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

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.

Keyphrases: Allometric scaling, Bioenergetic model, Biomass dynamics, Community ecology, Community functioning, Computational ecology, Consumer-resource model, Food webs, Graph theory