00630nas a2200181 4500008004100000022001300041245014500054210006900199260001600268300001400284490000800298100002200306700002200328700002100350700002100371700002000392856003600412 2019 eng d a0959652600aMussels or tunicates: That is the question. Evaluating efficient and sustainable resource use by low-trophic species in aquaculture settings0 aMussels or tunicates That is the question Evaluating efficient a cJan-09-2019 a132 - 1430 v2311 aFilgueira, Ramón1 aStrople, Leah, C.1 aStrohmeier, Tore1 aRastrick, Samuel1 aStrand, Øivind u//www.simulistics.com/node/439000937nas a2200205 4500008004100000022001400041245014800055210006900203260001600272300001600288490000800304100002200312700002200334700002300356700001900379700002200398700002900420700002300449856025900472 2018 eng d a0378-190900aThe effect of environmental conditions on Atlantic salmon smolts’ (Salmo salar) bioenergetic requirements and migration through an inland sea0 aeffect of environmental conditions on Atlantic salmon smolts Sal cJan-10-2018 a1467 - 14820 v1011 aStrople, Leah, C.1 aFilgueira, Ramón1 aHatcher, Bruce, G.1 aDenny, Shelley1 aBordeleau, Xavier1 aWhoriskey, Frederick, G.1 aCrossin, Glenn, T. uhttp://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.pdf02843nas a2200217 4500008004100000022001300041245010100054210006900155260001600224300001400240490000800254520196400262100001902226700002402245700002602269700002802295700002302323700002002346700002602366856023302392 2018 eng d a0048969700aShifts in wind energy potential following land-use driven vegetation dynamics in complex terrain0 aShifts in wind energy potential following landuse driven vegetat cJan-10-2018 a374 - 3840 v6393 a

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.

1 aFang, Jiannong1 aPeringer, Alexander1 aStupariu, Mihai-Sorin1 aPătru-Stupariu, Ileana1 aButtler, Alexandre1 aGolay, Francois1 aPorté-Agel, Fernando uhttps://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/plain01649nas a2200121 4500008004100000245019000041210006900231300000800300490002200308520114300330100001801473856003601491 2017 eng d00aUsing 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’s thesis).0 aUsing an individual based model to evaluate the effects of clima a2530 vMaster of Science3 a

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.

1 aFoley, J., L. u//www.simulistics.com/node/438800675nas a2200169 4500008003900000022001300039245014100052210006900193260001200262300001400274490000800288100002200296700002100318700002000339700001900359856012700378 2015 d a0025326X00aInforming Marine Spatial Planning (MSP) with numerical modelling: A case-study on shellfish aquaculture in Malpeque Bay (Eastern Canada)0 aInforming Marine Spatial Planning MSP with numerical modelling A c11/2015 a200 - 2160 v1001 aFilgueira, Ramón1 aGuyondet, Thomas1 aBacher, Cédric1 aComeau, Luc, A u//www.simulistics.com/publications/informing-marine-spatial-planning-msp-numerical-modelling-case-study-shellfish-aquacult02071nas a2200181 4500008003900000022001300039245013400052210006900186260001200255300001200267490000800279520141300287100001701700700001601717700001601733700001301749856012701762 2014 d a0924796300aA fully-spatial ecosystem-DEB model of oyster (Crassostrea virginica) carrying capacity in the Richibucto Estuary, Eastern Canada0 afullyspatial ecosystemDEB model of oyster Crassostrea virginica  c08/2014 a42 - 540 v1363 aThe 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– 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–phytoplankton–zooplankton–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.1 aFilgueira, R1 aGuyondet, T1 aComeau, L A1 aGrant, J u//www.simulistics.com/publications/fully-spatial-ecosystem-deb-model-oyster-crassostrea-virginica-carrying-capacity-richib02509nas a2200145 4500008003900000245012100039210006900160300001400229490000700243520199900250100002202249700001502271700002002286856005702306 2014 d00aImplementation of marine spatial planning in shellfish aquaculture management: modeling studies in a Norwegian fjord0 aImplementation of marine spatial planning in shellfish aquacultu a832–8430 v243 aShellfish 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.1 aFilgueira, Ramón1 aGrant, Jon1 aStrand, Øivind uhttp://www.esajournals.org/doi/pdf/10.1890/13-0479.102611nas a2200277 4500008003900000022001400039245008700053210006900140520178500209100001401994700001402008700001202022700001402034700001402048700001502062700001402077700001402091700001602105700001402121700001302135700001602148700002002164700001802184700001602202856011502218 2014 d a1091-649000aMultiscale digital Arabidopsis predicts individual organ and whole-organism growth0 aMultiscale digital Arabidopsis predicts individual organ and who3 aUnderstanding 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.1 aChew, Y H1 aWenden, B1 aFlis, A1 aMengin, V1 aTaylor, J1 aDavey, C L1 aTindal, C1 aThomas, H1 aOugham, H J1 aReffye, P1 aStitt, M1 aWilliams, M1 aMuetzelfeldt, R1 aHalliday, K J1 aMillar, A J uhttp://www.pnas.org/content/early/2014/08/27/1410238111.full.pdf+html?sid=66edb45d-8e99-4d84-a072-a47729a65e1402609nas a2200181 4500008003900000022001300039245009100052210006900143260001200212300001400224490000700238520204900245100001702294700001602311700001602327700001302343856007102356 2014 d a1470160X00aPhysiological indices as indicators of ecosystem status in shellfish aquaculture sites0 aPhysiological indices as indicators of ecosystem status in shell c04/2014 a134 - 1430 v393 aThe 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–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.1 aFilgueira, R1 aGuyondet, T1 aComeau, L A1 aGrant, J uhttp://www.sciencedirect.com/science/article/pii/S1470160X1300496201899nas a2200157 4500008003900000245009200039210006900131260001200200300001400212520131800226100002201544700002101566700001901587700001501606856012001621 2014 d00aStorm-induced changes in coastal geomorphology control estuarine secondary productivity0 aStorminduced changes in coastal geomorphology control estuarine  c01/2014 an/a - n/a3 aEstuarine 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'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'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.1 aFilgueira, Ramón1 aGuyondet, Thomas1 aComeau, Luc, A1 aGrant, Jon uhttp://onlinelibrary.wiley.com/doi/10.1002/2013EF000145/abstract;jsessionid=DBD0FB7B2443BD9C9D658F85A42F41FD.f04t0401946nas a2200157 4500008003900000245011100039210006900150300001200219490000600231520143500237100001701672700001301689700001401702700001501716856005701731 2013 d00aEcosystem modelling for ecosystem-based management of bivalve aquaculture sites in data‑poor environment0 aEcosystem modelling for ecosystembased management of bivalve aqu a117-1330 v43 aAlthough 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.1 aFilgueira, R1 aGrant, J1 aStuart, R1 aBrown, M S uhttp://www.int-res.com/abstracts/aei/v4/n2/p117-133/00507nas a2200145 4500008003900000245008700039210007100126300001000197490000600207100002200213700001500235700002000250700002000270856007100290 2012 d00aA physical–biogeochemical coupling scheme for modeling marine coastal ecosystems0 aphysical–biogeochemical coupling scheme for modeling marine coas a71-800 v71 aFilgueira, Ramón1 aGrant, Jon1 aBacher, Cédric1 aCarreau, Michel uhttp://www.sciencedirect.com/science/article/pii/S157495411100097501466nas a2200109 4500008003900000245010000039210006900139520099100208100002101199700001501220856012101235 2009 d00aA Box Model for Ecosystem-Level Management of Mussel Culture Carrying Capacity in a Coastal Bay0 aBox Model for EcosystemLevel Management of Mussel Culture Carryi3 a

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.

1 aFilgueira, Ramon1 aGrant, Jon u//www.simulistics.com/publications/box-model-ecosystem-level-management-mussel-culture-carrying-capacity-coastal-bay00709nas a2200205 4500008003900000245009900039210006900138100002000207700002500227700002500252700002400277700002600301700001800327700002100345700001800366700002200384700002300406700002000429856005400449 2008 d00aCONCEPT MAPS FOR COMBINING HARD AND SOFT SYSTEM THINKING IN THE MANAGEMENT OF SOCIO-ECOSYSTEMS0 aCONCEPT MAPS FOR COMBINING HARD AND SOFT SYSTEM THINKING IN THE 1 aSalerno, Franco1 aCuccillato, Emanuele1 aMuetzelfeldt, Robert1 aGiannino, Francesco1 aBajracharya, Birendra1 aCaroli, Paolo1 aViviano, Gaetano1 aStaiano, Anna1 aFabrizio Cartenì1 aMazzoleni, Stefano1 aTartari, Gianni uhttp://cmc.ihmc.us/cmc2008papers/cmc2008-p190.pdf01633nas a2200229 4500008003900000245011300039210006900152260001300221300001000234490000700244520085700251653002001108653002501128653001501153653001301168653001801181653001301199653002301212100002101235700002001256856012701276 2007 d00aEvaluation and comparison of models and modelling tools simulating nitrogen processes in treatment wetlands 0 aEvaluation and comparison of models and modelling tools simulati bElsevier a26-490 v163 a

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.

10aDenitrification10aEcological modelling10aEvaluation10aModelica10aNitrification10aNitrogen10aTreatment wetlands1 aEdelfeldt, Stina1 aFritzson, Peter u//www.simulistics.com/publications/evaluation-and-comparison-models-and-modelling-tools-simulating-nitrogen-processes-trea