Modelling Food Webs

We review theoretical approaches to the understanding of food webs. After an overview of the available food web data, we discuss three different classes of models. The first class comprise static models, which assign links between species according to some simple rule. The second class are dynamical models, which include the population dynamics of several interacting species. We focus on the question of the stability of such webs. The third class are species assembly models and evolutionary models, which build webs starting from a few species by adding new species through a process of "invasion" (assembly models) or "speciation" (evolutionary models). Evolutionary models are found to be capable of building large stable webs.Comment: 34 pages, 2 figures. To be published in "Handbook of graphs and networks" S. Bornholdt and H. G. Schuster (eds) (Wiley-VCH, Berlin

Complex dynamics in coevolution models with ratio-dependent functional response

We explore the complex dynamical behavior of two simple predator-prey models of biological coevolution that on the ecological level account for interspecific and intraspecific competition, as well as adaptive foraging behavior. The underlying individual-based population dynamics are based on a ratio-dependent functional response [W.M. Getz, J. Theor. Biol. 108, 623 (1984)]. Analytical results for fixed-point population sizes in some simple communities are derived and discussed. In long kinetic Monte Carlo simulations we find quite robust, approximate 1/f noise in species diversity and population sizes, as well as power-law distributions for the lifetimes of individual species and the durations of periods of relative evolutionary stasis. Adaptive foraging enhances coexistence of species and produces a metastable low-diversity phase and a stable high-diversity phase.Comment: 19 page

What does a bioenergetic network approach tell us about the functioning of ecological communities?

Les perturbations auxquelles font face les communautés écologiques, du fait des activités humaines, sont à l'origine de changements profonds dans ces communautés. Nombreuses caractéristiques des espèces sont altérées, de leur physiologie à leur occurrence même. Ces changements se répercutent sur la composition, la diversité et la structure des communautés, puisque les espèces n'interagissent pas tout le temps de la même manière en fonction des conditions. Prévoir le devenir de ces communautés émergentes, et des fonctions qu'elles soutiennent est un défi central de l'écologie et de nos sociétés. Différents cadres conceptuels ont été utilisés pour relever ce défi, basés sur différents mécanismes écologiques, et ont divergé en plusieurs domaines. D'un côté, l'analyse des chaînes trophiques utilise la consommation pour expliquer les effets de la diversité verticale (le nombre de niveaux trophiques) sur le fonctionnement, et de l'autre côté, les analyses biodiversité-fonctionnement lient compétition et effets de la diversité horizontale (la diversité au sein des niveaux trophiques isolés). Chacun de ces domaines a produit des résultats clés pour comprendre les conséquences fonctionnelles des changements de composition et diversité des communautés écologiques. Cependant, ils sont chacun basés sur différentes simplifications fortes des communautés. L'hypothèse qui sous-tend cette thèse est que la réconciliation en un même cadre de travail des résultats fondamentaux de ces champs conceptuels divergents, ainsi que des effets des changements de structure de la biodiversité, est une étape clé pour pouvoir améliorer notre compréhension du fonctionnement de communautés écologiques en changement. L'essor récent des méthodes d'analyse des réseaux trophiques, et des modèles permettant de simuler le fonctionnement de ces réseaux trophiques offre un cadre idéal pour cette réconciliation. En effet, les réseaux trophiques cartographient les échanges de matière entre toutes les espèces d'une communauté, permettant la mise en place d'interactions variées. Ils reflètent mieux la réalité complexe des communautés que les chaînes trophiques ou leurs niveaux trophiques isolés en intégrant notamment compétition et consommation. Un modèle ressource-consommateur bioénergétique classique, développé par Yodzis et Innes (1992), permet d'en simuler le fonctionnement, en intégrant des mécanismes et taux testés empiriquement. Au-delà d'utiliser ces outils, cette thèse se concentre aussi sur leur évaluation. Après un premier chapitre d'introduction, le second chapitre propose une plateforme ouverte, commune, solidement testée et efficace pour l'utilisation du modèle bioénergétique, permettant ainsi une synthèse plus rapide et aisée des résultats. Le troisième chapitre est une revue du corpus méthodologique d'analyse des réseaux trophiques, proposant une gamme de méthodes robustes et informatives, et soulignant leur domaine d'application et leurs limites. Enfin le quatrième chapitre met ce cadre méthodologique à l'épreuve. Dans ce chapitre, nous montrons l'existence d'une relation entre la complexité de la structure du réseau trophique des communautés et leur régime de fonctionnement, se traduisant par la réalisation de différentes prédictions issues de l'analyse des chaînes trophiques ou des analyses diversité-fonctionnement. Cette mise en évidence des conditions structurelles pour la réalisation de différentes prédictions nous permet de mieux comprendre quels mécanismes écologiques prédominent selon différentes conditions, dirigeant l'effet de la diversité sur le fonctionnement.Human-driven disturbances are causing profound changes in ecological communities, as many characteristics of species are altered, from their physiology to their very occurrence. These changes affect the composition, diversity and structure of communities, since species do not always interact in the same way under different conditions. Predicting the fate of these emerging communities, and the functions they support, is a central challenge for ecology and our societies. Diverging conceptual frameworks have been used to address this challenge, based on different ecological mechanisms. On the one hand, food chain analysis uses consumption to explain the effects of vertical diversity (the number of trophic levels) on functioning, and on the other hand, biodiversity-functioning analyses link competition and the effects of horizontal diversity (diversity within isolated trophic levels). Each of these domains has produced key results for understanding the functional consequences of changes in the composition and diversity of ecological communities. However, they are each based on different strong simplifications of communities. The hypothesis underlying this thesis is that reconciling the fundamental results of these divergent conceptual fields, as well as the effects of changes in the structure of biodiversity, into a single framework is a key step towards improving our understanding of the functioning of changing ecological communities. The recent development of food web analysis and of models to simulate food webs functioning provides an ideal framework for this reconciliation. Food webs map the exchange of matter between all species in a community, allowing for a variety of interactions to take place. They better reflect the complex reality of communities than food chains or their isolated trophic levels, notably by integrating competition and consumption. A classical consumer-resource bioenergetic model developed by Yodzis and Innes (1992) specifically makes it possible to realistically simulate their functioning, using empirically tested mechanisms and rates. Beyond using these tools, this thesis focuses on their evaluation and implementation. After a first, introductory chapter, the second chapter proposes an open, common, well-tested and efficient platform for the use of the bioenergetic model, allowing a faster and easier synthesis of the results. The third chapter is a review of the methodological corpus for ecological networks analysis, outlining a range of robust and informative methods, and highlighting their scope and limitations. Finally, the fourth chapter puts this methodological framework to the test. In this chapter, we show the existence of a relationship between the complexity of communities' food-web structure and functioning regime, resulting in the realization of different predictions from food chain analysis or diversity-functioning analyses. This demonstration of the structural conditions for the realization of different predictions allows us to better understand which ecological mechanisms predominate under different conditions, directing the effect of diversity on functioning

Modeling the ecology and evolution of communities: A review of past achievements, current efforts, and future promises

Background: The complexity and dynamical nature of community interactions make modeling a useful tool for understanding how communities develop over time and how they respond to external perturbations. Large community-evolution models (LCEMs) are particularly promising, since they can address both ecological and evolutionary questions, and can give rise to richly structured and diverse model communities. Questions: Which types of models have been used to study community structure and what are their key features and limitations? How do adaptations and/or invasions affect community formation? Which mechanisms promote diverse and table communities? What are the implications of LCEMs for management and conservation? What are the key challenges for future research? Models considered: Static models of community structure, demographic community models, and small and large community- evolution models. Conclusions: LCEMs encompass a variety of modeled traits and interactions, demographic dynamics, and evolutionary dynamics. They are able to reproduce empirical community structures. Already, they have generated new insights, such as the dual role of competition, which limits diversity through competitive exclusion, yet facilitates diversity through speciation. Other critical factors determining eventual community structure are the shape of trade-off functions, inclusion of adaptive foraging, and energy availability. A particularly interesting feature of LCEMs is that these models not only help to contrast outcomes of community formation via species assembly with those of community formation via gradual evolution and speciation, but that they can furthermore unify the underlying invasion processes and evolutionary processes into a single framework

Local flexibility in feeding behaviour and contrasting microhabitat use of an omnivore across latitudes

As the environment is getting warmer and species are redistributed, consumers can be forced to adjust their interactions with available prey, and this could have cascading effects within food webs. To better understand the capacity for foraging flexibility, our study aimed to determine the diet variability of an ectotherm omnivore inhabiting kelp forests, the sea urchin Echinus esculentus, along its entire latitudinal distribution in the northeast Atlantic. Using a combination of gut content and stable isotope analyses, we determined the diet and trophic position of sea urchins at sites in Portugal (42° N), France (49° N), southern Norway (63° N), and northern Norway (70° N), and related these results to the local abundance and distribution of putative food items. With mean estimated trophic levels ranging from 2.4 to 4.6, omnivory and diet varied substantially within and between sites but not across latitudes. Diet composition generally reflected prey availability within epiphyte or understorey assemblages, with local affinities demonstrating that the sea urchin adjusts its foraging to match the small-scale distribution of food items. A net “preference” for epiphytic food sources was found in northern Norway, where understorey food was limited compared to other regions. We conclude that diet change may occur in response to food source redistribution at multiple spatial scales (microhabitats, sites, regions). Across these scales, the way that key consumers alter their foraging in response to food availability can have important implication for food web dynamics and ecosystem functions along current and future environmental gradients

The robustness, link-species relationship and network properties of model food webs

New results are collected using the Webworld model which simulates evolutionary food web construction with population dynamics (Drossel et al., 2001 [1]). We show that it supports a link-species relationship of neither constant link-density nor constant connectance, and new properties for the food webs are calculated including clustering coefficients and stability in the sense of community robustness to species deletion. Time-series for more than 40 properties of the taxonomic and trophic webs are determined over the course of individual simulations. Robustness is found to be positively correlated with connectance, but negatively with diversity, and we study the long-term development of model webs including the distribution of extinction events in a simulation with 108 speciation event