Mathematical models with fixed parameters have a long history of use in describing the dynamics of populations in ecological interactions. However, in many instances, evolutionary changes in species characteristics can have a significant influence on these dynamics. Using evolutionary game theory, we incorporate evolution into population dynamic models and apply the resulting “Darwinian dynamic” models to study the effects that evolutionary changes can have on populations in several ecological scenarios. We start with a single species (Chapter 2), then add a competitor (Chapter 3), and a predator (Chapter 4). In Chapter 2, a rigorous mathematical analysis of the Darwinian logistic model for a single species shows that stable equilibria occur at strategies that maximize population size rather than growth rate. We apply this model to the data obtained from an experimental study on genetically perturbed populations of the flour beetle Tribolium castaneum. In Chapter 3, we apply a Darwinian dynamic modification of the Lotka-Volterra model to investigate circumstances under which evolution will change expected competitive outcomes. We compare the results of our Darwinian Lotka-Volterra model to studies in which unusual observations were made in studies of the flour beetles T. castaneum and T. confusum, including a reversal in the “winner” of competitive exclusion, and evolution from exclusion to coexistence. Chapters 2 and 3 provide one of the few examples in which evolutionary game theory has been successfully applied to empirical data. From a foundation provided by the Darwinian logistic equation, we build Darwinian dynamic models with two and three trophic levels to study effects of evolution on some basic ecological interactions in Chapter 4. We show how a consumer can cause a resource (producer) species to evolve to a mean strategy that increases its growth rate rather than its population size. We also briefly study how predation on the consumer species can affect equilibrium strategies of species lower in the food chain. Our results show how evolutionary game theoretic methods can be useful for studying both theoretical and applied problems that arise due to evolutionary processes, even when they occur on a ecological time scale. They provide a foundation for the future study of evolutionary effects in larger complex networks of interacting species.

Ecological systems are difficult to understand, let alone predict. The reason is their enormous complexity that arises from numerous organisms interacting with each other and their environment in a multitude of ways. However, this understanding is crucial to secure a plentitude of services that are provided by ecological systems. A substantial proportion of these services are carried out by microorganisms such as bacteria, fungi, and archaea. For example, microorganisms contribute to degradation of organic matter, water purification, and even regulation of the global climate. Therefore, a thorough understanding of the ecology of microorganisms is particularly relevant for our future well-being. While microorganisms are comparatively well-suited for experimental studies, owing also to recent technological advances in molecular biology, it is necessary to apply theory and modeling in order to fully benefit from the empirical data. A widely used theoretical method in microbial ecology is individual-based modeling, in which population or community dynamics emerge from the behavior and interplay of individual entities that are simulated according to a predefined set of rules. However, existing individual-based models of microbial communities are often specialized on particular research questions or require proficiency in specific programming languages or software. These limitations can be hampering for a broad and systematic application of individual-based modeling in microbial ecology. For this thesis, McComedy, a framework and software tool for the creation and running of individual-based models of microbial consumer-resource systems, was developed. It allows for fast and user-friendly model development by flexibly combining pre-implemented building blocks that represent physical, biological, and evolutionary processes. The ability of McComedy to capture the essential dynamics of microbial consumer-resource systems was demonstrated by reproducing and furthermore adding to the results of two distinct studies from the literature. McComedy was furthermore applied to study the evolution of metabolic interactions between bacteria. More specifically, it was assessed whether cooperative exchange of costly metabolites can evolve in bacterial multicellular aggregates. The results indicate that this is in principle possible, however, it depends on the mechanism by which the metabolites are exchanged. If metabolites are exchanged via diffusion through extracellular space, cooperation is not expected to evolve. On the other hand, if metabolites are transferred by contact-dependent means, for instance via intercellular nanotubes, cooperation is likely to evolve. Overall, contributions from this thesis comprise, first, a user-friendly modeling tool that can be used by microbial ecologists, second, insights into the evolution of metabolic interactions in bacterial systems, and, third, awareness of how the mechanistic consideration of a process can drastically affect the outcome of a modeling study.

Much research debates whether properties of ecological networks such as nestedness and connectance stabilise biological communities while ignoring key behavioural aspects of organisms within these networks. Here, we computationally assess how adaptive foraging (AF) behaviour interacts with network architecture to determine the stability of plant-pollinator networks. We find that AF reverses negative effects of nestedness and positive effects of connectance on the stability of the networks by partitioning the niches among species within guilds. This behaviour enables generalist pollinators to preferentially forage on the most specialised of their plant partners which increases the pollination services to specialist plants and cedes the resources of generalist plants to specialist pollinators. We corroborate these behavioural preferences with intensive field observations of bee foraging. Our results show that incorporating key organismal behaviours with well-known biological mechanisms such as consumer-resource interactions into the analysis of ecological networks may greatly improve our understanding of complex ecosystems.

Consumer-resource interactions are the basic building blocks of every food web. In spite of being a central research theme of longstanding interest in ecology, the mechanisms governing the stability and persistence of consumer-resource interactions are still not entirely understood. In particular, theoretical predictions on consumer-resource stability along gradients of temperature and nutrient enrichment diverge widely and are sometimes in conflict with empirical results. In this thesis I address these issues from the angle of the functional response, which describes a consumer’s feeding rate as a function of resource density. Specifically, I explore mechanistic, nutrient-based consumer-resource interaction models with respect to the influence of feeding behavior (the shape of the functional response), environmental temperature, nutrient enrichment, and resource quality on consumer-resource stability and persistence. In order to parameterize these models I performed extensive laboratory experiments with pairs of freshwater pelagic algae and grazers of the genus Daphnia, which are widespread, ecologically important model organisms. I found a sigmoidal type III functional response in every studied Daphnia-algae species pair. The exact form of its shape is described by an exponent b which is determined by fitting functional response models to the experimental data. A high value of b can stabilize consumer-resource systems under the otherwise destabilizing influence of nutrient enrichment, as predicted by a novel stability criterion relating b to the consumer’s prey handling time, food conversion efficiency and mortality. Estimated parameter values and, consequently, stability predictions are sensitive to the method of parameter estimation, and I propose a new estimation procedure that minimizes parameter uncertainty. Because many consumers’ feeding rates depend on temperature, warming is expected to strongly affect food web stability. In functional response experiments over a broad temperature gradient, I found that the attack rate coefficient and the maximum ingestion rate of Daphnia are hump-shaped functions of temperature. Moreover, the functional response exponent increases with warming towards stronger type III responses. Plugging these findings into a nutrient-based consumer-resource model, I found that predator persistence is a U-shaped function of temperature in nutrient enrichment-temperature space. Enrichment easily turns the system unstable when the consumer has a type II response, whereas a type III response opens up a large region of stability at intermediate, for the consumer optimal, temperatures. These findings reconcile seemingly conflicting results of earlier studies of temperature effects on consumer-resource dynamics, which can be mapped as special cases onto the enrichment-temperature space. I finally demonstrate the utility of three key model ingredients - temperature dependence of rate parameters, a mechanistic description of the dynamics of algal resources, and a type III functional response in Daphnia - by successfully implementing them in the description and explanation of phytoplankton-Daphnia dynamics in a mesocosm experiment exploring effects of warming on the spring succession of the plankton.

The objective of this thesis was to investigate the effects of mammalian grazers, such as microtine rodents and reindeer, (top-down effects) and nutrient availability (bottom- up effects) on the plant community of a tundra heath. I conducted a large-scale fertilization experiment and studied the impact of grazers using exclosures. I measured the effects of fertilization and grazing on soil microbial activity and nutrient cycling. I investigated the responses to fertilization of the invertebrate community, I studied the effects on the quality of bilberry as food for mammalian herbivores, and I looked at how concentrations of nutrients and carbon-based secondary defences against herbivory fluctuated between seasons in unfertilized and fertilized treatments. The results of my thesis show that the plant community investigated is exposed to a strong top-down control by mammalian herbivores. On the fertilized and grazed areas the aboveground biomass of the vascular plant community did not increase compared to unfertilized areas. However, the productivity of the plant community was clearly nutrient- limited. During the eight years of the experiment, on the fertilized areas plant biomass was significantly increased inside the herbivore exclosures In my study mammalian herbivores at comparatively low densities and grazing outside the growing season were sufficient to control the biomass of a heterogeneous plant community. Microtine rodents (Norwegian lemmings and grey-sided voles) preferred the fertilized areas for overwintering. The food plant quality of bilberry for grey-sided voles was improved on the fertilized areas throughout the year. Grazing decreased the nitrogen storage in the aboveground plant biomass. Reindeer and rodents had also important indirect effects on the plant community by decelerating soil nutrient cycling and soil microbial activity. This effect may be accelerated by the impact of herbivore on plant species composition. Graminoids, which contained the highest nitrogen concentrations in their tissues, increased rapidly on the fertilized areas, but their abundance was significantly lower on grazed fertilized areas. The invertebrate community was detritus-based and received their energy indirectly from the litter via soil microbes and detritivores. Fertilization increased the biomass of invertebrate carnivores, but had no effect on the biomass of invertebrate herbivores. Apparent competition between detritivores and invertebrate herbivores, mediated by carnivorous invertebrates predating on both of them, is supposed to keep the densities and grazing pressure of invertebrate herbivores low. Grazing damage by invertebrates was very low and only 0.021 % of the total vascular plant biomass was removed. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 2001, härtill 6 uppsstser.</p> / digitalisering@umu

Species diversity may simultaneously be a cause and a consequence of variability in population, community and ecosystem properties. Ecology has traditionally focused on elucidating the causes of biodiversity. However, in the last decade and a half ecologists have asked the opposite question: What are the consequences of species diversity? The majority of these studies elucidated the effects of species diversity within single trophic levels. Incorporating trophic complexity is the next step in this research program. In this dissertation I investigated the causes of resource species diversity, as well as the impacts that resource diversity has on rates of consumption and the stability of population, community and ecosystem properties over time in planktonic food webs. The high diversity of phytoplankton found in nature appears to defy the competitive exclusion principle, and elucidating the mechanisms which maintain this diversity continues to be a challenge. In general, variability in limiting factors is required to maintain non-neutral species diversity, but this variability can be generated by forces outside of the competitive community (i.e. exogenous), or may be the outcome of competitive interactions themselves (i.e. endogenous). Using microcosm experiments, I showed that endogenously generated variability in limiting factors was more effective at maintaining phytoplankton species diversity over the long-term, although the strength of this effect depended on the composition of the phytoplankton community. Existing resource diversity has been proposed to generally weaken consumer-resource interaction strengths and limit consumer control of resource biomass. This is because more diverse resource communities are more likely to contain inedible, unpalatable, toxic or non-nutritious species. However, when resource communities contain multiple palatable species, diversity may also accelerate consumption. Using grazing experiments with multiple zooplankton consumer species, I found that the mechanism, direction and magnitude of modulation of consumption depended on the feeding selectivity of the consumer and the composition of the resource community. By altering consumer-resource interaction strengths in the short-term, resource species diversity may impact the stability of consumer-resource dynamics in the long-term. In separate microcosm experiments, I investigated the influence of resource species diversity, community composition and consumer feeding selectivity on population, community, and ecosystem properties over time. Diversity had positive effects on phytoplankton population biomass, resource community biomass, the rate of photosynthesis, the standing stock of particulate nutrients, and the generalist consumer’s population density. It also stabilized resource community biomass and the stocks of particulate nutrients over time. Unexpectedly, diversity did not stabilize either of the consumer populations, regardless of feeding selectivity. This suggests that effects of diversity on resource community properties do not impact consumer dynamics linearly. Resource community composition was generally more important than resource species diversity in determining food web properties. The importance of community composition in determining both the causes and consequences of resource diversity in these experiments points to the importance of species’ traits and the outcomes of their interactions. I suggest that the use of complex adaptive systems theory and trait-based approaches in the future will allow a consideration of the feedbacks between the causes and consequences of species diversity in food webs. / Graduate

No description available.

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.