Two proposed models will be used to help answer a long observed question in the dynamics of \textit{Manduca sexta} and its related parasitoid wasps-Why is there a large difference in diversity in hyperparasitoid species between tobacco and other related plants such as tomato? Two stage structured differential equation models are presented. The first is a single patch model to study the changes in dynamics that occur between hosts, parasitoids, and hyperparasitoids as the amount of nicotine in the plant increases. The second is a two patch model that allows hyperparasitoids to choose between patches that are nicotine negative (i.e. tomato plants) and nicotine positive (i.e. tobacco plants). Both models will be used to investigate how host nicotine sequestration may impact hyperparasitoid diversity.

There are thousands of species of mosquitoes, but only a handful of these species carry pathogens that cause human diseases. Here, we study two species, Aedes albopictus and Aedes aegypti, which transmit infections such as dengue, Zika, Mayaro virus, and La Crosse virus. Curtailing these diseases is a good reason to consider control of mosquito populations. However, mosquitoes are quite hardy and spraying of pesticides is typically a short-term solution. Thus, more long-term solutions require careful thought about mosquito populations, including early juvenile aquatic stages: egg, larva, and pupa. In this dissertation, we examine the factors that affect the dynamics of aquatic stages by creating mathematical models. The goal is to assess what key biological features most impact the total population. Both Aedes albopictus and Aedes aegypti lay eggs in small containers, producing limitations on space and food. We investigate how restricting resources changes development time, survival to adulthood, and body mass at emergence. The interactions between these changes are complicated, so to disentangle their effects we create three different mathematical models. The first model is discrete in time and focuses on the best way to incorporate the influence of larval density. We compare the impact of larval density by inputting seven different functional forms altering survival and development time. Larval density used in the model is determined from the average of the population size over the past one to thirty-six days. The second model is also discrete in time but focuses on the interaction between survival, development time, and mass. This model considers three levels of mass. Here, we use the density-dependent function determined from our first model and fit the maximum value for development time from experimental data. Survival values are fit using constants and a density-dependent function. Finally, growth is built in as a function of food. Food decreases at each time point as a function of the total larvae in the environment. We compare between model formulations with Akaike information criterion. The third model examines the ramifications of constricting resources on growth verses death. We employ a partial differential equation that has three independent variables: time, age, and mass. We find that density dependence is highly influential in the maturation of mosquitoes, and it is more essential to include its impacts on development time than on survival. These findings can be incorporated into a larger framework of disease dynamics, and give insight into better control of mosquitoes and disease spread. / Doctor of Philosophy / There are thousands of species of mosquitoes, but only a handful of these species spread human diseases. We specifically study mosquitoes that transmit diseases such as dengue and Zika, which plague large portions of the world. One way to reduce disease spread by mosquitoes is to eliminate the mosquito population, but mosquitoes are becoming resistant to commonly used insecticides. Thus, additional ways to combat mosquitoes are needed. To do so requires a better understanding of how mosquito populations change. This necessitates incorporating information from all life stages of the mosquito, including the juvenile stages that live in the water. In this dissertation, we examine various factors that affect the population size and characteristics of young mosquitoes by creating mathematical models. The goal is to assess what key biological features most impact the population. As young mosquitoes live in aquatic environments, there are limitations on space and food. We investigate how restricting resources changes the time it takes for mosquitoes to develop into adults, how many survive to adulthood, and what their body mass is as new adults. These outcomes interact in complicated way. To disentangle this, we create three different mathematical models. The first model focuses on the best way to incorporate the influence of limiting space or density on population size. The second model focuses on the interaction between mosquito body mass, survival, and time spent as a juvenile. The third model examines how resources alter growth and death and the ensuing mass of mosquitoes. Models are fit to experimental data and validated based on how accurately they describe known patterns. We find that population density is highly influential in the maturation of juvenile mosquitoes and its most important effect is on time spent as a juvenile mosquito. By correlating growth of juvenile mosquitoes to density and resources, our second model is better able to reproduce data. These findings provide important understanding on mosquito populations, which provides insight into how to better control mosquitoes and the diseases they spread.

When intraspecific individuals differ in resource intake, scramble competition occurs among inferior individuals growing food-dependently. Scramble can be released through predation mortality. As a consequence of this release, production rates in inferior individuals increase and biomass overcompensation in the subsequent life-stages may occur. When intraspecific individuals do not differ in their resource intakes biomass overcompensation does not occur. If an individual changes its resource intake over ontogeny, the balance of intake and losses, its energetics, will change over ontogeny. Furthermore, differences will arise between the energetics of different life-stages. The predominant volume of interspecific competition theory is based on studies assuming no stage-specific differences in energetics, neglecting the influence of ontogeny on community dynamics altogether. We study how an stage-specific differences in energetics affect expectations from conventional competition theory. We use a stage-structured biomass model consistently translating individual life history processes, in particular food-dependent growth in body size, to the population level. The stage-structured population can be reduced to an unstructured population, if the energetics of all individuals are assumed to be equal.  The stage-structured model, however can also describe population dynamics when this equality is broken. We use the stage-structured biomass model to contrast the stage-specific differences resulting in a stage-structured population model, with an unstructured population model assuming no differences between stages. We show that stage-specific differences in energetics can affect competition on various trophic levels. I: In stead of outcompeting each other, a predator can be facilitated by another preying a scrambling prey life-stage of the same prey population. II: In coexistence with their prey, omnivores with an ontogenetic diet shift, where juvenile omnivores feed on resource and adults on prey, affect community structure only as predators, not as competitors to their prey. We show coexistence of omnivore and prey is not possible if the dominating interaction is competition. Feeding on prey, however, alleviates competition with prey and facilitates the introduction of omnivores. III: An ontogenetic diet shift creates niche partitioning, where without it this would result in neutral coexistence of two consumers competing for two resources. IV: Furthermore, predators can change resource requirements of diet shifters such that diet shifters can reduce resources to lower equilibria and sustain higher predator biomass than consumers without stage-specific differences in energetics. / LEREC

L'objectif de ce travail de thèse est de développer un modèle mathématique pour l'étude et la compréhension de la dynamique des populations d'un insecte ravageur, l'Eudémis de la vigne (Lobesia botrana Den. & Schiff.), dans son écosystème. Le modèle proposé est un système d'équations aux dérivées partielles de type hyperbolique qui décrit les variations numériques au cours du temps de la population en fonction des stades de développement, du sexe des individus et des conditions environnementales. La ressource alimentaire, la température, l'humidité et la prédation sont les principaux facteurs environnementaux du modèle expliquant les fluctuations du nombre d'individus au cours du temps. Les différences de développement qui existent dans une cohorte d'Eudémis sont aussi modélisées pour affiner les prédictions du modèle. A partir de données expérimentales obtenues par les entomologistes de l'INRA, situé à Bordeaux, les paramètres du modèle sont estimés. Ce modèle ainsi ajusté nous permet alors d’étudier quelques aspects biologiques et écologiques de l’insecte comme par exemple l'impact de scénarios climatiques sur la ponte des femelles ou sur la dynamique d’attaque de la vigne par les jeunes larves. Les analyses mathématique et numérique du modèle mathématique et des problèmes d'estimation des paramètres sont développées dans cette thèse. / The objective of the thesis is to develop a mathematical model for studying the population dynamics of the European grapevine moth (Lobesia botrana Den. & Schiff.) in its ecosystem. The model proposed is a system of hyperbolic equations that describe the numerical variations in time of the population with respect to developmental stage, the gender and the environmental conditions. The food, the temperature, the humidity and the predation are the main environmental factors of the model that explain the fluctuations of the population in time. The differences in growth inside a cohort are modeled in order to precise the model simulations. We use experimental data obtained by entomologists of the National Research Institut of Agronomy to estimate the parameters of the model. This ajusted model allows us to study some biological and ecological aspects of this pest like for example the impact of climate change on the female laying or on the young larvae dynamic, main actors in the depredation of the Vine. The mathematical analysis and the numerical analysis of the mathematical model and of the parameters estimation problems are presented in this thesis.

Codakia orbicularis est un mollusque bivalve appartenant à la famille des Lucinidae et établissant des symbioses avec des bactéries sulfo-oxydantes (symbiotes) au sein de ses branchies. Dans l’hypothèse où toute symbiose nécessite une régulation par des molécules de dialogue, une étude chimique exhaustive pourrait aboutir à la mise en évidence des métabolites impliqués. Le travail de ce manuscrit porte donc sur l'isolement de métabolites secondaires à partir des branchies de ce bivalve et sur l'évaluation de l'activité antibactérienne des molécules isolées. Douze composés ont été isolés des branchies de Codakia orbicularis et leurs structures ont été déterminées par les méthodes spectroscopiques usuelles. Parmi ces molécules, une seule est nouvelle et a été nommée orbicularisine. Elle présente un squelette indolone spirotetracyclique inédit. Parmi les molécules isolées, seules quatre d’entre elles présentent une activité antibactérienne à savoir le soufre S8, la 4-hydroxybenzaldéhyde et deux monoglycérolipides. L'orbicularisine est inactive contre un panel de lignées cellulaires cancéreuses et de kinases. Le nouveau squelette de l’orbicularisine pourrait permettre d'aboutir à une nouvelle famille de molécules par synthèse organique et ainsi d'accroître la diversité moléculaire autour de ce motif inédit. Il sera également intéressant de déterminer l'origine des molécules isolées (procaryote ou eucaryote), particulièrement pour l’orbicularisine, et leurs rôles dans le cadre de la symbiose. Les résultats chimiques obtenus sur C. orbicularis et sur les Lucinidae en général sont intéressants puisque les espèces côtières appartenant aux bivalves ont été peu exploitées en chimie jusqu’à ce jour. / Codakia orbicularis is a bivalve mollusk belonging to the family Lucinidae harboring sulfur-oxidizing bacterial endosymbionts within its gills. Considering that any symbiosis is most likely regulated by dialogue molecules, an exhaustive chemical study could lead to identify the involved metabolites. Thus, the aim of this thesis focuses on the isolation of secondary metabolites from the gills of this bivalve and the evaluation of the antibacterial activity of the isolated molecules. Twelve compounds were isolated from the gills of Codakia orbicularis and their structures were determined by usual spectroscopic methods. Among these molecules, only one presented a new structure and has been named orbicularisine. The latter presents an undescribed spirotetracyclic indolone skeleton. Regarding the biological activities, among the isolated molecules, only four of them identified as S8 sulfur, 4-hydroxybenzaldehyde and two monoglycerolipids presented an antibacterial activity. Orbicularisine was inactive against a panel of cell lines and kinase. The orbicularisine new skeleton is an interesting start for the synthesis of new family of molecules, thus enhancing its molecular diversity. It will be interesting to determine the origin of the isolated molecules (prokaryotic or eukaryotic), especially for the new orbicularisine, and their roles in the frame of the symbiosis. The chemical results obtained on C. orbicularis and on lucinids in general are interesting since the coastal species belonging to Bivalves have not been chemically explored.

There is a widespread distribution of possibly toxic heavy metals, such as zinc, in aquatic ecosystems. Simultaneously aquatic food webs are changing due to declining predatory fish stocks. In this study, I examine how such an alteration of the food chain, the disappearance of a top trophic level, can affect the uptake and transfer of pollutants in lower trophic levels. I investigate a tri-trophic food chain containing resources (zooplankton), consumer fish, and predatory fish and use zinc as an example pollutant. This is done by constructing and adding a pollutant module to a stage-structured biomass model. The combined model is based on a system of eight ordinary differential equations to study the zinc concentrations in the consumer fish population in two scenarios: in the presence or absence of predatory fish, i.e., the food chain consists of either three or two trophic levels. The results show that the removal of the predator affects the concentration of the pollutant in the consumer population. In the absence of predators, the uptake of zinc from food is smaller and the zinc concentration is lower in the consumer fish population. The results remain the same for different values of the pollutant-specific parameters, i.e., uptake rate from water, assimilation efficiency, and efflux rate. This could indicate that food chain dynamics have a strong influence on the uptake and transfer of pollutants. Furthermore, this means that even if the model is parametrized to zinc in this study, the modeling tool can also be used for other pollutants with similar biokinetics as zinc. The results from this study highlight the importance to include food chain structure and dynamics when studying the uptake and transfer of pollutants. The novel knowledge and the developed tool from this study could advantageously be included to a higher degree when discussing the impact of pollution on aquatic ecosystems and mitigation measures. / Det finns en utbredd spridning av potentiellt giftiga tungmetaller, som t.ex. zink, i akvatiska ekosystem. Samtidigt förändras akvatiska födovävar på grund av minskande rovfiskbestånd. I denna studie undersöker jag hur en sådan förändring av födoväven, ett försvinnande av en trofisk toppnivå, kan påverka upptaget och överföringen av föroreningari lägre trofinivåer. Jag undersöker en tritrofisk födokedja som innehåller resurser (zooplankton), konsumentfisk och rovfisk och använder zink som ett exempel på förorening. Detta görs genom att konstruera och addera en föroreningsmodul till en stegstrukturerad biomassamodell. Den kombinerade modellen bygger på ett system med åtta ordinära differentialekvationer för att studera zinkhalterna i konsumentfiskpopulationen i två scenarier: i närvaro eller frånvaro av predatorer, dvs. födokedjan innehåller antingen tre eller två trofiska nivåer. Resultaten visar att koncentrationen av föroreningen i konsumentpopulationen förändras när födokedjan ändras. När rovfiskar saknas i systemet är upptaget av zink från föda mindre och zinkkoncentrationen lägre i konsumentfiskpopulationen. Resultaten förblir detsamma för olika värden på de föroreningsspecifika parametrarna, d.v.s. upptagshastighet från vatten, assimileringseffektivitet och utflödeshastighet, vilket skulle kunna indikera att födokedjans dynamik har ett starkt inflytande på upptag och överföring av föroreningar. Vidare innebär detta att även om modellen har parametriserats till zink i denna studie, så kan modelleringsverktyget även användas för andra föroreningar som har en liknande biokinetik som zink. Resultaten från denna studie understryker vikten av att inkludera födokedjans struktur och dynamik när man studerar upptag och överföring av föroreningar. Den nya kunskapen och det utvecklade verktyget från denna studie skulle med fördel i högre grad inkluderas när man diskuterar föroreningars påverkan på akvatiska ekosystem och vilka åtgärder som bör sättas in för att minska problemen.

Increased temperatures due to anthropogenic-induced climate change may raise the threat of extinction for taxa with sessile life histories (e.g., plants) in the near future. Linking climate change models to demographic models may provide useful insights into the potential effects of environmental changes on rare plants, and therefore aid in their current and future conservation. Population demographers generally agree that mechanistic models from a reductionist perspective are necessary to test assumptions in population drivers. For the first study, I assessed the climate vulnerability of a rare plant species, Pyrrocoma radiata, with a mechanistic model of four climatically-similar populations. I used environmentally-driven demographic models to estimate vital rates and population sizes from a nonlinear, nonparametric regression with local climate variables. I assessed the utility of this environmentally-correlated, stage-structured population matrix model compared to a stationary model of independent and identically-distributed environmental stochasticity. I then simulated future population projections based on climate conditions predicted by General Circulation Models (GCMs) under opposing emission scenarios. The second study hopes to answer population-level questions using a traditionally community-level method, non-metric multidimensional scaling, which considers correlation structure between response variables and can be used to find environmental correlates of the ordination axes. Demographic data on a threatened perennial, Astragalus tyghensis, were collected from five sites in the Tygh Valley, OR. I considered correlation structure between demographic vital rates to find environmental correlates of the ordination axes. The search for an environmental driver of population vital rates was successful for the two study species. Previous year dry dormant season precipitation likely affects the fertility rates a year later in P. radiata populations, and dry growing season reference evapotranspiration rates positively correlated with a growth gradient in A. tyghensis. Based on predicted precipitation, P. radiata is expected to rapidly decline by 2050, but this may be due to biases in the two GCMs and reliance on only one environmental factor. The NMS ordination adequately captured most of the variation in transition elements for the years and populations from A. tyghensis demographics. I provided support to the claim that model predictions can improve with the inclusion of mechanistic relationships. The inclusion of abiotic drivers in models used to predict population trends is supported by our study and may enhance predictive power in population viability assessments under changing climates. / Graduation date: 2013