@misc{SiblyGrimmMartinetal.2013, author = {Sibly, Richard M. and Grimm, Volker and Martin, Benjamin T. and Johnston, Alice S. A. and Kulakowska, Katarzyna and Topping, Christopher J. and Calow, Peter and Nabe-Nielsen, Jacob and Thorbek, Pernille and DeAngelis, Donald L.}, title = {Representing the acquisition and use of energy by individuals in agent-based models of animal populations}, series = {Methods in ecology and evolution : an official journal of the British Ecological Society}, volume = {4}, journal = {Methods in ecology and evolution : an official journal of the British Ecological Society}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2041-210X}, doi = {10.1111/2041-210x.12002}, pages = {151 -- 161}, year = {2013}, abstract = {Agent-based models (ABMs) are widely used to predict how populations respond to changing environments. As the availability of food varies in space and time, individuals should have their own energy budgets, but there is no consensus as to how these should be modelled. Here, we use knowledge of physiological ecology to identify major issues confronting the modeller and to make recommendations about how energy budgets for use in ABMs should be constructed. Our proposal is that modelled animals forage as necessary to supply their energy needs for maintenance, growth and reproduction. If there is sufficient energy intake, an animal allocates the energy obtained in the order: maintenance, growth, reproduction, energy storage, until its energy stores reach an optimal level. If there is a shortfall, the priorities for maintenance and growth/reproduction remain the same until reserves fall to a critical threshold below which all are allocated to maintenance. Rates of ingestion and allocation depend on body mass and temperature. We make suggestions for how each of these processes should be modelled mathematically. Mortality rates vary with body mass and temperature according to known relationships, and these can be used to obtain estimates of background mortality rate. If parameter values cannot be obtained directly, then values may provisionally be obtained by parameter borrowing, pattern-oriented modelling, artificial evolution or from allometric equations. The development of ABMs incorporating individual energy budgets is essential for realistic modelling of populations affected by food availability. Such ABMs are already being used to guide conservation planning of nature reserves and shell fisheries, to assess environmental impacts of building proposals including wind farms and highways and to assess the effects on nontarget organisms of chemicals for the control of agricultural pests.}, language = {en} } @article{RadchukJohstGroeneveldetal.2013, author = {Radchuk, Viktoriia and Johst, Karin and Gr{\"o}neveld, Juergen and Grimm, Volker and Schtickzelle, Nicolas}, title = {Behind the scenes of population viability modeling predicting butterfly metapopulation dynamics under climate change}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {259}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2013.03.014}, pages = {62 -- 73}, year = {2013}, abstract = {Studies explaining the choice of model structure for population viability analysis (PVA) are rare and no such study exists for butterfly species, a focal group for conservation. Here, we describe in detail the development of a model to predict population viability of a glacial relict butterfly species, Boloria eunomia, under climate change. We compared four alternative formulations of an individual-based model, differing in the environmental factors acting on the survival of immature life stages: temperature (only temperature impact), weather (temperature, precipitation, and sunshine), temperature and parasitism, and weather and parasitism. Following pattern-oriented modeling, four observed patterns were used to contrast these models: one qualitative (response of population size to habitat parameters) and three quantitative ones describing population dynamics during eight years (mean and variability of population size, and magnitude of the temporal autocorrelation in yearly population growth rates). The four model formulations were not equally able to depict population dynamics under current environmental conditions; the model including only temperature was selected as the most parsimonious model sufficiently well reproducing the empirical patterns. We used all four model formulations to test a range of climate change scenarios that were characterized by changes in both mean and variability of the weather variables. All models predicted adverse effects of climate change and resulted in the same ranking of mean climate change scenarios. However, models differed in their absolute values of population viability measures, underlining the need to explicitly choose the most appropriate model formulation and avoid arbitrary usage of environmental drivers in a model. We conclude that further applications of pattern-oriented modeling to butterfly and other species are likely to help in identifying the key factors impacting the viability of certain taxa, which, ultimately, will aid and speed up informed management decisions for endangered species under climate change.}, language = {en} } @article{MeliAuclercPalmqvistetal.2013, author = {Meli, Mattia and Auclerc, Apolline and Palmqvist, Annemette and Forbes, Valery E. and Grimm, Volker}, title = {Population-level consequences of spatially heterogeneous exposure to heavy metals in soil an individual-based model of springtails}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {250}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, number = {1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2012.11.010}, pages = {338 -- 351}, year = {2013}, abstract = {Contamination of soil with toxic heavy metals poses a major threat to the environment and human health. Anthropogenic sources include smelting of ores, municipal wastes, fertilizers, and pesticides. In assessing soil quality and the environmental and ecological risk of contamination with heavy metals, often homogeneous contamination of the soil is assumed. However, soils are very heterogeneous environments. Consequently, both contamination and the response of soil organisms can be assumed to be heterogeneous. This might have consequences for the exposure of soil organisms and for the extrapolation of risk from the individual to the population level. Therefore, to explore how soil contamination of different spatial heterogeneity affects population dynamics of soil invertebrates, we developed a spatially explicit individual-based model of the springtail, Folsomia candida, a standard test species for ecotoxicological risk assessment. In the model, individuals were assumed to sense and avoid contaminated habitat with a certain probability that depends on contamination level. Avoidance of contaminated areas thus influenced the individuals' movement and feeding, their exposure, and in turn all other biological processes underlying population dynamics. Model rules and parameters were based on data from the literature, or were determined via pattern-oriented modelling. The model correctly predicted several patterns that were not used for model design and calibration. Simulation results showed that the ability of the individuals to detect and avoid the toxicant, combined with the presence of clean habitat patches which act as "refuges", made equilibrium population size due to toxic effects less sensitive to increases in toxicant concentration. Additionally, the level of heterogeneity among patches of soil (i.e. the difference in concentration) was important: at the same average concentration, a homogeneously contaminated scenario was the least favourable habitat, while higher levels of heterogeneity corresponded to higher population growth rate and equilibrium size. Our model can thus be used as a tool for extrapolating from short-term effects at the individual level to long-term effects at the population level under more realistic conditions. It can thus be used to develop and extrapolate from standard ecotoxicological tests in the laboratory to ecological risk assessments.}, language = {en} } @article{MartinJagerNisbetetal.2013, author = {Martin, Benjamin T. and Jager, Tjalling and Nisbet, Roger M. and Preuss, Thomas G. and Hammers-Wirtz, Monika and Grimm, Volker}, title = {Extrapolating ecotoxicological effects from individuals to populations - a generic approach based on Dynamic Energy Budget theory and individual-based modeling}, series = {Ecotoxicology}, volume = {22}, journal = {Ecotoxicology}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {0963-9292}, doi = {10.1007/s10646-013-1049-x}, pages = {574 -- 583}, year = {2013}, abstract = {Individual-based models (IBMs) predict how dynamics at higher levels of biological organization emerge from individual-level processes. This makes them a particularly useful tool for ecotoxicology, where the effects of toxicants are measured at the individual level but protection goals are often aimed at the population level or higher. However, one drawback of IBMs is that they require significant effort and data to design for each species. A solution would be to develop IBMs for chemical risk assessment that are based on generic individual-level models and theory. Here we show how one generic theory, Dynamic Energy Budget (DEB) theory, can be used to extrapolate the effect of toxicants measured at the individual level to effects on population dynamics. DEB is based on first principles in bioenergetics and uses a common model structure to model all species. Parameterization for a certain species is done at the individual level and allows to predict population-level effects of toxicants for a wide range of environmental conditions and toxicant concentrations. We present the general approach, which in principle can be used for all animal species, and give an example using Daphnia magna exposed to 3,4-dichloroaniline. We conclude that our generic approach holds great potential for standardized ecological risk assessment based on ecological models. Currently, available data from standard tests can directly be used for parameterization under certain circumstances, but with limited extra effort standard tests at the individual would deliver data that could considerably improve the applicability and precision of extrapolation to the population level. Specifically, the measurement of a toxicant's effect on growth in addition to reproduction, and presenting data over time as opposed to reporting a single EC50 or dose response curve at one time point.}, language = {en} } @article{MartinJagerNisbetetal.2013, author = {Martin, Benjamin T. and Jager, Tjalling and Nisbet, Roger M. and Preuss, Thomas G. and Grimm, Volker}, title = {Predicting population dynamics from the properties of individuals - a cross-level test of dynamic energy budget theory}, series = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, volume = {181}, journal = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences}, number = {4}, publisher = {Univ. of Chicago Press}, address = {Chicago}, issn = {0003-0147}, doi = {10.1086/669904}, pages = {506 -- 519}, year = {2013}, abstract = {Individual-based models (IBMs) are increasingly used to link the dynamics of individuals to higher levels of biological organization. Still, many IBMs are data hungry, species specific, and time-consuming to develop and analyze. Many of these issues would be resolved by using general theories of individual dynamics as the basis for IBMs. While such theories have frequently been examined at the individual level, few cross-level tests exist that also try to predict population dynamics. Here we performed a cross-level test of dynamic energy budget (DEB) theory by parameterizing an individual-based model using individual-level data of the water flea, Daphnia magna, and comparing the emerging population dynamics to independent data from population experiments. We found that DEB theory successfully predicted population growth rates and peak densities but failed to capture the decline phase. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small-and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detect gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology.}, language = {en} } @article{LiuSiblyGrimmetal.2013, author = {Liu, Chun and Sibly, Richard M. and Grimm, Volker and Thorbek, Pernille}, title = {Linking pesticide exposure and spatial dynamics an individual-based model of wood mouse (Apodemus sylvaticus) populations in agricultural landscapes}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {248}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, number = {2}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2012.09.016}, pages = {92 -- 102}, year = {2013}, abstract = {The wood mouse is a common and abundant species in agricultural landscape and is a focal species in pesticide risk assessment. Empirical studies on the ecology of the wood mouse have provided sufficient information for the species to be modelled mechanistically. An individual-based model was constructed to explicitly represent the locations and movement patterns of individual mice. This together with the schedule of pesticide application allows prediction of the risk to the population from pesticide exposure. The model included life-history traits of wood mice as well as typical landscape dynamics in agricultural farmland in the UK. The model obtains a good fit to the available population data and is fit for risk assessment purposes. It can help identify spatio-temporal situations with the largest potential risk of exposure and enables extrapolation from individual-level endpoints to population-level effects. Largest risk of exposure to pesticides was found when good crop growth in the "sink" fields coincided with high "source" population densities in the hedgerows.}, language = {en} } @article{LinBergerGrimmetal.2013, author = {Lin, Yue and Berger, Uta and Grimm, Volker and Huth, Franka and Weiner, Jacob}, title = {Plant interactions alter the predictions of metabolic scaling theory}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {2}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0057612}, pages = {6}, year = {2013}, abstract = {Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of -4/3 between mean individual biomass and density during density-dependent mortality (self-thinning). Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms' internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than -4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive.}, language = {en} } @unpublished{KreftPluggeGrimmetal.2013, author = {Kreft, Jan-Ulrich and Plugge, Caroline M. and Grimm, Volker and Prats, Clara and Leveau, Johan H. J. and Banitz, Thomas and Baines, Stephen and Clark, James and Ros, Alexandra and Klapper, Isaac and Topping, Chris J. and Field, Anthony J. and Schuler, Andrew and Litchman, Elena and Hellweger, Ferdi L.}, title = {Mighty small - observing and modeling individual microbes becomes big science}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {45}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1317472110}, pages = {18027 -- 18028}, year = {2013}, language = {en} } @article{JeltschBlaumBroseetal.2013, author = {Jeltsch, Florian and Blaum, Niels and Brose, Ulrich and Chipperfield, Joseph D. and Clough, Yann and Farwig, Nina and Geissler, Katja and Graham, Catherine H. and Grimm, Volker and Hickler, Thomas and Huth, Andreas and May, Felix and Meyer, Katrin M. and Pagel, J{\"o}rn and Reineking, Bj{\"o}rn and Rillig, Matthias C. and Shea, Katriona and Schurr, Frank Martin and Schroeder, Boris and Tielb{\"o}rger, Katja and Weiss, Lina and Wiegand, Kerstin and Wiegand, Thorsten and Wirth, Christian and Zurell, Damaris}, title = {How can we bring together empiricists and modellers in functional biodiversity research?}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {14}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, number = {2}, publisher = {Elsevier}, address = {Jena}, issn = {1439-1791}, doi = {10.1016/j.baae.2013.01.001}, pages = {93 -- 101}, year = {2013}, abstract = {Improving our understanding of biodiversity and ecosystem functioning and our capacity to inform ecosystem management requires an integrated framework for functional biodiversity research (FBR). However, adequate integration among empirical approaches (monitoring and experimental) and modelling has rarely been achieved in FBR. We offer an appraisal of the issues involved and chart a course towards enhanced integration. A major element of this path is the joint orientation towards the continuous refinement of a theoretical framework for FBR that links theory testing and generalization with applied research oriented towards the conservation of biodiversity and ecosystem functioning. We further emphasize existing decision-making frameworks as suitable instruments to practically merge these different aims of FBR and bring them into application. This integrated framework requires joint research planning, and should improve communication and stimulate collaboration between modellers and empiricists, thereby overcoming existing reservations and prejudices. The implementation of this integrative research agenda for FBR requires an adaptation in most national and international funding schemes in order to accommodate such joint teams and their more complex structures and data needs.}, language = {en} } @article{GergsZenkerGrimmetal.2013, author = {Gergs, Andre and Zenker, Armin and Grimm, Volker and Preuss, Thomas G.}, title = {Chemical and natural stressors combined from cryptic effects to population extinction}, series = {Scientific reports}, volume = {3}, journal = {Scientific reports}, number = {2}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep02036}, pages = {8}, year = {2013}, abstract = {In addition to natural stressors, populations are increasingly exposed to chemical pollutants released into the environment. We experimentally demonstrate the loss of resilience for Daphnia magna populations that are exposed to a combination of natural and chemical stressors even though effects on population size of a single stressor were cryptic, i.e. hard to detect statistically. Data on Daphnia population demography and along with model-based exploration of our predator-prey system revealed that direct trophic interactions changed the population size-structure and thereby increased population vulnerability to the toxicant which acts in a size selective manner. Moreover, population vulnerability to the toxicant increases with predator size and predation intensity whereas indirect trait-mediated interactions via predator kairomones may buffer chemical effects to a certain extent. Our study demonstrates that population size can be a poor endpoint for risk assessments of chemicals and that ignoring disturbance interactions can lead to severe underestimation of extinction risk.}, language = {en} } @article{FranzRomanowskiJohstetal.2013, author = {Franz, Kamila W. and Romanowski, Jerzy and Johst, Karin and Grimm, Volker}, title = {Ranking landscape development scenarios affecting natterjack toad (Bufo calamita) population dynamics in Central Poland}, series = {PLoS one}, volume = {8}, journal = {PLoS one}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0064852}, pages = {8}, year = {2013}, abstract = {When data are limited it is difficult for conservation managers to assess alternative management scenarios and make decisions. The natterjack toad (Bufo calamita) is declining at the edges of its distribution range in Europe and little is known about its current distribution and abundance in Poland. Although different landscape management plans for central Poland exist, it is unclear to what extent they impact this species. Based on these plans, we investigated how four alternative landscape development scenarios would affect the total carrying capacity and population dynamics of the natterjack toad. To facilitate decision-making, we first ranked the scenarios according to their total carrying capacity. We used the software RAMAS GIS to determine the size and location of habitat patches in the landscape. The estimated carrying capacities were very similar for each scenario, and clear ranking was not possible. Only the reforestation scenario showed a marked loss in carrying capacity. We therefore simulated metapopulation dynamics with RAMAS taking into account dynamical processes such as reproduction and dispersal and ranked the scenarios according to the resulting species abundance. In this case, we could clearly rank the development scenarios. We identified road mortality of adults as a key process governing the dynamics and separating the different scenarios. The renaturalisation scenario clearly ranked highest due to its decreased road mortality. Taken together our results suggest that road infrastructure development might be much more important for natterjack toad conservation than changes in the amount of habitat in the semi-natural river valley. We gained these insights by considering both the resulting metapopulation structure and dynamics in the form of a PVA. We conclude that the consideration of dynamic processes in amphibian conservation management may be indispensable for ranking management scenarios.}, language = {en} } @misc{BecherOsborneThorbeketal.2013, author = {Becher, Matthias A. and Osborne, Juliet L. and Thorbek, Pernille and Kennedy, Peter J. and Grimm, Volker}, title = {Towards a systems approach for understanding honeybee decline - a stocktaking and synthesis of existing models}, series = {Journal of applied ecology : an official journal of the British Ecological Society}, volume = {50}, journal = {Journal of applied ecology : an official journal of the British Ecological Society}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0021-8901}, doi = {10.1111/1365-2664.12112}, pages = {868 -- 880}, year = {2013}, abstract = {1. The health of managed and wild honeybee colonies appears to have declined substantially in Europe and the United States over the last decade. Sustainability of honeybee colonies is important not only for honey production, but also for pollination of crops and wild plants alongside other insect pollinators. A combination of causal factors, including parasites, pathogens, land use changes and pesticide usage, are cited as responsible for the increased colony mortality. 2. However, despite detailed knowledge of the behaviour of honeybees and their colonies, there are no suitable tools to explore the resilience mechanisms of this complex system under stress. Empirically testing all combinations of stressors in a systematic fashion is not feasible. We therefore suggest a cross-level systems approach, based on mechanistic modelling, to investigate the impacts of (and interactions between) colony and land management. 3. We review existing honeybee models that are relevant to examining the effects of different stressors on colony growth and survival. Most of these models describe honeybee colony dynamics, foraging behaviour or honeybee - varroa mite - virus interactions. 4. We found that many, but not all, processes within honeybee colonies, epidemiology and foraging are well understood and described in the models, but there is no model that couples in-hive dynamics and pathology with foraging dynamics in realistic landscapes. 5. Synthesis and applications. We describe how a new integrated model could be built to simulate multifactorial impacts on the honeybee colony system, using building blocks from the reviewed models. The development of such a tool would not only highlight empirical research priorities but also provide an important forecasting tool for policy makers and beekeepers, and we list examples of relevant applications to bee disease and landscape management decisions.}, language = {en} } @article{BailleulGrimmChionetal.2013, author = {Bailleul, Frederic and Grimm, Volker and Chion, Clement and Hammill, Mike}, title = {Modeling implications of food resource aggregation on animal migration phenology}, series = {Ecology and evolution}, volume = {3}, journal = {Ecology and evolution}, number = {8}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.656}, pages = {2535 -- 2546}, year = {2013}, abstract = {The distribution of poikilotherms is determined by the thermal structure of the marine environment that they are exposed to. Recent research has indicated that changes in migration phenology of beluga whales in the Arctic are triggered by changes in the thermal structure of the marine environment in their summering area. If sea temperatures reflect the spatial distribution of food resources, then changes in the thermal regime will affect how homogeneous or clumped food is distributed. We explore, by individual-based modelling, the hypothesis that changes in migration phenology are not necessarily or exclusively triggered by changes in food abundance, but also by changes in the spatial aggregation of food. We found that the level of food aggregation can significantly affect the relationship between the timing of the start of migration to the winter grounds and the total prey capture of individuals. Our approach strongly indicates that changes in the spatial distribution of food resources should be considered for understanding and quantitatively predicting changes in the phenology of animal migration.}, language = {en} }