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Positive and negative interactions within and between species may occur simultaneously, with the net effect depending on population densities. For instance, at low densities plants may ameliorate stress, while competition for resources dominates at higher densities. Here, we propose a simple two-species model in which con- and heterospecifics have a positive effect on per capita growth rate at low densities, while negative interactions dominate at high densities. The model thus includes both Allee effects (intraspecific positive effects) and mutualism (interspecific positive effects), as well as intra- and interspecific competition. Using graphical methods we derive conditions for alternative stable states and species coexistence. We show that mutual non-invasibility (i.e. the inability of each species to invade a population of the other) is more likely when species have a strong positive effect on the own species or a strong negative effect on the other species. Mutual non-invasibility implies alternative stable states, however, there may also be alternative stable states at which species coexist. In the case of species symmetry (i.e. when species are indistinguishable), such alternative coexistence states require that if the positive effect exerted at low densities at the own species is stronger than on the other species, the negative effect at higher densities is also stronger on the own species than on the other species, or, vice versa, if the interspecific positive effects at low densities are stronger than the intraspecific effects, the negative effects at higher densities are also stronger between species than within species. However, the reachability of alternative stable states is restricted by the frequency and density at which species are introduced during community assembly, so that alternative stable states do not always represent alternative endstates of community assembly.

We developed the individual-based model PHYLLOSIM to explain observed variation in the size of bacterial clusters on plant leaf surfaces (the phyllosphere). Specifically, we tested how different ‘waterscapes’ impacted the diffusion of nutrients from the leaf interior to the surface and the growth of individual bacteria on these nutrients. In the ‘null’ model or more complex ‘patchy’ models, the surface was covered with a continuous water film or with water drops of equal or different volumes, respectively. While these models predicted the growth of individual bacterial immigrants into clusters of variable sizes, they were unable to reproduce experimentally derived, previously published patterns of dispersion which were characterized by a much larger variation in cluster sizes and a disproportionate occurrence of clusters consisting of only one or two bacteria. The fit of model predictions to experimental data was about equally poor (, PLoS ONE, 8 (10), ISSN:1932-6203

Nile perch (Lates niloticus) suddenly invaded Lake Victoria between 1979 and 1987, 25 years after its introduction in the Ugandan side of the lake. Nile perch then replaced the native fish diversity and irreversibly altered the ecosystem and its role to lakeshore societies: it is now a prised export product that supports millions of livelihoods. The delay in the Nile perch boom led to a hunt for triggers of the sudden boom and generated several hypotheses regarding its growth at low abundances – all hypotheses having important implications for the management of Nile perch stocks. We use logistic growth as a parsimonious null model to predict when the Nile perch invasion should have been expected, given its growth rate, initial stock size and introduction year. We find the first exponential growth phase can explain the timing of the perch boom at the scale of Lake Victoria, suggesting that complex mechanisms are not necessary to explain the Nile perch invasion or its timing. However, the boom started in Kenya before Uganda, indicating perhaps that Allee effects act at smaller scales than that of the whole Lake. The Nile perch invasion of other lakes indicates that habitat differences may also have an effect on invasion success. Our results suggest there is probably no single management strategy applicable to the whole lake that would lead to both efficient and sustainable exploitation of its resources.

Variations in abundance and survival of larvae of the major fish species, bream, roach, pikeperch, perch and smelt were studied in shallow eutrophic lake Tjeukemeer (1986-1988). Except for smelt, the size of the spawning stock and the abundance of larvae were not related. Both the timing of appearance of larvae and their growth rate were determined by water temperature as was shown by a growth model developed earlier for Tjeukemeer fishes. In cyprinids and percids the survival of the larvae was hypothesized to be negatively related to the duration of the earliest stages. Except in cyprinids, the abundance of 0+ juvenile fish could be explained by the number of larvae. In cyprinids 0+ juvenile abundance at the end of the year was not related to the number of larvae in May and June. The cyprinid juvenile survival rates are hypothesized to be related to the size of the main cyprinid predator, 0+ pikeperch. [KEYWORDS: recruitment; spawning stock; 0+ juvenile fish; temperature; 0+ growth model; mortality; predation; starvation; cyprinids; percids Population-dynamics; rutilus-rutilus; cyclopoid redation; daphnia-hyalina; abramis-brama; south bay; growth; temperature; size; recruitment]

A general framework for the implementation of ecological models directed towards the falsification of knowledge, as opposed to models directed at making predictions, is proposed. The framework is constructed by defining a set of classes, with their interrelationships, in an object-oriented programming language. The classes represent the major levels of the so- called levels-of-integration hierarchy: individual, population and system. The abiotic physical and chemical environment is implemented by the classes condition and resource, respectively. Class habitat is used to represent the spatial structure of an ecosystem. The simulation is controlled by a class called analyser. The simulation mechanism is implemented by deriving all these real-life objects from a more abstract class simobject. The engine of the simulation is formed by a dynamic list of references to simobjects, sorted according to the time each simobject should be activated next, The data of each object are implemented in class dataobject, from which simobject is derived. The applicability of this framework, called OSIRIS (object-oriented simulation framework for individual-based simulations), is shown for a population dynamical study on daphnids, The effects of variation among individual daphnids on the growth rate and structure of a population of daphnids are studied by comparing the results of the individual-based model with those of a life table. Moreover, variation in population growth rate over time, which parameter cannot be derived from a life table, is calculated. Finally, the sensitivity of the model for the number of modelled individuals and the sampling interval is analysed. [KEYWORDS: model; falsification versus prediction; levels of integration individuals versus ecosystem Shallow eutrophic lake; models; fish; system; growth;variability; temperature; tjeukemeer; cucullata; hybrid]

In the light of ongoing land use changes, it is important to understand how multitrophic communities perform at different land use intensities. The paradox of enrichment predicts that fertilization leads to destabilization and extinction of predator-prey systems. We tested this prediction for a land use intensity gradient from natural to highly fertilized agricultural ecosystems. We included multiple aboveground and belowground trophic levels and land use-dependent searching efficiencies of insects. To overcome logistic constraints of field experiments, we used a successfully validated simulation model to investigate plant responses to removal of herbivores and their enemies. Consistent with our predictions, instability measured by herbivore-induced plant mortality increased with increasing land use intensity. Simultaneously, the balance between herbivores and natural enemies turned increasingly towards herbivore dominance and natural enemy failure. Under natural conditions, there were more frequently significant effects of belowground herbivores and their natural enemies on plant performance, whereas there were more aboveground effects in agroecosystems. This result was partly due to the "boom-bust'' behavior of the shoot herbivore population. Plant responses to herbivore or natural enemy removal were much more abrupt than the imposed smooth land use intensity gradient. This may be due to the presence of multiple trophic levels aboveground and belowground. Our model suggests that destabilization and extinction are more likely to occur in agroecosystems than in natural communities, but the shape of the relationship is nonlinear under the influence of multiple trophic interactions. Citation: Meyer KM, Vos M, Mooij WM, Hol WHG, Termorshuizen AJ, et al. (2012) Testing the Paradox of Enrichment along a Land Use Gradient in a Multitrophic Aboveground and Belowground Community.

Complex lake ecosystem models can assist lake managers in developing management plans counteracting the eutrophication symptoms that are expected to be a result of climate change. We applied the ecological model PCLake based on 22 years of data from shallow, eutrophic Lake Søbygaard, Denmark and simulated multiple combinations of increasing temperatures (0–6 ◦C), reduced external nutrient loads (0%–98%) with and without internal phosphorus loading.Simulations suggest nitrogen to be the main limiting nutrient for primary production, reflecting ample phosphorus release from the sediment. The nutrient loading reduction scenarios predicted increased diatom dominance, accompanied by an increase in the zooplankton:phytoplankton biomass ratio. Simulations generally showed phytoplankton to benefit from a warmer climate and the fraction of cyanobacteria to increase. In the 6 ◦C warming scenario, a nutrient load reduction of as much as 60% would be required to achieve summer chlorophyll-a levels similar to those of the baseline scenario with present-day temperatures.

Diversity is expected to increase the resilience of ecosystems. Nevertheless, highly diverse ecosystems have collapsed, as did Lake Victoria's ecosystem of cichlids or Caribbean coral reefs. We try to gain insight to this paradox, by analyzing a simple model of a diverse community where each competing species inflicts a small mortality pressure on an introduced predator. High diversity strengthens this feedback and prevents invasion of the introduced predator. After a gradual loss of native species, the introduced predator can escape control and the system collapses into a contrasting, invaded, low-diversity state. Importantly, we find that a diverse system that has high complementarity gains in resilience, whereas a diverse system with high functional redundancy gains in resistance. Loss of resilience can display early-warning signals of a collapse, but loss of resistance not. Our results emphasize the need for multiple approaches to studying the functioning of ecosystems, as managing an ecosystem requires understanding not only the threats it is vulnerable to but also pressures it appears resistant to. [KEYWORDS: LAKE VICTORIA STABLE STATES

Here, we communicate a point of departure in the development of aquatic ecosystem models, namely a new community-based framework, which supports an enhanced and transparent union between the collective expertise that exists in the communities of traditional ecologists and model developers. Through a literature survey, we document the growing importance of numerical aquatic ecosystem models while also noting the difficulties, up until now, of the aquatic scientific community to make significant advances in these models during the past two decades. Through a common forum for aquatic ecosystem modellers we aim to (i) advance collaboration within the aquatic ecosystem modelling community, (ii) enable increased use of models for research, policy and ecosystem-based management, (iii) facilitate a collective framework using common (standardised) code to ensure that model development is incremental, (iv) increase the transparency of model structure, assumptions and techniques, (v) achieve a greater understanding of aquatic ecosystem functioning, (vi) increase the reliability of predictions by aquatic ecosystem models, (vii) stimulate model inter-comparisons including differing model approaches, and (viii) avoid 're-inventing the wheel', thus accelerating improvements to aquatic ecosystem models. We intend to achieve this as a community that fosters interactions amongst ecologists and model developers. Further, we outline scientific topics recently articulated by the scientific community, which lend themselves well to being addressed by integrative modelling approaches and serve to motivate the progress and implementation of an open source model framework. © 2011 Springer Science+Business Media B.V.

1. We studied the effect of size-selective predation on the outcome of competition between two differently sized prey species in a homogenous environment.2. Using a physiologically structured population model, we calculated equilibrium food concentrationsfor a range of predation scenarios defined by varying maximum predation intensity and size-selectivity, the latter being characterized by the neutral selection length (NSL), where negativeselection of small prey size-classes turns into positive selection of larger prey. We parameterized the model according to the well-studied example of fish predation on two differently sizedcladoceran species, Daphnia pulicaria and Daphnia galeata.3. Although the larger D. pulicaria was principally the better competitor for food, competitive superiority shifted to the smaller D. galeata under certain predation scenarios. The lowest predationintensity needed to induce a shift from D. pulicaria to D. galeata was found at NSL values in between the sizes at maturity of both species.4. Analysing the per capita mortality rates as a result of the underlying parameters of the mortality model, NSL and maximum predation intensity, revealed that the tolerable mortality rate of daphnids decreased as NSL increases towards values close to the size at maturity. This effect was most pronounced in D. pulicaria, thus explaining a higher vulnerability of the larger speciesto size-selective predation.5. A reduction of the size at maturity in the smaller species (D. galeata) as a phenotypic response to the presence of fish resulted not only in an increased capability to withstand predation, butalso in competitive dominance shifts over the larger D. pulicaria at lower predation intensities and a much wider range of NSL as a trait-mediated indirect effect.6. Overall, our results demonstrate that shifts in dominance of differently sized herbivores under size-selective predation regimes may be facilitated by the demonstrated alteration in competitivecapacities and thus might not be exclusively caused by direct predation effects.

For more than 20 years scientists of the ‘Food-chain studies’ Group of the former Limnological Institute have been studying interactions within the pelagic food web. Purpose of research was to explain the structure and dynamics of the zooplankton and fish communities in lakes and reservoirs in relation to biotic and abiotic environmental factors. A so-called multi-species approach was used, in which all common and abundant species within a specific ecosystem were studied on the individual and population level with the same degree of detail. The recent results and the scientific approach used are evaluated and the main gaps in knowledge about food-web dynamics in shallow eutrophic lakes are identified and discussed. It is concluded that instead of the purely functional approach used so far, future studies should also include evolutionary aspects which determine the success of an organism in a given environment and that more attention should be paid to central questions in ‘community ecology’.

A one-dimensional ecological model of the meromictic brackish Lake Shira (Russia, Khakasia) was developed. The model incorporates state-of-the-art knowledge about the functioning of the lake ecosystem using the most recent field observations and ideas from PCLake, a general ecosystem model of shallow freshwater lakes. The model of Lake Shira presented here takes into account the vertical dynamics of biomasses of the main species of algae, zooplankton and microbial community, as well as the dynamics of oxygen, detritus, nutrients and hydrogen sulphide from spring to autumn. Solar radiation, temperature and diffusion are modelled using real meteorological data. The parameters of the model were calibrated to the field data, after applying different methods of sensitivity analysis to the model. The resulting patterns of phytoplankton and nutrients dynamics show a good qualitative and quantitative agreement with the field observations during the whole summer season. Results are less satisfactory with respect to the vertical distribution of zooplankton biomass. We hypothesize that this is due to the fact that the current model does not take the sex and age structure of zooplankton into account. The dynamics of oxygen, hydrogen sulphide and the modelled positions of the chemocline and thermocline are again in good agreement with field data. This resemblance confirms the validity of the approach we took in the model regarding the main physical, chemical and ecological processes. This general model opens the way for checking various hypotheses on the functioning of the Lake Shira ecosystem in future investigations and for analysing options for management of this economically important lake.

In meromictic lakes such as Lake Shira, horizontal inhomogeneity is small in comparison with vertical gradients. To determine the vertical distribution of temperature, salinity, and density of water in a deep zone of a Lake Shira, or other saline lakes, a one-dimensional (in vertical direction) mathematical model is presented. A special feature of this model is that it takes into account the process of ice formation. The model of ice formation is based on the one-phase Stefan problem with the linear temperature distribution in the solid phase. A convective mixed layer is formed under an ice cover due to salt extraction in the ice formation process. To obtain analytical solutions for the vertical distribution of temperature, salinity, and density of water, we use a scheme of vertical structure in the form of several layers. In spring, the ice melts as top and bottom. These processes are taken into account in the model. The calculated profiles of salinity and temperature of Shira Lake are in good agreement with field measurement data for each season. Additionally, we focussed on the redox zone, which is the zone in which the aerobic layers of a water column meet the anaerobic ones. Hyperactivity of plankton communities is observed in this zone in lakes with hydrogen sulphide monimolimnion, and Lake Shira is among them. The location of the redox zone in the lake, which is estimated from field measurements, coincides with a sharp increase in density (the pycnocline) during autumn and winter. During spring and summer, the redox zone is deeper than the pycnocline. The location of pycnocline calculated with the hydro physical model is in good agreement with field measurement data.

Addressing complex ecological research questions often requires complex empirical experiments. However, due to the logistic constraints of empirical studies there is a trade-off between the complexity of experimental designs and sample size. Here, we explore if the simulation of complex ecological experiments including stochasticity-induced variation can aid in alleviating the sample size limitation of empirical studies. One area where sample size limitations constrain empirical approaches is in studies of the above- and belowground controls of trophic structure. Based on a rule- and individual-based simulation model on the effect of above- and belowground herbivores and their enemies on plant biomass, we evaluate the reliability of biomass estimates, the probability of experimental failure in terms of missing values, and the statistical power of biomass comparisons for a range of sample sizes. As expected, we observed superior performance of setups with sample sizes typical of simulations (n = 1000) as compared to empirical experiments (n = 10). At low sample sizes, simulated standard errors were smaller than expected from statistical theory, indicating that stochastic simulation models may be required in those cases where it is not possible to perform pilot studies for determining sample sizes. To avoid experimental failure, a sample size of n = 30 was required. In conclusion, we propose that the standard tool box of any ecologist should comprise a combination of simulation and empirical approaches to benefit from the realism of empirical experiments as well as the statistical power of simulations.

International audience; Spatial self-organization is the main theoretical explanation for the global occurrence of regular or otherwise coherent spatial patterns in ecosystems. Using mussel beds as a model ecosystem, we provide an experimental demonstration of spatial self-organization. Under homogeneous laboratory conditions, mussels developed regular patterns, similar to those in the field. An individual-based model derived from our experiments showed that interactions between individuals explained the observed patterns. Furthermore, a field study showed that pattern formation affected ecosystem-level processes in terms of improved growth and resistance to wave action. Our results imply that spatial self-organization is an important determinant of the structure and functioning of ecosystems, and it needs to be considered in their conservation.

We followed adaptation of the chytrid parasite Zygorhizidium planktonicum during 200 generations of growth on its host, the freshwater diatom Asterionella formosa, in a serial passage experiment. Evolution of parasite fitness was assessed both on a homogenous and heterogeneous host population, consisting of respectively a single new and ten different new host strains. These 10 host strains were genetically different and also varied in their initial susceptibility to the parasite. Parasite fitness increased significantly and rapidly on the new, genetically homogenous host population, but remained unaltered during 200 generations of growth on the heterogeneous host population. Enhanced parasite fitness was the result of faster and more efficient transmission, resulting in higher values of R-0 (number of secondary infections). Consequently, parasites that evolved within the uniclonal host population infected significantly more of these hosts than did their ancestors. We thus provide experimental evidence for the widely held view that host genetic diversity restricts evolution of parasites and moderates their harmful effects. Genetically uniform host populations are not only at increased risk from fungal epidemics because they all share the same susceptibility, but also because new parasite strains are able to adapt quickly to new host environments and to improve their fitness.

We studied costs and benefits of life history shifts of water fleas (genus Daphnia) in response to infochemicals from planktivorous fish. We applied a dynamic energy budget model to investigate the resource allocation patterns underlying the observed life history shifts and their adaptive value under size selective predation in one coherent analysis. Using a published data set of life history shifts in response to fish infochemicals we show that Daphnia invests less energy in somatic growth in the fish treatment. This observation complies with theoretical predictions on optimal resource allocation. However, the observed patterns of phenotypic plasticity cannot be explained by changes in resource allocation patterns alone because our model-based analysis of the empirical data clearly identified additional bioenergetic costs in the fish treatments. Consequently, the response to fish kairomone only becomes adaptive if the intensity of size selective predation surpasses a certain critical level. We believe that this is the first study that puts resource allocation, energetic costs, and adaptive value of predator induced life-history shifts – using empirical data – into one theoretical framework.

Many lakes have experienced a transition from a clear into a turbid state without macrophyte growth due to eutrophication. There are several measures by which nitrogen (N) and phosphorus (P) concentrations in the surface water can be reduced. We used the shallow lake model PCLake to evaluate the effects of three measures (reducing external nutrient loading, increasing relative marsh area, and increasing exchange rate between open water and marsh) on water quality improvement. Furthermore, the contribution of different retention processes was calculated. Settling and burial contributed more to nutrient retention than denitrification. The model runs for a typical shallow lake in The Netherlands showed that after increasing relative marsh area to 50%, total phosphorous (TP) concentration in the surface water was lower than the Maximum Admissible Risk (MAR, a Dutch government water quality standard) level, in contrast to total nitrogen (TN) concentration. The MAR levels could also be achieved by reducing N and P load. However, reduction of nutrient concentrations to MAR levels did not result in a clear lake state with submerged vegetation. Only a combination of a more drastic reduction of the present nutrient loading, in combination with a relatively large marsh cover (approximately 50%) would lead to such a clear state. We therefore concluded that littoral marsh areas can make a small but significant contribution to lake recovery.

We studied how chemicals obtained as filtrates from algal monocultures (algal chemicals) and from rotifer cultures with or without algae (rotifer chemicals) affected feeding rates of the rotifer Brachionus calyciflorus on its food algae, both directly and indirectly (through chemical-induced changes in algal morphology). Algal chemicals had a strong stimulating effect on the feeding rate of B. calyciflorus, but these effects were counteracted by rotifer chemicals. In functional response experiments, rotifer chemicals lowered maximum ingestion rates and had strong effects on assimilation rates and assimilation efficiencies of B. calyciflorus, probably due to the release of unspecific (auto)toxic metabolites. Furthermore, rotifer chemicals induced colony formation in the food alga Scenedesmus obliquus. Above the optimum particle size for ingestion by B. calyciflorus, larger algal colony sizes increased the food-handling time, thus lowering ingestion and assimilation rates. Through their effects on trophic interactions, infochemicals may play a role in structuring and the functioning of aquatic food webs.

Mismatches between predator and prey due to climate change have now been documented for a number of systems. Ultimately, a mismatch may have far-reaching consequences for ecosystem functioning as decoupling of trophic relationships results in trophic cascades. Here, we examine the potential for climate change induced mismatches between zooplankton and algae during spring succession, with a focus on Daphnia and its algal food. Whereas the development of an overwintering population of daphnids may parallel shifts in phytoplankton phenology due to climate warming, changes in the photoperiod-temperature interaction may cause the emerging population of daphnids to hatch too late and mismatch their phytoplankton prey. A decoupling of the trophic relationship between the keystone herbivore Daphnia and its algal prey can result in the absence of a spring clear water phase. We extended an existing minimal model of seasonal dynamics of Daphnia and algae and varied the way the Daphnia population is started in spring, i.e., from free swimming individuals or from hatching resting eggs. Our model results show that temperature affects the timing of peak abundance in Daphnia and algae, and subsequently the timing of the clear water phase. When a population is started from a small inoculum of hatching resting eggs, extreme climate warming (+6 degrees C) results in a decoupling of trophic relationships and the clear water phase fails to occur. In the other scenarios, the trophic relationships between Daphnia and its algal food source remain intact. Analysis of 36 temperate lakes showed that shallow lakes have a higher potential for climate induced match-mismatches, as the probability of active overwintering daphnids decreases with lake depth. Future research should point out whether lake depth is a direct causal factor in determining the presence of active overwintering daphnids or merely indicative for underlying causal factors such as fish predation and macrophyte cover.

Global average surface temperatures are expected to rise by about 1.4-5.8 degrees C from the present until the year 2100. This temperature increase will affect all ecosystems on earth. For shallow lakes-which can be either in a clear water or a turbid state-this climate change will expectedly negatively affect water transparency though the prediction is far from conclusive and experimental investigations elucidating the potential climatic effects on shallow lakes are still rare. The aim of this study was to further shape and sharpens hypotheses on the impact of climate change on shallow lakes by applying an existing and well-calibrated ecosystem model, PCLake. We focused on asymptotic model behaviour for a range of temperature and loading scenarios in a factorial design. We conclude that climate change will likely lead to decreased critical nutrient loadings. Combined with an expected increase in the external nutrient loading, this will increase the probability of a shift from a clear to a turbid state. As the model predicts a higher summer chlorophyll-a concentration, a stronger dominance of cyanobacteria during summer and a reduced zooplankton abundance due to climate change, the turbid state itself is likely to become even more severe.

1. Theoretical studies have shown that inducible defences have the potential to affect population stability and persistence in bi- and tritrophic food chains. Experimental studies on such effects of prey defence strategies on the dynamics of predator–prey systems are still rare. We performed replicated population dynamics experiments using the herbivorous rotifer Brachionus calyciflorus and four strains of closely related algae that show different defence responses to this herbivore. 2. We observed herbivore populations to fluctuate at a higher frequency when feeding on small undefended algae. During these fluctuations minimum rotifer densities remained sufficiently high to ensure population persistence in all the replicates. The initial growth of rotifer populations in this treatment coincided with a sharp drop in algal density. Such a suppression of algae by herbivores was not observed in the other treatments, where algae were larger due to induced or permanent defences. I 3. A variety of alternative mechanisms could explain differential herbivore persistence in the different defence treatments. Our analysis showed the density and fraction of highly edible algal particles to better explain herbivore persistence and extinctions than total algal density, the fraction of highly inedible food particles or the accumulation of herbivore waste products or autotoxins. 4. We argue that the rotifers require a minimum fraction and density of edible food particles for maintenance and reproduction. We conjecture that induced defences in algae may thus favour larger zooplankton species such as Daphnia spp. that are less sensitive to shifts in their food size spectrum, relative to smaller zooplankton species, such as rotifers and in this way contributes to the structuring of planktonic communities. [KEYWORDS: consumer–resource interactions ; inducible defences ; phenotypic plasticity ; Scenedesmus ; trait-mediated interactions.]

Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern- oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity

This chapter reviews the predicted effects of induced defenses on trophic structure and two aspects of stability, “local” stability and persistence, as well as presenting novel results on a third, resilience. Food webs are structures of populations in a given location organized according to their predator–prey interactions. Interaction strengths and, therefore, prey defenses are generally recognized as important ecological factors affecting food webs. Despite this, surprisingly, little light has been shed on the food web-level consequences of inducible defenses. Inducible defenses occur in many taxa in both terrestrial and aquatic food webs. They include refuge use, reduced activity, adaptive life history changes, the production of toxins, synomones and extrafloral nectar, and the formation of colonies, helmets, thorns, or spines. In the chapter, theoretical results for the effects of inducible defenses on trophic structure and the three aspects of stability are reviewed. This is done, in part, using bifurcation analysis—a type of analysis that is applied to nonlinear dynamic systems described by a set of ordinary differential or difference equations. The work presented in the chapter suggests that heterogeneity, as caused by induced defenses in prey species, has major effects on the functioning of food webs. Inducible defenses occur in many species in both aquatic and terrestrial systems, and theoretical work indicates they have major effects on important food web properties such as trophic structure, local stability, persistence, and resilience.

The allelopathic potential of exudates from the aquatic macrophyte Stratiotes aloides on the growth of phytoplankton was investigated. A selection of phytoplankton species, occurring in habitats similar to that of Stratiotes, was used: two cyanobacterial strains (toxic and non-toxic Microcystis aeruginosa), one green alga (Scenedesmus obliquus) and one eustigmatophyte (Nannochloropsis limnetica). The results indicate allelopathic effects of Stratiotes on phytoplankton in six of the eight cases, expressed in an extended duration of the initial biovolume doubling time. The overall inhibitory effect (8–51%) was strain-specific for the two cyanobacteria. We also studied the effect of irradiance on the allelopathic potential of exudates from Stratiotes. Irradiance influenced the response of Scenedesmus only. The inhibitory effect of Stratiotes exudates on the growth of this green alga was stronger at 35 µmol m-2 s-1 than at 105 µmol m-2 s-1. We conclude that Stratiotes has allelopathic effects on phytoplankton, and that irradiance can, but does not always determine the extent of the allelopathic inhibition. In our experiments, the sensitivity of cyanobacteria to Stratiotes exudates was not higher than for other phytoplankton strains, but within cyanobacteria, the toxic strain was more sensitive than the non-toxic one. [KEYWORDS: Allelopathy ; Exudate ; Growth inhibition ; Initial biovolume doubling time ; Irradiance ; Lag phase]

Uncertainty in estimates of survival of dispersing animals is a vexing difficulty in conservation biology. The current notion is that this uncertainty decreases the usefulness of spatially explicit population models in particular. We examined this problem by comparing dispersal models of three levels of complexity: (1) an event-based binomial model that considers only the occurrence of mortality or arrival, (2) a temporally explicit exponential model that employs mortality and arrival rates, and (3) a spatially explicit grid-walk model that simulates the movement of animals through an artificial landscape. Each model was fitted to the same set of field data. A first objective of the paper is to illustrate how the maximum-likelihood method can be used in all three cases to estimate the means and confidence limits for the relevant model parameters, given a particular set of data on dispersal survival. Using this framework we show that the structure of the uncertainty for all three models is strikingly similar. In fact, the results of our unified approach imply that spatially explicit dispersal models, which take advantage of information on landscape details, suffer less from uncertainly than do simpler models. Moreover, we show that the proposed strategy of model development safeguards one from error propagation in these more complex models. Finally, our approach shows that all models related to animal dispersal, ranging from simple to complex, can be related in a hierarchical fashion, so that the various approaches to modeling such dispersal can be viewed from a unified perspective [KEYWORDS: dispersal models, uncertainty; dispersal mortality; dispersal success; individual-based modeling; landscape details; likelihood, maximum; managing endangered species; model complexity; population models; random grid-walk models; spatially explicit modeling; suitable habitat]

Surface waterblooms of toxic cyanobacteria (scums) interfere with the use of lakes, for instance in the production of drinking water or for recreation. Routine monitoring data are not sufficient for early warning due to the large temporal and spatial variability in the occurrence of surface waterblooms, and the time lag between the formation of the scum and the availability of relevant information for risk management. We combined a “traditional” dynamic simulation model based upon differential equations with fuzzy logic to describe the three main conditions governing surface waterbloom formation: (1) a preexisting population of cyanobacteria, (2) buoyancy of the cells, and (3) stability of the water column. The attributes and membership functions of the fuzzy model were based on earlier field studies of diel changes in buoyancy and vertical distribution of cyanobacteria. The model was applied without further calibration to the large lake IJsselmeer (1200 km2) in the Netherlands, and we validated the model output using 12 years of NOAA-AVHRR (National Oceanic and Atmospheric Administration–Advanced Very High Resolution Radiometers) satellite images on which surface blooms are discernible as an enhanced vegetation index or increased surface water temperature. Existing surface blooms were predicted with high accuracy, but additional blooms were also predicted. A statistical test (Cohen's Kappa) showed that correct predictions of the absence or presence of surface blooms were highly unlikely to have occurred by chance only. The model can be used to predict the occurrence of surface waterblooms in advance on the basis of the long-term weather forecast, leaving time for appropriate management of the problem. The lake management has expressed interest in converting the present model into a fully operational–online–early warning system [KEYWORDS: algal blooms; early warning; blue-green algae; cyanobacteria; ecological models; eutrophication; fuzzy logic; Microcystis; remote sensing; scums; water management]

We investigated the relative importance of a behavioural defence (refuge use through diel vertical migration) and a life history change (a reduced size at first reproduction) that are used by daphnids to decrease the risk of predation by visually hunting fish. We used an individual based model of a Daphnia population in a stratified lake to quantify the effects of these inducible defences on Daphnia predation-mortality and the resulting Daphnia population dynamics. Our analysis shows that diel vertical migration (DVM) confers a much stronger protection against fish predation than a reduced size at first reproduction (SFR). DVM allows daphnids to withstand a higher predation pressure in the epilimnion and it decelerates a Daphnia population decline more strongly than a reduced SFR. DVM effectively reduces the (P/B) flow of carbon from daphnids to fish. Many theoretical studies have only considered the fitness benefits of DVM above ‘staying up’ in the epilimnion of a lake. Our results suggest that ‘staying down’ in the hypolimnion would confer an even stronger fitness benefit to Daphnia than DVM at times of peak predation risk. Daphnids that remain in the hypolimnion avoid the predation suffered by migrating daphnids around dusk and dawn. Staying down could prevent a Daphnia population decline, while DVM and a reduced SFR can only decelerate th

The paper aims at exploring the viability of the Florida snail kite population under various drought regimes in its wetland habitat. The population dynamics of snail kites are strongly linked with the hydrology of the system due to the dependence of this bird species on one exclusive prey species, the apple snail, which is negatively affected by a drying out of habitat. Based on empirical evidence, it has been hypothesised that the viability of the snail kite population critically depends not only on the time interval between droughts, but also on the spatial extent of these droughts. A system wide drought is likely to result in reduced reproduction and increased mortality, whereas the birds can respond to local droughts by moving to sites where conditions are still favourable. This paper explores the implications of this hypothesis by means of a spatially-explicit individual-based model. The specific aim of the model is to study in a factorial design the dynamics of the kite population in relation to two scale parameters, the temporal interval between droughts and the spatial correlation between droughts. In the model high drought frequencies led to reduced numbers of kites. Also, habitat degradation due to prolonged periods of inundation led to lower predicted numbers of kites. Another main result was that when the spatial correlation between droughts was low, the model showed little variability in the predicted numbers of kites. But when droughts occurred mostly on a system wide level, environmental stochasticity strongly increased the stochasticity in kite numbers and in the worst case the viability of the kite population was seriously threatened. [KEYWORDS: Conservation; Everglades; Rostrhamus sociabilis; Spatially explicit individual based model; Habitat quality; Hydrology; Inundation; Succession]

Spatially explicit population models (SEPMs) are a means for studying the dynamics and viability of populations on landscapes (e.g., Pulliam et al. 1992; Turner et al. 1995). Because of their capabilities for modeling populations on realistic, heterogeneous landscapes (using geographic information system data, for example), SEPMs have been applied in conservation biology (e.g., Wolff 1994; Schippers et al. 1996; DeAngelis et al. 1998). Concerns have been raised by some authors (Wennergren et al. 1995; Groom & Pascual 1997; Meir & Kareiva 1997; Ruckelshaus et al. 1997), however, that such models are "likely to be highly unreliable given our uncertainties about dispersal behavior and rates" (Wennergren et al. 1995). This pessimism seems to be justified by simulations with an abstract landscape model performed by Ruckelshaus et al. (1997). These authors investigated the effects of input data errors in a model of animals dispersing on a landscape. They deduced from their model that small errors in the mortality associated with dispersal leads to disproportionately large errors in predicting overall survival and conclude "that the dispersal modules of spatially explicit models are staggeringly sensitive to the details of dispersal behavior" (Ruckelshaus et al. 1997). The model of Ruckelshaus et al. (1997) describes a landscape composed of 118 X 118 cells, with patches of suitable habitat randomly distributed over the grid. Model organisms moved randomly over the grid until they reached a patch of suitable habitat. For a given size and shape of the patches and fraction of suitable habitat, 400 individuals were simulated sequentially. This resulted in frequency distributions of steps it takes an individual to reach a patch of suitable habitat. To study the effect of dispersal mortality on overall dispersal success

Formation of year-class strength of bream Abramis brama, the most abundant fish in shallow eutrophic Lake Tjeukemeer, was studied during a 14-year period. Although the size of the spawning stock of bream was rather stable during this period, analysis of length-frequency distributions indicates that it comprised only a few year-classes. The strength of a year-class was determined at a fork length of about ii cm, at the end of the second summer. Mortality rates of fish larger than 11 cm were low (

The interactions between the higher trophic levels in a shallow eutrophic lake were studied during the course of a year. Three fish species determined the main pathways of organic matter flow within the system: the predominantly planktivorous bream (Abramis brama), the obligate planktivorous smelt (Osmerus eperlanus), and the piscivorous pikeperch (Stizostedion lucioperca). Of the thirteen common zooplankton taxa Daphnia hyalina and cyclopoid copepods were utilized most by the planktivorous fish, while the large production of small cladocerans is almost left unutilized. The seasonal variations of production and consumption are large. This is mainly affected by seasonal variation of the water temperature. The production of O + smelt is efficiently utilized by the pikeperch. Being the most important zooplankton consumer, as well as the most important prey group, O + fish plays a key role in the Tjeukemeer food web.

A feature of meromictic lakes is that several physicochemical and biological gradients affect the vertical distribution of different organisms. The vertical stratification of physical, chemical and biological components in saline, fishless meromictic lakes Shira and Shunet (Siberia, Russia) is quite different mainly because both mean depth and maximum depth of lakes differ as well as their salinity levels differ. The chemocline of the Lake Shira, as in many meromictic lakes, is inhabited by bacterial community consisting of purple sulphur and heterotrophic bacteria. As the depth of the chemocline is variable, the bacterial community does not attain high densities. The mixolimnion in Lake Shira, which is thermally stratified in summer, also creates different habitat for various species. The distribution of phytoplankton is non-uniform with its biomass peak in the metalimnion. The distribution of zooplankton is also heterogeneous with rotifers and juvenile copepods inhabiting the warmer epilimnion and older copepods found in the cold but oxic hypolimnion. The amphipod Gammarus lacustris which can be assigned to the higher trophic link in the fishless lake’s ecosystem, such as Lake Shira, is also distributed non-uniformly, with its peak density generally observed in the thermocline region. The chemocline in Lake Shunet is located at the depth of 5 m, and unlike in Lake Shira, due to a sharp salinity gradient between the mixolimnion and monimolimnion, this depth is very stable. The mixolimnion in Lake Shunet is relatively shallow and the chemocline is inhabited by (1) an extremely dense bacterial community; (2) a population of Cryptomonas sp.; and (3) ciliate community comprising several species. As the mixolimnion of Lake Shunet is not thermally stratified for long period, the phytoplankton and zooplankton populations are not vertically stratified. The gammarids, however, tend to concentrate in a narrow layer located 1–2 m above the chemocline. We believe that in addition to vertical inhomogeneities of both physicochemical parameters, biological and physical factors also play a role in maintaining these inhomogeneities. We conclude that the stratified distributions of the major food web components will have several implications for ecosystem structure and dynamics. Trophic interactions as well as mass and energy flows can be significantly impacted by such heterogeneous distributions. Species spatially separated even by relatively short distances, say a few centimetres will not directly compete. Importantly, we demonstrate that not only bacteria, phytoflagellates and ciliate tend to concentrate in thin layers but also larger-sized species such Gammarus (amphipods) can also under certain environmental conditions have stratified distribution with maxima in relatively thin layer. As the vertical structure of the lake ecosystem is rather complex in such stratified lakes as ours, the strategy of research, including sampling techniques, should consider potentially variable and non-homogeneous distributions.

Shallow lakes have the potential to switch between two alternative stable states: a clear macrophyte-dominated and a turbid phytoplankton-dominated state. Observational and experimental studies show that in some lakes herbivory by birds may severely decrease macrophyte biomass, while in other lakes, the removed biomass by herbivory is compensated by regrowth. These contradictory outcomes might arise because of interplay between top-down control by bird herbivory and bottom-up effects by nutrient loading on macrophytes. Here, we use the ecosystem model PCLake to study top-down and bottom-up control of macrophytes by coots and nutrient loading. Our model predicted that (1) herbivory by birds lowers the critical nutrient loading at which the regime shift occurs; (2) bird impact on macrophyte biomass through herbivory increases with nutrient loading; and (3) improved food quality enhances the impact of birds on macrophytes, thus decreasing the resilience of the clear-water state even further. The fact that bird herbivory can have a large impact on macrophyte biomass and can facilitate a regime shift implies that the presence of waterfowl should be taken into account in the estimation of critical nutrient loadings to be used in water quality management.

Intra- and interspecific differences in pigmentation between finfold larvae of the three most abundant cyprinids in Dutch eutrophic waters, bream, white bream and roach, were studied, using laboratory-raised larvae in the length range 8–11 mm. Because the internal pigmentation of the larvae has been used for identification, some attention is paid to the effects of different ways of fixation and preservation on transparency. The size and the shape of the melanophores, as described in the literature, could not be used as identification characters because of too much intraspecific variation and the effects of light conditions at the moment of fixation. Three characters proved to be significant for the identification of the larvae of the three species. Roach can be distinguished from bream and white bream by the pattern of melanophores on the belly. A second character is the pigmentation of the ventral aorta, which is only found in white bream. Lastly bream shows an irregular pattern of melanophores on the dorsal side, in contrast to roach which has a regular pattern.

Peatlands are important sinks for atmospheric carbon (C), yet the role of plant functional types (PFTs) for C sequestration under climatic perturbations is still unclear. A plant-removal experiment was used to study the importance of vascular PFTs for the net ecosystem CO2 exchange (NEE) during (i.e., resistance) and after (i.e., recovery) an experimental drought. The removal of PFTs caused a decrease of NEE, but the rate differed between microhabitats (i.e., hummocks and lawns) and the type of PFTs. Ericoid removal had a large effect on NEE in hummocks, while the graminoids played a major role in the lawns. The removal of PFTs did not affect the resistance or the recovery after the experimental drought. We argue that the response of Sphagnum mosses (the only PFT present in all treatments) to drought is dominant over that of coexisting PFTs. However, we observed that the moment in time when the system switched from C sink to C source during the drought was controlled by the vascular PFTs. In the light of climate change, the shifts in species composition or even the loss of certain PFTs are expected to strongly affect the future C dynamics in response to environmental stress.

There is ample evidence that tube-dwelling invertebrates such as chironomids significantly alter multiple important ecosystem functions, particularly in shallow lakes. Chironomids pump large water volumes, and associated suspended and dissolved substances, through the sediment and thereby compete with pelagic filter feeders for particulate organic matter. This can exert a high grazing pressure on phytoplankton, microorganisms, and perhaps small zooplankton and thus strengthen benthic-pelagic coupling. Furthermore, intermittent pumping by tube-dwelling invertebrates oxygenates sediments and creates a dynamic, three-dimensional mosaic of redox conditions. This shapes microbial community composition and spatial distribution, and alters microbe-mediated biogeochemical functions, which often depend on redox potential. As a result, extended hotspots of element cycling occur at the oxic-anoxic interfaces, controlling the fate of organic matter and nutrients as well as fluxes of nutrients between sediments and water. Surprisingly, the mechanisms and magnitude of interactions mediated by these organisms are still poorly understood. To provide a synthesis of the importance of tube-dwelling invertebrates, we review existing research and integrate previously disregarded functional traits into an ecosystem model. Based on existing research and our models, we conclude that tube-dwelling invertebrates play a central role in controlling water column nutrient pools, and hence water quality and trophic state. Furthermore, these tiny ecosystem engineers can influence the thresholds that determine shifts between alternate clear and turbid states of shallow lakes. The large effects stand in contrast to the conventional limnological paradigm emphasizing predominantly pelagic food webs. Given the vast number of shallow lakes worldwide, benthic invertebrates are likely to be relevant drivers of biogeochemical processes at regional and global scales, thereby mediating feedback mechanisms linked to climate change.

Learning animals are predicted to use a flexible patch-leaving threshold (PLT) while foraging in a depletable environment under exploitative competition. This prediction was tested in flock-feeding Bewick's swans (Cygnus columbianus bewickii) depleting hidden tubers of fennel pondweed (Potamogeton pectinatus) in a two-dimensional, continuous environment. The swans' patch residence time was measured by combining recordings of the foraging behaviour and movement paths. The tuber biomass density was measured before and after the period of exploitation, using the presumable foraging window of the swans as the scale of measurement. Swan foraging was simulated in order to predict the effects of flexible and fixed PLTs, respectively, on the patch residence time and the spatial heterogeneity of the tuber biomass density. Flexible PLTs were predicted to lead to short and decreasing patch residence times and a decrease in the coefficient of variation in tuber biomass densities, whereas the reverse was generally the case for fixed PLTs. Observed patch residence times did not decrease with time and were intermediate between those predicted for swans with flexible and fixed PLTs. Furthermore, an increase of the coefficient of variation in the tuber biomass density was observed. Given the observed giving-up biomass densities the most likely model was one with swans with a fixed rather than a flexible PLT. These results point at factors that may affect the spacing behaviour or constrain the use of a flexible PLT in swans.

All over the world freshwater ecosystems like ponds, ditches and lakes suffer from nutrient-driven regime shifts from submerged plants to dominance by algae or free-floating plants. Although freshwaters are often connected and part of a network, most of our current knowledge on regime shifts comes from studies of isolated ecosystems. The few studies that have assessed the spatial manifestation of regime shifts overlooked the hydrological fact that the water flow through connected waters typically increases in the downstream direction. Here, we use a complex ecosystem model to show that this increase in flow does not lead to spatial differences in ecosystem state. We support these findings with a simple, analytically tractable, nutrient retention model on connected waterbodies. The model shows that all bodies have the same nutrient concentration despite spatial gradients in the flow of water as well as nutrients carried by the water. As a consequence, each connected waterbody is equally vulnerable to a regime shift, implying a regime shift to be system-wide. Furthermore, it appeared that each connected waterbody behaves the same as an isolated waterbody, implying that the vast body of theory on isolated systems, like alternative stable states theory, can still be useful for connected systems. Although these findings are violated when there is heterogeneity in lateral runoff or waterbody characteristics—leading to spatial differences in ecosystem state and therefore to differences in the vulnerability to a regime shift—they show that the typical downstream build-up of water flow does not necessarily lead to differences in ecological state, and thereby provide a basic concept to better understand the ecology of connected freshwaters.

In contradiction with field observations, theory predicts that the number of coexisting plankton species at equilibrium cannot exceed the number of limiting resources, which is called the "paradox of the plankton". Recently, Huisman & Weissing (1999, 2000) showed, in a model study, that the number of coexisting species may exceed the number of limiting resources when internal system feedback induces oscillations or chaos. In this paper, we use the term "supersaturated coexistence" for this phenomenon. On the basis of these findings, they claimed that the paradox of the plankton is solved. We investigated the prerequisites for supersaturated coexistence in the same model. Our results indicate that supersaturated coexistence is a rare phenomenon in parameter space, requires a very precise parameterization of the community members and is sensitive to the introduction of new species and the removal of the present species. This raises the question of whether supersaturated coexistence is likely to occur in nature. We conclude that the claim by Huisman & Weissing (1999, 2000) is premature. [KEYWORDS: biodiversity; chemostat; chaos; model;multiple resource competition; oscillations; persistence phytoplankton; supersaturated coexistence Phytoplankton; biodiversity; competition]

Stockholm University, Department of Systems Ecology, SE-10691, Stockholm, Sweden Aquatic Ecology and Water Quality Management Group, Department of Environmental Sciences, Wageningen University, P.O. Box 47, NL-6700 AA Wageningen, Netherlands Netherlands Environmental Assessment Agency, P.O. Box 303, 3720 AH Bilthoven, Netherlands Institute of Biology, Leiden University, Sylviusweg 72, 2300 RA Leiden, Netherlands Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, P.O. Box 338, 6700 AH Wageningen, Netherlands Department of Aquatic Ecology, Netherlands Institute of Ecology, P.O. Box 50, NL-6700 AB, Wageningen, Netherlands