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In simulation models of populations or communities, individual plants have often been obfuscated in favor of aggregated vegetation. This simplification comes with a loss of biological detail and a smoothing out of the demographic noise engendered by stochastic individual-scale processes and heterogeneities, which is significant among others when studying the viability of small populations facing challenging fluctuating environmental conditions. This consideration has motivated the development of precise plant-centered models. The accuracy gained in the representation of plant biology has then, however, often been balanced by the disappearance in models of important plant-soil interactions (esp. water dynamics) due to the inability of most individual-based frameworks to simulate complex continuous processes. In this study, we used a hybrid modeling approach, namely integrated System Dynamics (SD)—Individual-based (IB), to illustrate the importance of individual plant dynamics to explain spatial self-organization of vegetation in arid environments. We analyzed the behavior of this model under different parameter sets either related to individual plant properties (such as seed dispersal distance and reproductive age) or the environment (such as intensity and yearly distribution of precipitation events). While the results of this work confirmed the prevailing theory on vegetation patterning, they also revealed the importance therein of plant-level processes that cannot be rendered by reaction-diffusion models. Initial spatial distribution of plants, reproductive age, and average seed dispersal distance, by impacting patch size and vegetation aggregation, affected pattern formation and population survival under climatic variations. Besides, changes in precipitation regime altered the demographic structure and spatial organization of vegetation patches by affecting plants differentially depending on their age and biomass. Water availability influenced non-linearly total biomass density. Remarkably, lower precipitation resulted in lower mean plant age yet higher mean individual biomass. Moreover, seasonal variations in rainfall greater than a threshold (here, ±0.45 mm from the 1.3 mm baseline) decreased mean total biomass and generated limit cycles, which, in the case of large variations, were preceded by chaotic demographic and spatial behavior. In some cases, peculiar spatial patterns (e.g., rings) were also engendered. On a technical note, the shortcomings of the present model and the benefit of hybrid modeling for virtual investigations in plant science are discussed.

Modelling the inter-relationships between litter accumulation and plant–soil feedback is a major challenge to predict natural and agricultural ecosystem dynamics. At increasing levels of undecomposed plant litter, seedling growth tends to show a multi-faceted response trend, characterised by a peak of positive stimulation at lower dosage followed by inhibition at higher dosage. In this study, a new logistic model was developed to describe such trend and disentangle substrate-specific positive and negative effects of plant litter. The model was tested on 35 litter types applied to the common phytometer Lepidium sativum; all litter types were collected in Mediterranean shrublands of Campania region (southern Italy). Model fitting resulted to be generally higher relative to the widely used linear log response model, although in only half of the cases it also gave more parsimonious results in terms of minimising information loss. Positive and negative effects of plant litter resulted to be uncorrelated, showing that the overall trend is probably the result of the combined action of separate factors rather than the effect of a single factor behaving differently at the different doses. The results of this work provide new tools to finely tune the optimal doses in experiments on hormesis and litter phytotoxicity, through the identification of the most suited doses to centre the range of nearly linear response to litter concentration. A wide screening is also presented on the phytotoxicity profiles of a number of spontaneous plant species widely distributed in the Mediterranean area.

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.

Ring shaped patches of clonal plants fascinated plant ecologists since long time. In this work we review the reports on the occurrence of ring pattern in different environmental conditions, the growth forms of ring-forming plants, the mecha- nisms underlying ring formation, and the consequences for species diversity at community scale. Rings formed by 83 species of clonal vascular plants have been found in grasslands, deserts, bare substrates of lava flow, harvested peat lands, salt marshes, and sand dunes. Four causal hypotheses have been proposed for the emergence of ring patterns: i. occurrence of architectural constraints for ramets development; ii. induction by fire, drought, trampling or overgrazing; iii. nutrient and water depletion by competition inside the ring; and iv. onset of species-specific negative plant-soil feedback in the inner zone of the clone. Since almost all the available studies are observations of ring structure or modelling exercises, none of the putative mechanisms for ring formation emerged from the literature as either generally applicable or suitable for rejection. Therefore, long-term field experiments are needed to investigate the relative prevalence of different mechanisms in different environments. Ring formation bears important consequences at community scale, because ring forming plants often act as “nurses”, enhancing the recruitment and development of different plant species. In fact, ring establishment modifies above- and below-ground environmental con- ditions, providing specialized safe sites for beneficiaries in the inner zone of the clones. Such interspecific facilitation by ring forming plants, particularly in chronically stressed environments, contributes to increase plant species richness and can locally promote the successional dynamics.

Spatial patterns and self-organization of plants has been a subject of fascination because the underlying mechanisms have been hard to determine, raising different explanatory hypotheses. Plant–soil negative feedback (PSNF) – defined as the induction of negative conditions for conspecific establishment – has been widely studied in both field and laboratory conditions, and conceptually demonstrated by some modelling works. We present a mechanistic model, integrating individual plants inside an agent-based framework, to explore the effects of PSNF on the spatial and temporal dynamics of virtual populations and communities of plants of diverse growth forms. This endeavour led to the reproduction of well-known vegetation patterns observed at various scales, demonstrating for the first time a unified mechanism behind the spatial patterns of Janzen–Connell seedlings’ distribution, ring formation, and the high species mobility in species-rich grasslands. These results support the ecological relevance of PSNF in the regulation of spatial organization and biodiversity dynamics in plant communities. More specifically, PSNF due to autoxicity seems most coherent with the spatio-temporal scale of dynamics displayed here.

The broad diffusion and active management by man of the sweet chestnut in past centuries has resulted in the establishment of the species at the limits of its potential ecological range in many European mountain areas. This raises the hypothesis that the chestnut tree has considerable plasticity, enabling the species to adapt to very different sites and conditions. In order to test this hypothesis, we applied the pipe-model approach, postulating the constancy of the leaf area/sapwood area (LA/SA) relationship for single portions of a tree. We analysed the variation of the LA/SA coefficient among chestnut trees subjected to different sites conditions (e.g., convex vs. concave sites) in order to gain insight into the plasticity of the species. The results confirmed that the sweet chestnut is able to greatly vary the allocation of resources with respect to environmental conditions. In particular, the LA/SA coefficient was high when trees were growing in sites with good water supply (e.g., concave sites or gentle slopes) and low in water stressed convex or steep sites.

A predator's foraging performance is related to its ability to acquire sufficient information on environmental profitability. This process can be affected by the patchy distribution and clustering of food resources and by the food intake process dynamics. We simulated body mass growth and behaviour in a forager acting in a patchy environment with patchy distribution of both prey abundance and body mass by an individual-based model. In our model, food intake was a discrete and stochastic process and leaving decision was based on the estimate of net energy gain and searching time during their foraging activities. The study aimed to investigate the effects of learning processes and food resource exploitation on body mass and survival of foragers under different scenarios of intra-patch resource distribution. The simulation output showed that different sources of resource variability between patches affected foraging efficiency differently. When prey abundance varied across patches, the predator stayed longer in poorest patches to obtain the information needed and its performance was affected by the cost of sampling and the resulting assessment of the environment proved unreliable. On the other hand, when prey body mass, but not abundance, varied among the patches the predator was quickly able to assess local profitability. Both body mass and survival of the predator were greatly affected by learning processes and patterns of food resource distribution.

Understanding how animals forage has always been a fundamental issue in Ethology and has become critical more recently in Environmental Conservation. Since the formalization of optimal foraging theory, theoretical models intended to depict the behavior of a generic forager have served as the main tools to analyze and ultimately comprehend the mechanisms of foraging. Due to complexity and technical constraints, these models have traditionally focused on single aspects of foraging, leaving out other concurrent processes that may also interplay. The recent inclusion of several facets inside united models has given rise to interesting results on the importance of interacting factors such as memory and resource heterogeneity. In this paper, we present a hybrid model integrating metabolism, foraging decisions, memory, as well as spatially explicit movement and resource distribution. We use it to examine the effects of spatial resource distribution – an aspect often neglected in favor of probabilistic resource heterogeneity – on the viability of a generic random-walking forager, and rely on the model to devise an ecological metric that can explain and render the relative profitability of given spatial distributions. Furthermore, we assess the significance of memory properties relatively to the profitability of resource distributions. Most notably, we reveal contrasted effects of memory depending on the aspect of resource varied in space (i.e. prey abundance, or prey body mass). On the whole, a general comparison of our findings with results obtained with spatially implicit models leads us to stress the complex interaction between memory and spatial resource distribution as well as the criticality of spatial representation in the modeling of foraging. Accordingly, we conclude with a discussion on the ecological implications of these results, as well as the advantages of hybrid modeling for the accurate simulation of foraging.

Development of a comprehensive theory of the formation of vegetation patterns is still in progress. A prevailing view is to treat water availability as the main causal factor for the emergence of vegetation patterns. While successful in capturing the occurrence of multiple vegetation patterns in arid and semiarid regions, this hypothesis fails to explain the presence of vegetation patterns in humid environments. We explore the rich structure of a toxicity-mediated model of the vegetation pattern formation. This model consists of three PDEs accounting for a dynamic balance between biomass, water, and toxic compounds. Different (ecologically feasible) regions of the model???s parameter space give rise to stable spatial vegetation patterns in Turing and non-Turing regimes. Strong negative feedback gives rise to dynamic spatial patterns that continuously move in space while retaining their stable topology.

This paper focuses on fire and grazing with an emphasis on work in Mediterranean environments. Fire and grazing accounted for more variation than the combination of all other environmental and spatial variables. Fire and grazing may have antagonistic effects over relatively short timescales. Grazing reduces plant growth and removes available fuel, thus reducing the intensity of fire, and their combined effect is thus less than expected from the sum of their individual impacts. The modelling exercises in this chapter show the power of existing modelling tools to examine some of the complex interactions of ecological processes, such as the combined effects of grazing, fire and dispersal processes, on patterns of plant competition. The level of model integration achieved allows the theoretical investigation of well-known ecological processes such as the successional patterns under different disturbance regimes and the effects of the introduction of exotic species on the diversity of natural vegetation.

DNA is usually known as the molecule that carries the instructions necessary for cell functioning and genetic inheritance. A recent discovery reported a new functional role for extracellular DNA. After fragmentation, either by natural or artificial decomposition, small DNA molecules (between ∼50 and ∼2000 bp) exert a species specific inhibitory effect on individuals of the same species. Evidence shows that such effect occurs for a wide range of organisms, suggesting a general biological process. In this paper we explore the possible molecular mechanisms behind those findings and discuss the ecological implications, specifically those related to plant species coexistence.

Ring shaped patches of clonal plants have been reported in different environments, but the mechanisms underlying such pattern formation are still poorly explained. Water depletion in the inner tussocks zone has been proposed as a possible cause, although ring patterns have been also observed in ecosystems without limiting water conditions. In this work, a spatially explicit model is presented in order to investigate the role of negative plant-soil feedback as an additional explanation for ring formation. The model describes the dynamics of the plant biomass in the presence of toxicity produced by the decomposition of accumulated litter in the soil. Our model qualitatively reproduces the emergence of ring patterns of a single clonal plant species during colonisation of a bare substrate. The model admits two homogeneous stationary solutions representing bare soil and uniform vegetation cover which depend only on the ratio between the biomass death and growth rates. Moreover, differently from other plant spatial patterns models, but in agreement with real field observations of vegetation dynamics, we demonstrated that the pattern dynamics always lead to spatially homogeneous vegetation covers without creation of stable Turing patterns. Analytical results show that ring formation is a function of two main components, the plant specific susceptibility to toxic compounds released in the soil by the accumulated litter and the decay rate of these same compounds, depending on environmental conditions. These components act at the same time and their respective intensities can give rise to the different ring structures observed in nature, ranging from slight reductions of biomass in patch centres, to the appearance of marked rings with bare inner zones, as well as the occurrence of ephemeral waves of plant cover. Our results highlight the potential role of plant-soil negative feedback depending on decomposition processes for the development of transient vegetation patterns.

Modeling could be summed up as the task of reproducing the structure and imitating the behavior of complex real-life systems with components interacting with one another at different scales. In many disciplines of ecology, System Dynamics and more recently Individual-Based modeling have emerged as the major tools to support this task. These techniques have usually been considered until now as exclusive alternatives instead of synergistic tools. The present paper starts by presenting the two approaches, and compares them to identify their strong and weak points depending on the type of components constituting the system under consideration. Then we isolate a class of systems difficult or in some cases impossible to model dynamically using any of these approaches alone, because of conceptual limitations. We further point out the usefulness of merging the two paradigms inside of a hybrid modeling framework to handle this class of systems, and present what we consider as the elementary combination patterns of System Dynamics and Individual-Based modeling. Since the power of this promising approach has been unexplored in most fields of ecology, we suggest some possible applications illustrating its usefulness.

Current theories may not fully explain why latitudinal patterns of plant diversity differ between terrestrial and flooded ecosystems. Moreover, the co-occurrence of hyper diverse stands in lowland tierra firma (not inundated) forests and almost monospecific stands in mangroves and gallery riparian vegetation within the tropics remains enigmatic. Building on evidence from ecology and agriculture, we present a new model investigating the hypothesis that, besides the general positive feedback of plant growth by nutrients release, litter decomposition builds up an intra-specific negative feedback functionally linked with tree diversity. The model results were compared with extensive published data sets both across and within latitudinal zones. The model predicts correctly the biomass production and decomposition process, as well as the number of tree species, their relative abundance in all environmental conditions providing a novel, putative explanation also for the diversity variations observed within the tropics. The model demonstrates a possible mechanistic link between the carbon cycle and biodiversity patterns, which is interesting in the debate about advancing in the direction of a unifying ecosystem theory.

Diversity of forest trees ranges from monospecific stands to the astonishing richness of tierra firma tropical forests. Such patterns are observed along gradients of latitude, altitude, soil fertility and rainfall. So far, the proposed coexisting mechanisms do not provide a comprehensive and unequivocal explanation of these patterns at the community level. We propose a new theory linking species diversity with organic matter cycle and negative plant-soil feedback induced by litter autotoxicity. This approach focuses on resource-waste rather than resource-only dynamics. High diversity does occur where litter decomposition is rapid and ecosystem nutrient cycles are closed. On the other hand, single species dominance is found where litter decomposition is slow and/or autotoxicity is removed from the nutrient cycle pathway. Unlike previous theoretical views, the one we present proves potentially capable of explaining differences in species diversity both along environmental gradients and within the tropics.

Different mechanisms, including equilibrium and non-equilibrium processes, have been taken into account as possible theoretical explanations of species coexistence. Despite the ample evidence on the existence of negative plant–soil feedback in both agriculture and natural vegetation, the role of these processes in the organization and dynamics of plant communities has so far been neglected. In this study, simulations by an individual-based competition model show how the intensity of negative feedback on individual plant performance can produce faster successional dynamics and allow species coexistence in two- and multi-species systems. The results show that even low levels of negative plant–soil feedback can enable species coexistence and often produce cyclic population dynamics. Moreover, the model highlights how negative feedback can generate positive reciprocal interspecific interactions at the population level, despite the fact that only competitive interactions is present between individual plants. In fact, competitive effects occur on a short-term scale, but positive reciprocal species interactions emerge only if negative feedback affects all species and if longer periods of simulation, more than the species life span, are considered. An important outcome of the model is the evidence that the effects at population level are timescale-dependent, thus showing the limitation of short-term species removal experiments used in traditional competition studies.

High mountains have sensitive social-ecological systems (SESs) characterized by fragility, complexity, and marginality. The local economies of these environments mainly rely on primary production, tourism, and leisure activities; thus human-ecosystem interactions are intricately linked. Many authors stress that this strict relationship must be assisted with a participatory approach involving interested stakeholders in the conceptualization, specification, and synthesis of knowledge and experience into useable information for the express purpose of addressing a problem complex. This paper presents experience garnered with a participatory modeling framework combining hard and soft methodology in 2 case studies: the Sagarmatha National Park and Buffer Zone (Nepal) and the Central Karakoram National Park (Pakistan). The modeling framework was developed based on local stakeholders' demands and needs; it consists of 5 modules, briefly presented here along with their conceptual background. In developing the framework, particular emphasis was given to considering the needs of decision-makers at the local level, rather than simply providing technical solutions to abstract problems. From the development of this modeling process, a need emerged to structure a management-oriented research module in order to generate management knowledge that is both stakeholder-relevant and evidence-based. The application of the framework in the 2 cases studies showed that the modeling can trigger valuable discussion among stakeholders as well as guidance for management-oriented research and feedback loops ensuring validation of knowledge. In addition, the resulting scenarios can help decision-makers in defining pathways for sustainable development in mountain areas, where people's livelihoods are closely dependent on ecosystems. The framework was developed in such a way that it can be replicated in other mountain areas with similar challenges.