MANAGEMENT OF SOCIO-ECOSYSTEMS}, year = {2008}, url = {http://cmc.ihmc.us/cmc2008papers/cmc2008-p190.pdf}, author = {Franco Salerno and Emanuele Cuccillato and Robert Muetzelfeldt and Francesco Giannino and Birendra Bajracharya and Paolo Caroli and Gaetano Viviano and Anna Staiano and Fabrizio Carten{\`\i}, and Stefano Mazzoleni and Gianni Tartari} } @article {1537, title = {Evaluation and comparison of models and modelling tools simulating nitrogen processes in treatment wetlands }, journal = {Simulation Modelling Practice and Theory}, volume = {16}, year = {2007}, note = {

From Bachelor thesis, http://liu.diva-portal.org/smash/record.jsf?pid=diva2:20221

Modelica was compared with Simile, Stella and PowerSim

It would be interesting to evaluate the comments on Simile.

}, pages = {26-49}, publisher = {Elsevier}, abstract = {

In this paper, two ecological models of nitrogen processes in treatment wetlands have been evaluated and compared. These models were implemented, simulated, and visualized using the Modelica modelling and simulation language [P. Fritzson, Principles of Object-Oriented Modelling and Simulation with Modelica 2.1 (Wiley-IEEE Press, USA, 2004).] and an associated tool. The differences and similarities between the MathModelica Model Editor and three other ecological modelling tools have also been evaluated. The results show that the models can well be modelled and simulated in the MathModelica Model Editor, and that nitrogen decrease in a constructed treatment wetland should be described and simulated using the Nitrification/Denitrification model as this model has the highest overall quality score and provides a more variable environment.

}, keywords = {Denitrification, Ecological modelling, Evaluation, Modelica, Nitrification, Nitrogen, Treatment wetlands}, doi = {doi:10.1016/j.simpat.2007.08.010 }, author = {Stina Edelfeldt and Peter Fritzson} }