Long-term population dynamics across heterogeneous environments can be a major factor in determining species’ ability to expand their ranges and persist in novel environments. Whether and how the relative performance of populations in different microsites over time impacts invasion into new microsites is poorly understood. Though largely restricted to disturbed semi-shaded microhabitats in its home range, the invasive herb Alliaria petiolata (garlic mustard) successfully invades intact forest understories – a novel microhabitat – in its introduced range, where it is known to impact above and below ground community composition. To test the hypothesis that source-sink metapopulation dynamics may be promoting A. petiolata’s incursion into the forest understory, I utilized two multi-season field surveys – approximately a decade apart – to evaluate trait variation, biomass allocation, and long-term population demographics of A. petiolata growing at the forest edge, within the intact forest understory, and in the intermediate transition zone between the two. My results show that adult plants in the edge were taller and branchier, produced more fruits, and had higher total and reproductive biomass than plants in the intermediate and forest microhabitats. Over time, seedling density remained highest in the edge microhabitat compared to the forest and intermediate microhabitats, which had similar densities. Reproductive adult densities were similar among all microhabitats at the beginning of the study, but a decade later, all microhabitats exhibited a decline in the number of adult plants they supported. Populations in the intermediate microhabitat displayed the steepest decline in reproductive adults between sampling periods but still supported more adult plants than the forest microhabitat. Populations in all microhabitats were predicted to grow (λ>1) at the onset of the study. A decade later, declines in population size were only predicted in the forest understory (λ1). Since edge and intermediate patches had higher densities of adult plants which produced the most fruit and had larger reproductive biomass, it appears that the edge populations, and possibly the intermediate populations, have sustained the low-density forest populations through source-sink dynamics at my study sites.

The purpose of this research was to uncover factors responsible for the prolific growth of various filamentous microorganisms in the bulking activated sludge at the Hoechst Celanese wastewater treatment plant. First, futile attempts were made to isolate the filamentous bacterium, <i>Nostocoida limicola II</i>, from activated sludge for purposes of its characterization. Chemostat and batch experiments were also performed in an effort to determine conditions favoring its growth, but the filament’s growth could not be sustained in any of the conditions provided. Second, several CSTRs were operated in which single cationic concentrations were varied to try to isolate the actual effects of the different cations on activated sludge microorganisms. Though the objectives of these CSTR experiments were not accomplished because bulking conditions could not be maintained in the reactors, insight was gained as to possible factors significantly impacting filamentous growth. A full-scale study followed, in which microbial population shifts in the activated sludge at the Hoechst Celanese wastewater treatment plant were tracked with changes in the operating conditions at the plant. The results of this study suggested the existence of relationships between the abundances of certain filaments and DO concentration and/or F/M ratio in the activated sludge environment. To isolate the individual effects of these two factors on activated sludge microorganisms, two modified batch studies were performed. The results of these studies indicated that the growth of most of the filaments present in the Hoechst Celanese activated sludge is primarily affected by F/M ratio, though DO concentration strongly impacts the growth of some. The findings in the DO and F/M experiments were combined with the findings in the full-scale study to estimate DO concentration and/or F/M ratio ranges in which growth of the following activated sludge filamentous organisms may be favored: <i>Haliscomenobacter hydrossis</i>, <i>Microthrix parvicella</i>, <i>Nocardia species</i>, <i>Nostocoida limicola II</i>, and Types 0041, 0581, 1851, and 1863. / Master of Science

Bottlenose dolphins of the Kvarnerić (NE Adriatic Sea) live in an area of increasing human impact, through tourism and small-scale fisheries. This thesis aimed to assess the status of the local population and to inform managers on factors affecting their distribution and abundance, using data from 1995-2003. Habitat modelling indicated a significant negative impact of proximity to the main ‘marine highway’ and to marine petrol stations. Evidence was found that dolphins may recently have reached a tolerance limit to the number of boats using the area and that they remember crowded areas from one year to the next. Dolphin presence was positively related to particular depths and trawling areas. Apparent adult survival rate was estimated to be significantly lower than for any other bottlenose dolphin population and first year calf survival was also low. A decreasing trend in fecundity rate was found. The population showed a considerable rate of non-random temporary emigration from the study area. The estimated size of the population was small and similar to two other European bottlenose dolphin populations (Moray Firth in Scotland and Shannon Estuary in Ireland). A significant decrease in abundance of about 39% from 1995 was estimated. PVA confirmed the importance of female adult survival to population viability and indicated that the current rate of human-induced mortality is unsustainable. Local extinction risk within three generations was estimated to be high (35%). Applying the IUCN Red List Criteria, the Kvarnerić population should be listed as Endangered under Criterion C and E. This study gives an important insight into the ecology of Adriatic bottlenose dolphins and indicates the need for a regionally and locally synergistic approach to conserve this population.

À partir d'un modèle existant de dynamique de populations de pucerons, nous avons développé une méthode permettant de quantifier la contribution de parasitoïdes à la réduction du maximum de densité de pucerons. La méthode a été validée, sur deux ans en champ de soya, en utilisant le modèle biologique composé du puceron du soya (Aphis glycines Matsumura) et de Aphelinus certus Jasnosh, son parasitoïde le plus abondant au nord-est de l'Amérique du Nord. La méthode a estimé que les densités naturelles de A. certus n'avait réduit les pics de densités de pucerons que de 1-6%. La cause de cette faible régulation est associée à un établissement tardif des populations de A. certus en champ de soya, mais les mécanismes sous-jacents restent inconnus. À cet effet, les proportions d'hyperparasitisme sur A. certus, avant le pic de densité de pucerons, étaient trop faible pour que l'hyperparasitisme puisse en être tenu responsable. Concernant la dynamique des populations de pucerons, nous avons proposé une re-paramétrisation du modèle mentionné précédemment afin de faciliter l'interprétation de ses paramètres lorsque la colonisation des champs par les pucerons n'était pas simultanée. Cette stratégie nous a permis d'établir que l'occurrence du pic de densité de puceron du soya est facilement prédictible de sa date de colonisation en champ. Nous recommandons l'utilisation de modèles afin de prédire les pics de densité de pucerons et d'utiliser la méthode d'estimation de l'impact afin d'incorporer des stratégies de relâchers augmentatifs de parasitoïdes aux programmes de lutte existants contre les pucerons. / Building upon an existing aphid population dynamics model, we develop a method to quantify the contribution of parasitoids in reducing the maximum aphid density. We validated the method, over a two years study in soybean fields, using the biological model made of the soybean aphid (Aphis glycines Matsumura) and Aphelinus certus Jasnosh, its most abundant parasitoid in north-eastern North America. The method estimated that natural populations of A. certus reduced peak soybean aphid densities by only 1-6%. The cause of this low regulation is associated to the late establishment of A. certus population in soybean field, although the underlying mechanisms remains unknown. Proportion hyperparasitism on A. certus, before peak soybean aphid densities, were too low for hyperparasitism to be accounted for the poor efficacy of A. certus in regulating the soybean aphid. Regarding aphid population dynamics, we proposed a re-parameterisation of the aforementioned model to facilitate the interpretation of its parameters when field colonization by aphids is not simultaneous. This allowed us to identify a high predictability in peak aphid densities from colonization time for the soybean aphid. We recommend using models to forecast peak aphid densities and to use the impact assessment method to incorporate augmentative parasitoid release strategies into aphid management programmes.

The evolution of metabolism regulation is an intertwined process, where different strategies are constantly being developed towards a cognitive ability to perceive and respond to an environment. Organisms depend on an orchestration of a complex set of chemical reactions: maintaining homeostasis with a changing environment, while simultaneously sending material and energetic resources to where they are needed. The success of an organism requires efficient metabolic regulation, highlighting the connection between evolution, population dynamics and the underlying biochemistry. In this work, I represent organisms as coupled information-processing networks, that is, gene-regulatory networks receiving signals from the environment and acting on chemical reactions, eventually affecting material flows. I discuss the mechanisms through which metabolism control is improved during evolution and how the nonlinearities of competition influence this solution-searching process. The propagation of the populations through the resulting landscapes generally point to the role of the rhythm of cell division as an essential phenotypic feature driving evolution. Subsequently, as it naturally follows, different representations of organisms as oscillators are constructed to indicate more precisely how the interplay between competition, maturation timing and cell-division synchronisation affects the expected evolutionary outcomes, not always leading to the \"survival of the fastest\".

Réalisé en cotutelle avec l'Université Montpellier II / L’étude qualitative et quantitative du mode de développement des plantes envahissantes est actuellement considérée comme une étape clef dans la compréhension des phénomènes d’invasion. L’objectif de ce travail est de préciser les relations qui existent entre la structure architecturale des buissons et leur caractère proliférant. Nous avons sélectionné cinq espèces buissonnantes (Cornus sericea L., Cornaceae ; Prunus virginiana L., Rosaceae ; Rhamnus cathartica L., Rhamnaceae ; Rhus typhina L., Anacardiaceae ; Zanthoxylum americanum Mill., Rutaceae) qui sont connues pour leur aptitude à bloquer la succession végétale sous certaines conditions au Sud du Québec (Canada). L’analyse architecturale a permis chez ces espèces de caractériser les unités structurelles et leurs modifications ontogéniques. Ces modifications ontogéniques doivent être prise en compte afin d’obtenir une description complète de la plasticité phénotypique chez ces espèces. L’analyse des différentes unités structurelles révèle qu’elles ne possèdent pas la même signification fonctionnelle : les niveaux d’organisation les plus grands sont responsables majoritairement des capacités de plasticité phénotypique de la plante et de sa compétition. Ces analyses ont abouti à la définition de trois stratégies architecturales correspondant à des comportements individuels et qui sont également pertinentes pour expliquer la prolifération des populations. / Qualitative and quantitative studies of the pattern of invasive plant development is now considered a key aspect in understanding invasiveness. This work was performed to determine relationships between shrub architectural plasticity and proliferating behaviour. We selected five shrub species (Cornus sericea L., Cornaceae ; Prunus virginiana L., Rosaceae ; Rhamnus cathartica L., Rhamnaceae ; Rhus typhina L., Anacardiaceae ; Zanthoxylum americanum Mill., Rutaceae) known to arrest plant succession under certain conditions in Southern Québec, Canada. Architectural analysis revealed species’ structural units and their ontogenic changes. These ontogenic changes need to be calibrated if a full description of phenotypic plasticity is to be obtained. Analysis of the plant structural units reveals that they are of different functional significance: the higher the level of organization, the greater the capacity for phenotypic plasticity and competition. We defined three architectural strategies related to individual behaviours and which can relevantly explain the population proliferation of shrubs.

La dynamique globale des systèmes parasites-hôte (SPH) ‘trématode digènes - coque Cerastoderma edule’ a été étudiée simultanément à Merja Zerga (Maroc) et dans le Bassin d’Arcachon (France). La dynamique de populations de la coque a montré une variabilité intra et inter-site et a été expliquée essentiellement par la température, la prédation, la compétition et la dynamique sédimentaire. Dans les deux lagunes, le recrutement s’opère à une température de 19°C avec un décalage temporel en relation avec les positions latitudinales des sites (avril-mai à Merja Zerga et juin-juillet à Arcachon). Les taux de croissance restent comparables pour les deux populations de coque (K=1,5 an-1) mais les performances de croissance sont plus élevées à Arcachon (F’=3,3) qu’à Merja Zerga (F’=3,1). La production était plus élevée à Merja Zerga (36-65 g poids sec.m-2.an-1). P/B est faible sur les deux sites et légèrement plus élevée à Arguin (1,1-1,5 contre 1,0-1,1 an-1). Les deux sites présentent deux riches communautés parasitaires regroupant à Merja Zerga (11 espèces) et à Arguin (13 espèces), respectivement, 69% et 81% de la richesse parasitaire (digènes) connue des coques. Les communautés parasitaires restent comparables et l’éloignement géographique et climatique n’a eu qu’un faible retentissement sur la structure des peuplements parasitaires. La comparaison latitudinale de la structure et de la dynamique des SPH a permis de relativiser l’importance de la température dans la dynamique de l’hôte et des parasites, du moins dans cet intervalle climatique. A Merja Zerga, la température ne semble pas être un facteur limitant de l’infestation contrairement aux sites plus au nord. Mais finalement, les niveaux d’infestation des coques adultes sont similaires. Les échinostomatidés et les gymnophalidés ont été les plus contributives dans la mortalité parasito- dépendante observée. L’impact des parasites digènes en situation normale se traduit par une augmentation de E/B, cependant plus marqué à Merja Zerga. Cette différence d’effet dénote d’un gradient positif de virulence en allant du nord vers le sud. La présence d’herbiers, la situation ‘intertidal versus subtidal’ et la densité des coques ont un effet modéré sur l’infestation parasitaire. / The global dynamics of the parasites-host systems (PHS) ‘digenean trematodes – cockle Cerastoderma edule’ was simultaneously studied in Merja Zerga (Morocco) and Arcachon Bay (France). Cockle population dynamics exhibited an intra- and inter-site variability mostly explained by temperature, predation, competition and sedimentary dynamics. In both lagoons, recruitment occurred at 19° C, with a temporal delay due to latitudinal position (April-May at Merja Zerga, and June-July at Arcachon). Growth rates were similar in both cockle populations (K=1.5 an-1) but growth performances were higher at Arcachon (F’=3.3) than at Merja Zerga (F’=3.1). Production was higher at Merja Zerga (36-65 g dry weight.m-2.yr-1). P/B was low in both sites and slighly higher at Arguin (1.1-1.5 contre 1.0-1.1 yr-1). Both sites exhibited rich parasite communities with 11 species at Merja Zerga and 13 species at Arguin, corresponding to 69 and 81% of the identified cockle parasite species richness (digeneans). Great distances and climate differences did not alter the structure of parasite communities. Structure and dynamics of PHS related to latitude showed the moderate effect of temperature, within this climate range. At Merja Zerga, temperature was not a limiting factor for parasite infestation, in contrast with what happens in northern countries. But eventually, parasite loads in adult cockles were similar in both sites. Echinostomatids and gymnophallids were the most contributive families explaining parasite- dependent mortality. Digenean impact on cockle resulted in an increasing of E/B, with a higher effect at Merja Zerga. This difference could be linked to a higher virulence in southern sites. The presence of seagrass beds, the position between subtidal and intertidal and the cockle density remained secondary factors in controlling parasite infestation.

This study is aimed at analysis of long-term and short-term changes in numbers of Red-crested Pochard (Netta rufina) in Třeboň region. This species is increasing in long-term period and it is also spreading into new localities in the Czech Republic. There were recorded two waves of arrival of Red-crested Pochard arrive, i.e. in April and in May. The total numbers were decreasing at the end of breeding season (from the beginning of July) in study area. The water surface area and area of littoral vegetation were found to be the most important factors affecting preference of individual ponds in pre-breeding season. Furthermore, water transparency seems to be important factor affecting numbers of broods, ducklings and adults in post-breeding season. Low numbers of broods per 1 female were recorded in years with high numbers of Red- crested Pochard at the start of breeding season. However, the frequency of brood parasitism was higher in these years. Key words: Netta rufina, Red-crested Pochard, population dynamics, ducks, breeding, numbers, brood parasitism, south Bohemia

Nous introduisons un modèle mathématique d'évolution d'une maladie cancéreuse à l'échelle de l'organisme, prenant en compte les métastases ainsi que leur taille et permettant de simuler l'action de plusieurs thérapies telles que la chirurgie, la chimiothérapie ou les traitements anti-angiogéniques. Le problème mathématique est une équation de renouvellement structurée en dimension deux. Son analyse mathématique ainsi que l'analyse fonctionnelle d'un espace de Sobolev sous-jacent sont effectuées. Existence, unicité, régularité et comportement asymptotique des solutions sont établis dans le cas autonome. Un schéma numérique lagrangien est introduit et analysé, permettant de prouver l'existence de solutions dans le cas non-autonome. L'effet de la concentration de la donnée au bord en une masse de Dirac est aussi envisagé.Le potentiel du modèle est ensuite illustré pour des problématiques cliniques telles que l'échec des anti-angiogéniques, les protocoles temporels d'administration pour la combinaison d'une chimiothérapie et d'un anti-angiogénique et les chimiothérapies métronomiques. Pour tenter d'apporter des réponses mathématiques à ces problèmes cliniques, un problème de contrôle optimal est formulé, analysé et simulé. / We introduce a mathematical model for the evolution of a cancer disease at the organism scale, taking into account for the metastases and their sizes as well as action of several therapies such as primary tumor surgery, chemotherapy and anti-angiogenic therapy. The mathematical problem is a renewal equation with bi-dimensional structuring variable. Mathematical analysis and functional analysis of an underlying Sobolev space are performed. Existence, uniqueness, regularity and asymptotic behavior of the solutions are proven in the autonomous case. A lagrangian numerical scheme is introduced and analyzed. Convergence of this scheme proves existence in the non-autonomous case. The effect of concentration of the boundary data into a Dirac mass is also investigated.Possible applications of the model are numerically illustrated for clinical issues such as the failure of anti-angiogenic monotherapies, scheduling of combined cytotoxic and anti-angiogenic therapies and metronomic chemotherapies. In order to give mathematical answers to these clinical problems an optimal control problem is formulated, analyzed and simulated.

Depuis sa première signalisation en 2005, le cténophore Mnemiopsis leidyi a été régulièrement observé dans l'Étang de Berre et a profité d'un écosystème planctonique perturbé. En effet, la régulation des apports en eau douce provenant de la centrale hydroélectrique EDF de Saint-Chamas (2006) a entraîné une augmentation de la salinité moyenne de la lagune, ainsi qu'une diversification et une « marinisation » des communautés planctoniques de la lagune. Leurs caractéristiques et la dynamique de la population de M. leidyi ont été étudiées au cours d'un suivi in situ réalisé en 2010-11. Les données obtenues lors de ce suivi, associées à une étude de son métabolisme (i.e. ingestion, respiration, excrétion et croissance), ont permis d'identifier les principaux facteurs contrôlant sa population (i.e. température, salinité, concentration et nature des proies). Son cycle de vie est étroitement lié à la température, les larves cyddipides apparaissant en hiver, suivies par les stades de transition en hiver/printemps et par les adultes du printemps à l'automne. Les conditions saumâtre et eutrophe semblent contribuer à sa présence dans la lagune, avec une salinité optimale pour son développement et une forte concentration en proies (i.e. zooplancton pour les adultes). En raison de la sélection active de proies (i.e. nauplii de copépodes et copépodites) et l'absence de seuil de satiété, M. leidyi a un impact important sur les populations de copépodes entraînant la chute drastique de leur abondance suite à ses proliférations. De nouvelles modifications des conditions hydrologiques (i.e. évolution vers une lagune marine) pourraient continuer à transformer le fonctionnement de la lagune. / The ctenophore Mnemiopsis leidyi has established a sustainable population in the Berre Lagoon since its first observation in 2005. This invasive species took advantage of a plankton ecosystem disturbed particularly by successive modifications of the hydrohalin conditions of the lagoon. Indeed, regulation of the freshwater inputs through the hydroelectric power plant of Saint-Chamas (2006) leads to an increase of the mean salinity, resulting in a more diversified and a more marine plankton community. Characteristics of the plankton ecosystem and population dynamics of M. leidyi was studied during an in situ survey in 2010-11. Metabolism (ingestion, respiration, excretion and growth) of the ctenophore adult and transition stages were studied in controlled conditions. Temperature influences the life cycle of M. leidyi with cyddipid larvae observed in winter, then transitional stages in winter/spring and adults from spring to autumn. The ctenophore seems to prefer brackish and eutrophic environments linked with its optimal salinity conditions (between 10 and 30) and its need for an important prey concentration (copepods nauplii and copepodites). The active selectivity of prey and the lack of a satiety level can largely explain the drop in copepod abundance following M. leidyi proliferations. New hydrological modifications (evolution towards a marine lagoon) will certainly continue to transform in the future the functioning of the Berre Lagoon.