Évaluer les stratégies d’histoire de vie d’espèces est indispensable à leur conservation. Un total de 3651 colonies de corail de feu, Millepora platyphylla, ont été mesurées, géoréférencées et collectées dans 5 habitats différents à Moorea afin d’évaluer le contexte biologique et écologique du maintien et du renouvellement des populations. Ce travail de thèse a démontré que la structure des populations diverge entre le lagon et la pente externe. À l’aide de marqueurs microsatellites nouvellement développés, nous avons démontré que cette espèce se reproduit principalement par fragmentation (80%) et que les fragments sont distribués en parfait alignement avec la dispersion des vagues. Les clones d’une même lignée clonale partagés entre habitats expriment différents phénotypes selon leur exposition aux vagues. Surprenamment, M. platyphylla affiche une morphologie vulnérable à la fragmentation dans les habitats exposés à la houle. L’analyse de parenté a révélé une forte contribution de l'autorecrutement (58%), une faible dispersion des propagules sexuées et une tendance à l’agrégation d’individus issus de mêmes parents. Enfin, nous avons démontré de la variabilité génétique intracoloniale, principalement due aux mutations somatiques (mosaïcisme), qui contribue ainsi à augmenter la diversité génétique dans la population. L’interaction de ces processus engendre une diversité génétique et phénotypique élevée dans la population et permet également le renouvellement local et la persistance de cette espèce à Moorea; habitat marginal. Ces stratégies d’histoire de vie augmentent ainsi le potentiel d’adaptation et la résilience de M. platyphylla face aux changements environnementaux. / Evaluating life history of species carries important implications for conservation biology. A total of 3651 colonies of the fire coral Millepora platyphylla was measured, georeferenced and collected in 5 different habitats in Moorea to evaluate the biological and ecological context of the population maintenance and renewal. This thesis has demonstrated that the population structure of this species varies greatly between lagoonal and fore reef habitats. Using newly developed microsatellite markers, we have shown that M. platyphylla relies heavily on clonal reproduction via fragmentation (80%) and that the fragments are distributed in perfect alignment with wave energy dispersal. Clonal lineages with clones shared among habitats revealed the ability of a single genotype to express different phenotypes depending on its exposure to swell wave energy. Surprisingly, M. platyphylla invests in a vulnerable morphology to wave-induced breakage in high energy reef habitats. Furthermore, parentage analysis revealed a high contribution from self-seeding (58%), limited dispersal of sexual propagules and sibling aggregations. At last, we have demonstrated intracolonial genotypic variability, mostly from somatic mutations (mosaicism), which creates novel genetic diversity within the population. The interaction of these processes generates a high level of genetic and phenotypic variation within the population and allows for local replenishment and the persistence of this fire coral species in Moorea, a marginal habitat. These life history strategies thus increase the adaptive potential and resilience of M. platyphylla in response to rapid and unpredictable environmental changes.

Les fibres optiques dont on façonne la réponse spectrale incorporent des ions luminescents, des ions de terres rares (TR), dans des nanoparticules (NP) formées in situ dans un verre de silice par séparation de phase. Cette ingénierie nécessite de comprendre le lien entre la composition des NP et l’environnement des TR.En Dynamique Moléculaire, les potentiels interatomiques existants pèchent à reproduire la séparation de phase observée expérimentalement. Le mélange xMgO-(1-x)SiO2 présente un domaine où coexistent deux phases mixtes, riche en Mg ou en Si. Une telle séparation de phase ne se modélise qu’avec un potentiel interatomique prenant en compte la ionicité des liaisons, réalisé ici par l’ajustement des charges des Oxygène selon l’environnement local. Ce modèle adaptatif, transférable, permet de suivre pour la 1ère fois la formation de NP amorphes de quelques nm. Mixtes et riches en Mg, elles se séparent d’une matrice riche en Si.Le dopage TR (Er3+ ou Eu3+) montre que leur voisinage dépend de la taille des NP les contenant : plus les NP sont grosses, plus les fractions de TR et de Mg augmentent. Ce voisinage riche en Mg permet à ces TR d’augmenter leur coordinence en Oxygène et elles n’ont plus besoin de s’agréger entre elles pour satisfaire cette tendance naturelle.Une simulation de l’étirage à chaud d’un verre de silice confirme l’existence d’une anisotropie dans la fibre optique, venant de l’orientation persistante des petits anneaux de silice, et se manifeste par une anisotropie élastique. Les effets que ces conditions extrêmes induisent sur les NP seront étudiés ultérieurement.La mise en œuvre d'un modèle de champ cristallin corrélera les modifications de l'environnement des TR avec leur réponse spectrale. / Optical fibers with tailored spectral response are doped with luminescent ions, rare-earth ions (re), embedded in nanoparticles (np) formed in situ in silica glass through a phase separation process. This engineering requires to understand the relation between the np composition and the re environment. In molecular dynamics, the existing interatomic potentials fail to reproduce the phase separation as experimentally observed. The system xmgo-(1-x)sio2 exhibits a domain inside of which two mixed phases coexist, mg-rich either si-rich. Such a phase separation can only be modeled by an interatomic potential that takes into account bond ionicity, and the transferability isEnabled here by the adaptation of oxygen charges according to the local environment. This adaptive model allows for the 1st time to track the formation of amorphous np of few nanometers. Mixed and mg-rich, they separate from a si-rich matrix. The re doping (er3+ or eu3+) shows that re environment depends on the size of the containing np: the bigger it is, the more the proportions of embedded re and mg increase. Thus, this mg-rich environment enables re ions to increase their oxygen coordination and to no more aggregate to each other to satisfy this natural trend. A simulation of the high-temperature drawing of silica-glass confirms the existence of an anisotropy in optical fiber, explained by the persistent orientation that small silica rings acquire in this fiber, and manifests itself by an elastic anisotropy. The nontrivial effects induced on np by these extreme conditions of temperature and stress can be studied later. The crystal-field model can be used to correlate the changes of the re environment with their spectral response.

Slum development in the Global South continues at a rapid pace, leading to a search for solutions to the severe environmental, social, and economical challenges facing these settlements. Informal economic activities are central to these communities’ survival and structure. Ownership policies have been initiated that contribute to security for residents, and there is evidence that this can lead to increased social and economic productivity. However, studies have also shown that broad ranging titling reforms may destroy existing networks, practices, and livelihoods of residents. This raises a fundamental question on how land titling and formalization of business ownership can be accomplished, while still maintaining local social networks and livelihoods. This thesis calls attention to the need to develop policy approaches that are context specific while also taking into account the complex economic networks that develop in informal settlements. / text

L’adaptation d’un champignon pathogène à son milieu, ainsi que l’évolution et la structuration des populations qui en découlent, sont fortement influencés par ses traits d’histoire de vie qui conditionnent sa fitness. C’est ce que nous avons illustré chez Melampsora larici-populina, l’agent de la rouille du peuplier. Ainsi, nous avons mis en évidence que le volume des spores du champignon évolue de manière répétable au cours des épidémies annuelles dans la vallée de la Durance, et ce sous l’effet de la sélection naturelle, signe que ce trait intervient directement dans le processus adaptatif du champignon. Par conséquent, les contraintes génétiques conditionnant le potentiel adaptatif du champignon en lien avec les traits d’histoire de vie ont été étudiées en laboratoire, au sein d’une descendance S1 issue de l’autofécondation d’une souche de référence. Les résultats obtenus suggèrent que M. larici-populina présente un potentiel adaptatif élevé. Enfin, une carte génétique à haute résolution du champignon, comprenant 18 chromosomes, a été construite afin d’étudier le déterminisme génétique de ces traits d'histoire de vie. Un locus de virulence ainsi que des QTL intervenant dans l’expression de la taille des lésions ont pu être détectés et positionnés avec précision sur cette carte. Ce travail a mis en évidence le rôle des traits quantitatifs dans l’adaptation et la structuration des populations de M. larici-populina en réponse aux pressions de sélection du milieu, en lui conférant un potentiel adaptatif élevée, essence de l’adaptation des organismes. Il ouvre également de nombreuses perspectives de recherche visant à identifier les bases génétiques de l’adaptation de ce champignon pathogène à son hôte, éléments indispensables à l’élaboration de stratégies de lutte durables / Adaptation of a phytopathogenic fungus to its environment, as well as the resulting evolution and structuration of its populations, are strongly influenced by its life history traits which condition its fitness. This is illustrated here with the poplar rust fungus Melampsora larici-populina. Hence, we showed that spore volume repeatedly evolved through natural selection, during annual epidemics in the Durance River valley, showing the implication of this trait in the fungus adaptive processes. Consequently, genetic constraints conditioning the adaptive potential of the fungus, in connection with life history traits, were studied in laboratory, over a progeny resulting from a selfing of a reference strain. Results suggest that M. larici-populina has a high adaptive potential. Finally, a high resolution genetic map of the fungus, comprising 18 chromosomes, has been built in order to study genetic determinism of these traits. One locus of virulence and three QTL involved in the expression of the lesion size were detected and accurately mapped on this map. This work emphasizes the role of quantitative traits in adaptation and structuration of M. larici-populina populations in response to the environmental selective pressures, by conferring an adaptive potential, the basis of organisms’ adaptation. It also opens many opportunities to identify the genetic bases of adaptation of this fungus, these elements being essential for the development of sustainable strategies of disease control

The Heat Shock Protein 90 (Hsp90) is an essential and highly conserved chaperone that facilitates the maturation of a wide array of client proteins, including many kinases. These clients in turn regulate a wide array of cellular processes, such as signal transduction, and transcriptional reprogramming. As a result, the activity of Hsp90 has the potential to influence physiology, which in turn may influence the ability to adapt to new environments. Previous studies using a deep mutational scanning approach, (EMPIRIC) identified multiple substitutions within a 9 amino acid substrate-binding loop of yeast Hsp90 that provides a growth advantage for yeast under elevated salinity conditions and costs of adaptation under alternate environments. These results demonstrate that genetic alterations to a small region of Hsp90 can contribute to evolutionary change and promote adaptation to specific environments. However, because Hsp90 is a large, highly dynamic and multi-functional protein the adaptive potential and evolutionary constraints of Hsp90 across diverse environments requires further investigation. In this dissertation I used a modified version of EMPIRIC to examine the impact of environmental stress on the adaptive potential, costs and evolutionary constraints for a 118 amino acid functional region of the middle domain of yeast Hsp90 under endogenous expression levels and the entire Hsp90 protein sequence under low expression levels. Endogenous Hsp90 expression levels were used to observe how environment may affect Hsp90 mutant fitness effects in nature, while low expression levels were used as a sensitive readout of Hsp90 function and fitness. In general, I found that mutations within the middle domain of Hsp90 have similar fitness effects across many environments, whereas, under low Hsp90 expression I found that the fitness effects of Hsp90 mutants differed between environments. Under individual conditions multiple variants provided a growth advantage, however these variants exhibited growth defects in other environments, indicating costs of adaptation. When comparing experimental results to 261 extant eukaryotic sequences I find that natural variants of Hsp90 support growth in all environments. I identified protein regions that are enriched in beneficial, deleterious and costly mutations that coincides with residues involved in co-chaperone-client-binding interactions, stabilization of Hsp90 client-binding interfaces, stabilization of Hsp90 interdomains and ATPase chaperone activity. In summary, this thesis uncovers the adaptive potential, costs of adaptation and evolutionary constraints of Hsp90 mutations across several environments. These results complement and extend known structural and functional information, highlighting potential adaptive mechanisms. Furthermore, this work elucidates the impact environment can have on shaping Hsp90 evolution and suggests that fluctuating environments may have played a role in the long-term evolution of Hsp90.