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Understanding the impact of warming on organisms, communities and ecosystems is a central problem in ecology. Although species responses to warming are well documented, our ability to scale up to predict community and ecosystem properties is limited. Improving understanding of the mechanisms that link patterns and processes over multiple levels of organisation and across spatial and temporal scales promises to enhance our ability to predict whether the biosphere will exacerbate, or mitigate, climate warming. In this thesis, I combine ideas from metabolic theory with a variety of experimental approaches to further our understanding of how warming will impact photosynthesis and respiration across scales. Firstly, I show how phytoplankton can rapidly evolve increased thermal tolerance by downregulating rates of respiration more than photosynthesis. This increased carbon-use efficiency meant that evolved populations allocated more fixed carbon to growth. I then explore how constraints on individual physiology and community size structure influence phytoplankton community metabolism. Using metabolic theory, I link community primary production and respiration to the size- and temperature- dependence of individual physiology and the distribution of abundance and body size. Finally, I show that selection on photosynthetic traits within and across taxa dampens the effects of temperature on ecosystem-level gross primary production in a set of geothermal streams. Across the thermal-gradient, autotrophs from cold streams had higher photosynthetic rates than autotrophs from warm streams. At the ecosystem-level, the temperature-dependence of gross primary productivity was similar to that of organism-level photosynthesis. However, this was due to covariance between biomass and stream temperature; after accounting for the effects of biomass, gross primary productivity was independent of temperature. Collectively, this work emphasises the importance of ecological, evolutionary and physiological mechanisms that shape how metabolism responds to warming over multiple levels of organisation. Incorporating both the direct and indirect effects of warming on metabolism into predictions of the biosphere to climate futures should be considered a priority.

Understanding the processes responsible for gradients in biodiversity is a central goal of ecological research. In order to elucidate the processes responsible for community assembly and structure, it is useful to adopt a functional trait approach to community ecology. This is because species names provide little information regarding how constituent species interact. In addition, assembly rules based on species names are likely to become intractably complex with increasing species richness but rules based on traits can provide simple, broadly applicable. In turn, generality is gained by emphasizing functional traits. Here I first build from a previously published model that merged metabolic theory with a model of community evolution and assembly to derive a general assembly rule based on a continuous functional trait and compare this rule with a broad suite of empirical data (Chapter 1). However, linking metabolism to macroevolutionary rates and patterns has thus far been limited to non-ecological, static models. These models are not inconsistent with empirical data, but are relatively limited in their predictive ability (Chapter 2). I thus next develop a fully dynamic `metabolic theory of biodiversity' (MTB) that explicitly implements the qualitative framework proposed in Allen et al. (2007). With this model I examine the influence of temperature dependent mutation rate on speciation rate, extinction rate and species richness (Chapter 2). The model predicts a variable influence of temperature, but the processes responsible for this variation are not immediately clear. I subsequently conduct a detailed analysis elucidating the key processes that allow/constrain a strong influence of temperature dependent mutation rate on species richness (Chapter 3). In addition to mutation rate, temperature-dependent metabolism can influence ecological (feeding and mortality) and ecosystem (e.g. decomposition and in turn nutrient supply) rates. As such, I extend the model developed in chapters 1-3 to incorporate these additional temperature dependencies and derive predictions for the influence of temperature over species richness (Chapter 4).

The combined effect of temperature, moisture and phosphorus availability on soil organic matter mineralization in permafrost affected soils of northern circumpolar region was investigated. This study was a part of research activities of the European project CryoCARB and it was primarily focused on the cryoturbated organic horizons of permafrost affected soils. During this study, the temperature sensitivity of the organic matter mineralization and its relation to the soil moisture and phosphorus availability was investigated using series of incubation experiments and field measurements.

Testing ecological theory at macroecological scales may be useful for disentangling abiotic influences from anthropogenic disturbances, and thus provide insights into fundamental processes that structure ecological communities. In tropical coral reef systems, our understanding of community structure is limited to small-scale studies conducted in moderately degraded regions, while larger regional or ocean scale analyses have typically focused on identifying human drivers of reef degradation. In this thesis, my collaborators and I combined stable isotope specimens, underwater visual censuses, and remote sensing data from 43 Pacific islands and atolls in order to examine the relative roles of natural environmental variation and anthropogenic pressures in structuring coral reef fish and benthic communities. First, at unexploited sites on Kiritimati Atoll (Kiribati), isotope estimates indicated that trophic level increased with body size across species and individuals, while negative abundance ~ body size relationships (size spectra) revealed distinct energetic constraints between energy-competing carnivores and energy-sharing herbivores. After demonstrating size structuring of reef fish communities in the absence of humans, we then examined evidence for size-selective exploitation impacts on coral reefs across the Pacific Ocean. Size spectra 'steepened' as human population density increased and proximity to market center decreased, reflecting decreases in large-bodied fish abundance, biomass, turnover rate, and mean trophic level. Depletion of large fish abundances likely diminishes functions such as bioerosion by grazers and food chain connectivity by top predators, further degrading reef community resilience. Next, we considered the relative strengths of abiotic, biotic and anthropogenic influences in determining reef benthic state across spatial scales. We found that from fine (0.25 km2) to coarse (1,024 km2) grain scales the phase shift index (a multivariate metric of the relative cover of hard coral and macroalgal) was primarily predicted by local abiotic and bottom-up influences, such that coral-dominated reefs occurred in warm, productive regions at sites exposed to low wave energy, irrespective of grazing or human impacts. Our size- based analyses of reef fish communities revealed novel exploitation impacts at ocean-basin scales, and provide a foundation for delineating energetic pathways and feeding interactions in complex tropical food webs. Furthermore, we demonstrate that abiotic constraints underpin natural variation among fish and benthic communities of remote uninhabited reefs, emphasizing the importance of accounting for local environmental conditions when developing quantitative baselines for coral reef ecosystems. / Graduate / 0329

The ant colony, known as a self-organized system, can adapt to the environment by a series of negative and positive feedbacks. There is still a lack of mechanistic understanding of how the factors, such as temperature and food, coordinate the labor of ants. According to the Metabolic Theory of Ecology (MTE), the metabolic rate could control ecological process at all levels. To analyze self-organized process of ant colony, we constructed an agent-based model to simulate the energy and population dynamics of ant colony. After parameterizing the model, we ran 20 parallel simulations for each experiment and parameter sweeps to find patterns and dependencies in the food and energy flow of the colony. Ultimately this model predicted that ant colonies can respond to changes of temperature and food availability and perform differently. We hope this study can improve our understanding on the self-organized process of ant colony.

No description available.

Cette thèse a pour objectif de combiner plusieurs théories opérant à différentes échelles spatiales afin de mieux prédire l'effet des changements globaux, tels que la modification du climat, l’exploitation intensive des ressources ou la disparition des espaces naturels, sur la structure et le fonctionnement des écosystèmes. L'originalité de ce travail est l'utilisation de la masse corporelle des espèces pour caractériser à la fois leur dynamique spatiale, leurs interactions trophiques ainsi que les flux de biomasse au sein de l’écosystème. Cette approche offre l'avantage de relier les propriétés des écosystèmes à un trait fonctionnel mesurable à l'échelle de l'espèce, voire même de l'individu.J'étudie dans un premier temps le lien entre la diversité des écosystèmes et leur stabilité, qui est une question centrale dans le domaine de l’écologie. Il a été démontré que les écosystèmes très diversifiés en espèces ne devraient pas perdurer du fait de leur trop grande sensibilité aux perturbations, ce qui soulève un paradoxe puisque les écosystèmes riches en espèces abondent dans la nature. Grâce à la compilation et à l'analyse d'un important jeu de données d'écosystèmes empiriques, je montre qu'il n'existe pas de relation entre la stabilité, la diversité et la complexité des écosystèmes. Une analyse détaillée des données démontre que la structure très organisée des flux de biomasse observés entre les prédateurs et leurs proies est l’un des principaux fondements de la stabilité des écosystèmes.Je relie ensuite ces propriétés stabilisantes à des caractéristiques mesurables à l’échelle de l’espèce. À partir de la masse corporelle des espèces, je détermine les interactions trophiques, les besoins énergétiques ainsi que les biomasses à l’équilibre des espèces d’un écosystème afin de modéliser des réseaux trophiques réalistes. Je trouve que les écosystèmes composés d’espèces de masses corporelles très différentes sont caractérisés par un nombre important d'interactions proie-prédateur de faible intensité et sont plus stables que ceux possédant des espèces de masse corporelle similaires.J'étudie enfin l’effet de la taille et de l’isolement d’un habitat sur la moyenne et la variance de la masse corporelle des espèces qui y coexistent à partir de modèles intégrant les différences interspécifiques de dispersion, de vulnérabilité aux extinctions et la position trophique des espèces. Je compare les prédictions des modèles aux distributions de masse corporelle observées dans les assemblages de poissons récifaux tropicaux en me basant sur une base de données globale. L'analyse de ces données démontre que les assemblages locaux de poissons ne correspondent pas à un sous-ensemble aléatoire du pool régional et valident les prédictions de la théorie allométrique et trophique de la biogéographie des îles.L’intégration de l’écologie fonctionnelle, de la biogéographie et de la théorie sur la stabilité des systèmes dynamiques ouvre de nouvelles perspectives pour la conservation des écosystèmes puisqu'elle met en évidence l'effet de la fragmentation des espaces naturels sur la diversité fonctionnelle, et par extension sur la structure et le fonctionnement des écosystèmes. / The general objective of this thesis is to combine theories acting at different spatial scales in order to better predict the effect of global changes, such as such as resource overexploitation, climate change or habitat fragmentation, on ecosystem functioning. The unique feature of this work is the use of species body mass to describe both spatial dynamics, trophic interactions and biomass flows between the species of an ecosystem. An advantage to this approach is that it links ecosystem properties to a functional trait, measured at the species or even the individual level.First, I study the relationship between the diversity and the stability of ecosystems. It has been demonstrated that species-rich, complex ecosystems should be too sensitive to perturbations to persist through time, which raises a paradox as many species-rich ecosystems are observed in nature. With the compilation and the analysis of a large dataset of empirically measured ecosystems, I show that there is no relationship between stability and diversity or complexity in real ecosystems. A further analysis demonstrates that the non-random organization of energy flows between predators and prey allows complex ecosystem to be stable.A second step is to link this stabilizing structure to species functional traits. I derive food web topology, species energetic needs and equilibrium densities from body mass to build quantitative realistic food webs. I find that food webs composed of species with very different body masses are characterized by a high number of weak trophic interactions and are more stable than food webs with more similar species.Finally, I study the effect of habitat area and isolation of the mean and variance of species body mass distribution, using models integrating the interspecific variability of dispersal ability, vulnerability to extinctions and trophic position. I compare model predictions to observed body mass distributions of fish assemblages found on tropical reefs with a global database. I find that body mass distribution in local fish assemblages does not correspond to a random sample of the regional species pool, which confirms the predictions of the allometric and trophic theory of island biogeography.The integration of functional ecology, island biogeography and theory on the stability of complex systems open new perspectives in the fields of macroecology and ecosystem management since it highlights the potential impact of habitat destruction and fragmentation on the functional reorganization of species assemblages and therefore on the structure and functioning of ecosystems.

Biodiversity trends (such as the relationship between species richness and temperature or productivity) are always defined for a particular taxon at a specific area (the entire range of the taxon or often just a region arbitrarily chosen by researchers). The form of these trends varies between taxa and regions. The weak relationship between richness and temperature or productivity is sometimes interpreted as a counterevidence for the hypothesis explaining diversity patterns by these variables. However, the delimitation of taxa or region may play a crucial role for the form of the trends. The aim of this thesis is to determine whether some taxon properties (its size) or region properties (its area, range of explanatory variables, the temperature-productivity relationship or average temperature) affect the strength and slope of the richness-temperature and richness-productivity relationships. 46 data sets of species richness for a wide range of plants, invertebrates and ectothermic vertebrates within different regions of the world were used for the analysis. While the taxon size is likely to affect the strength and slope of the relationship when comparing individual (nested) subclades within larger clade, the comparison of different taxa in different regions of the world shows only the effect of the region...

Understanding how temperature affects biological systems is a central question in ecology and evolutionary biology. Anthropogenic climate change adds urgency to this topic, as the demise or success of species under climate change is expected to depend on how temperature affects important aspects of organismal performance, such as growth, development, survival and reproduction. Rates of biological processes generally increase with increasing temperature up to some maximal temperature. Variation in the slope of the initial, rising phase has attracted considerable interest and forms the focus of this thesis. I explore variation in growth rate-temperature relationships over several levels of biological organization, both between and within species, over individuals’ lifetime, depending on the ecological context and in relation to important life history characteristics such as generation length and winter dormancy.       Specifically, I examine how a clade of temperate damselflies have adapted to their thermal environment along a 3,600 km long latitudinal transect spanning from Southern Spain to Northern Sweden. For each of six species, I sampled populations from close to the northern and southern range margin, as well from the center of the latitudinal range. I reared larvae in the laboratory at several temperatures in order to measure indiviudal growth rates. Very few studies of thermal adaptation have employed such an extensive sampling approach, and my finding reveal variation in temperature responses at several levels of organization.       My main finding was that temperature responses became steeper with increasing latitude, both between species but also between latitudinal populations of the same species. Additional genetic studies revealed that this trend was maintained despite strong gene flow. I highlight the need to use more refined characterizations of latitudinal temperature clines in order to explain these findings. I also show that species differ in their ability to acclimate to novel conditions during ontogeny, and propose that this may reflect a cost-benefit trade-off driven by whether seasonal transitions occur rapidly or gradually during ontogeny.       I also carried out a microcosm experiment, where two of the six species were reared either separately or together, to determine the interacting effects of temperature and competition on larval growth rates and population size structure. The results revealed that the effects of competition can be strong enough to completely overcome the rate-depressing effects of low temperatures. I also found that competition had stronger effects on the amount of variation in growth rates than on the average value.       In summary, my thesis offers several novel insights into how temperature affects biological systems, from individuals to populations and across species’ ranges. I also show how it is possible to refine our hypotheses about thermal adaptation by considering the interacting effects of ecology, life history and environmental variation.