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1	Population genomics of pollinating fig wasps and their natural enemies Cooper, Lisa Suzanne January 2018 (has links) The advent of next generation sequencing technologies has had a major impact on inference methods for population genetics. For example, community ecology studies can now assess species interactions using population history parameters estimated from genomic scale data. Figs and their pollinating fig wasps are obligate mutualists thought to have coevolved for some 75 million years. This relationship, along with additional interactions with many species of non-pollinating fig wasps (NPFW), makes this system an excellent model for studying multi-trophic community interactions. A common way of investigating the population histories of a community's component species is to use genetic markers to estimate demographic parameters such as divergence times and effective population sizes. The extent to which histories are congruent gives insights into the way in which the community has assembled. Because of coalescent variance, using thousands of loci from the genomes of a small number of individuals gives more statistical power and more realistic estimates of population parameters than previous methods using just a handful of loci from many individuals. In this thesis, I use genomic data from eleven fig wasp species, which are associated with three fig species located along the east coast of Australia, to characterise community assembly in this system. The first results chapter describes the laboratory and bioinformatic protocols required to generate genomic data from individual wasps, and assesses the level of genetic variation present across populations using simple summaries. The second results chapter presents a detailed demographic analysis of the pollinating fig wasp, Pleistodontes nigriventris. The inferences were made using a likelihood modelling framework and the pairwise sequentially Markovian coalescent (PSMC) method. The final results chapter characterises community assembly by assessing congruence between the population histories inferred for eight fig wasp species. The population histories were inferred using a new composite likelihood modelling framework. I conclude by discussing the implications of the results presented along with potential future directions for the research carried out in this thesis.
2	Systèmes de particules en interaction, approche par flot de gradient dans l'espace de Wasserstein / Interacting particles systems, Wasserstein gradient flow approach Laborde, Maxime 01 December 2016 (has links) Depuis l’article fondateur de Jordan, Kinderlehrer et Otto en 1998, il est bien connu qu’une large classe d’équations paraboliques peuvent être vues comme des flots de gradient dans l’espace de Wasserstein. Le but de cette thèse est d’étendre cette théorie à certaines équations et systèmes qui n’ont pas exactement une structure de flot de gradient. Les interactions étudiées sont de différentes natures. Le premier chapitre traite des systèmes avec des interactions non locales dans la dérive. Nous étudions ensuite des systèmes de diffusions croisées s’appliquant aux modèles de congestion pour plusieurs populations. Un autre modèle étudié est celui où le couplage se trouve dans le terme de réaction comme les systèmes proie-prédateur avec diffusion ou encore les modèles de croissance tumorale. Nous étudierons enfin des systèmes de type nouveau où l’interaction est donnée par un problème de transport multi-marges. Une grande partie de ces problèmes est illustrée de simulations numériques. / Since 1998 and the seminal work of Jordan, Kinderlehrer and Otto, it is well known that a large class of parabolic equations can be seen as gradient flows in the Wasserstein space. This thesis is devoted to extensions of this theory to equations and systems which do not have exactly a gradient flow structure. We study different kind of couplings. First, we treat the case of nonlocal interactions in the drift. Then, we study cross diffusion systems which model congestion for several species. We are also interested in reaction-diffusion systems as diffusive prey-predator systems or tumor growth models. Finally, we introduce a new class of systems where the interaction is given by a multi-marginal transport problem. In many cases, we give numerical simulations to illustrate our theorical results. Distance de Wasserstein Flots de gradient Schéma JKO Splitting Dérive non locale Diffusions non linéaires Diffusions croisées Systèmes de réaction-Diffusion Équations d'Hele-Shaw Transport optimal Transport multi-Marges Formule de Benamou-Brenier Lagrangien augmenté Mouvement de foules Espèces en interaction Wasserstein distance Gradient flows JKO scheme Splitting Nonlocal drift Nonlinear diffusions Cross-Diffusion Reaction-Diffusion systems Hele-Shaw equation Optimal transport Multi-Marginal transport Benamou-Brenier formula Augmented lagrangian Crowd motions Interacting species 519.2

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Population genomics of pollinating fig wasps and their natural enemies

Systèmes de particules en interaction, approche par flot de gradient dans l'espace de Wasserstein / Interacting particles systems, Wasserstein gradient flow approach