Biofilms are colonies of bacteria attached to the surface at a solid-fluid interface. Bacteria in biofilm produce exopolysaccharides (EPS) that form a gel-like matrix in which the bacteria are embedded. Biofilms have numerous consequences in industrial and medical settings, both positive (bioreactors, digestion) and negative (blocking, as corrosive damage of materials/devices, food contamination, clinical infection). The use of antibiotics or mechanical clearing can be effective at removing biofilms, but such treatments are not always effective or appropriate in all situations. Recently, non-thermal atmospheric plasma treatments have been proposed as an alternative (or complementary) form of treatment, that can target sites of infection with minimal damage to the surroundings (e.g. host cells in a clinical setting). These plasmas generate a multitude of chemical species, most of which are very short lived, that can infiltrate and diffuse into the biofilm killing the bacteria within. The aim of this thesis is to develop a multi-dimensional mathematical model to investigate the effect of a non- thermal plasma on biofilms in time and space and to identify key factors that determine effectiveness of the treatment. Most of the chemical products of cold plasmas are too short lived, or too reactive, to be effective in killing the biofilms, it is the longer live species, e.g. ozone, hydrogen peroxide, acid species, that penetrated the biofilm and do the most damage. However, the EPS in biofilms is an effective barrier against ozone and hydrogen peroxide. No published biofilm model combines multi-dimensional growth with a detailed description of EPS production, hence a new mathematical model is developed and applied to simulating plasma treatment. The thesis is split broadly into two parts. The first part presents a new biofilm model framework that simulates growth in response to any number of substrates (e.g. nutrient, oxygen). The model combines an Individual based model (IbM) description of bacteria (individuals or clusters) and substrates are described as a continuum. Novel features of the framework are the assumption that EPS forms a continuum over the domain and the explicit consideration of cellular energy (ATP). Simulations of this model demonstrate the contrast between biofilm grown with topical nutrient sources (forming irregular, bumpy biofilm) and basal nutrient source with topical oxygen such as biofilm grown on agar (forming regular spatially uniform biofilms). The former is in broad agreement with experiments whilst the latter, to our knowledge, has been the subject of very little experimental study. The second part extends the modelling framework to consider the effect of the plasma species. The simulations demonstrate that penetration is a key factor in their effectiveness, for which EPS plays a key role in preventing spread within and beyond the plasma treated zone. The simulations provide estimates of the timescale of equilibration of the main plasma species, predict the effect of combining these species and demonstrate how the constituents of the biofilm can change following treatment. A number of recommended suggestions for future theoretical and experimental study are discussed in the conclusions.

Population replenishment through recruitment is an essential process for the long term viability of corals and their associated communities, particularly under increasing stresses that threaten their vitality. Although many researchers have identified specific factors that influence individual processes in the early life cycle of corals, few studies to date have attempted to determine the cumulative success of a cohort's progression through these stages in natural reef settings. Specifically, there is a paucity of knowledge regarding appropriate and realistic techniques to forecast the success of recruitment in natural settings, while taking into account both the individual and environmental factors that regulate these recruitment dynamics at local scales. Because of this need, the overall goals of this dissertation research were to (1) assess key life stage processes leading to recruitment - specifically, settlement and early post-settlement processes - for which previous knowledge was limited or absent; and (2) using this knowledge, develop a local-scale recruitment model that assessed the cumulative success of a cohort's progression through all the early life stages and identified those processes that had a strong relative influence on regulating recruitment dynamics. Focusing on the common western Atlantic brooding coral, Porites astreoides, this dissertation research was divided into three main sections to address the overall objectives: (1) identification and quantification of recruitment patterns in natural reef settings, in order to guide the development and testing of the recruitment model (Chapter 2); (2) assessment of the focal species' behaviors, survivorship rates, and factors affecting those rates during its progression through the primary early life stage processes (i.e., basic habitat preferences during the settlement stage, Chapter 3; early post-settlement survivorship, Chapters 4 and 5); and (3) development of a local recruitment model that accounted for the full complement of early life stage processes in a spatially-explicit simulation framework (Chapter 6). While unique study-specific insights were gained from each of the individual chapters, a few general insights emerged with respect to the overarching study objectives from this dissertation research. First, larval supply is a key driver for recruitment, where a high degree of larval loss, either through direct larval mortality or export from the reef, occurs prior to settlement on the substrate. Rates of loss were 96-99% in the model analyses, and as such represent the first major population bottleneck for this species and others with similar life histories. Compounding this larval loss is a second population bottleneck during the early post-settlement stage, where mortality was typically greater than 75% within the first week after settlement. Such high rates of loss have important implications for future population dynamics, as relatively minor changes to these rates of loss can have relatively strong influences on future dynamics. Second, habitat influences on recruitment were found to be relatively minimal when compared to high rates of mortality in both the larval supply and early post-settlement stages. Although the relative influence of habitat may be strong under unique situations where substantial space preemption limits settlement (e.g., high macroalgal cover, sedimentation, or adult coral cover), these effects may not be reflective of average systems. However, the influence of habitat may still be crucial for ensuring that the few individuals who survive the larval supply and the early post-settlement bottlenecks recruit into the future adult population, and these influences may interact with other density-dependent processes as adult cover increases. Overall, this research presents valuable and novel insights on a number of the under-studied early life stage processes. By identifying the key processes which regulate recruitment, this work highlights those stages whose responses to environmental change will have strong impacts on recruitment and subsequent population dynamics. In addition to the process-based insights gained on these dynamics, this work provides informative criteria for managers on the stages most responsive to conservation efforts aimed at promoting resilience and recovery.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18497号 / 理博第4012号 / 新制||理||1578(附属図書館) / 31383 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 山内 淳, 教授 工藤 洋, 教授 田村 実 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Sea-level rise is a concern for the future of coastal marsh obligate species such as the Clapper Rail (Rallus crepitans). Clapper Rails possess the potential to indicate changes to marsh ecological state due to population variation related to habitat features exhibited in previous study. Estimates for Clapper Rail survival are among the key missing parameters to create predictive models for Clapper Rail populations. I estimated Clapper Rail survival using data collected from six automated telemetry towers located in two Mississippi marshes. Thirty adult rails were harnessed with radio transmitters around telemetry towers to provide evidence of a rail’s status, alive or dead. Using survival estimates in conjunction with existing empirical data, I created an individual-based model that incorporated existing Sea-level Affecting Marsh Models, which predict changing land cover. These models showed that Clapper Rails will likely persist, though at decreased populations, through changes in habitat due to sea-level rise.

A ocorrência de distúrbios impacta a diversidade de estratégias de vida em comunidades e a evolução de estratégias de vida em populações. Na Ecologia, o distúrbio é estudado enquanto fator ambiental que altera a disponibilidade de recursos e a abundância das populações, ocasionando a exclusão competitiva de espécies menos favorecidas a depender da intensidade e da frequência de sua ocorrência. Na Biologia Evolutiva, o distúrbio é avaliado enquanto pressão que, dependendo de sua regularidade no ambiente, determina a intensidade da resposta evolutiva das espécies e, assim, a adaptação a estratégias de vida de maior aptidão. Ainda que haja separação entre as duas áreas, a dinâmica ecológica influencia a dinâmica evolutiva e vice-versa. Estudos que integram Ecologia e Evolução têm sido cada vez mais recorrentes, no entanto, poucos ou nenhum consideram o distúrbio. Neste trabalho, utilizamos um modelo baseado em indivíduo para criar cenários nos quais os processos de adaptação e exclusão competitiva de espécies possam ocorrer, tanto conjunta quanto isoladamente, a fim de entender como o distúrbio determina as estratégias de vida presentes em comunidades sob dinâmicas ecológicas, evolutivas e eco-evolutivas. No modelo, as estratégias de vida são atributos herdáveis definidos por um trade-off entre longevidade e fecundidade. O cenário evolutivo foi composto por populações (apenas uma espécie) com mutação; o cenário ecológico, por diversas espécies sem mutação e o cenário eco-evolutivo, por diversas espécies com mutação. Observamos que o distúrbio esteve positivamente relacionado com a predominância de indivíduos fecundos em todos os cenários, mas o efeito do distúrbio sobre a diversidade de estratégias variou. Nos cenários evolutivo e eco-evolutivo, a diversidade de estratégias aumentou com a intensificação do distúrbio, enquanto no cenário ecológico a diversidade caiu. Isso indica a importância da mutação como fonte de novas variantes da estratégia quando há alta renovação de indivíduos da comunidade, condicionada pela mortalidade elevada. Apenas no cenário eco-evolutivo houve um pico de heterogeneidade de estratégias em níveis intermediários de distúrbio. Neste cenário, o isolamento reprodutivo das espécies, em contraposição à pan-mixia que ocorre dentro das populações, permite que as espécies difiram em relação à sua estratégia de vida média. Em paralelo, a entrada constante de variantes de estratégias por mutação previne a extinção definitiva das estratégias do sistema. Assim, quando o nível de distúrbio é intermediário, tanto espécies mais fecundas quanto espécies mais longevas conseguem coexistir na comunidade. Dado que os diferentes cenários resultaram em padrões distintos de frequência relativa de estratégias de vida, este trabalho evidencia a importância de estudarmos o efeito do distúrbio na estrutura e na dinâmica de comunidades unindo processos que são tipicamente estudados de forma isolada pela Ecologia e pela Biologia Evolutiva / Disturbance events impact life strategy diversity in communities and life strategy evolution in populations. In the field of Ecology, disturbance occurrence is studied while an environmental factor that alters resource availability and populations abundance, causing competitive exclusion of less favorable life strategies depending on disturbance frequency and intensity. In the field of Evolutionary Biology, disturbance is evaluated as a pressure, depending on its spatial and temporal regularity, that determines the intensity of species\' evolutionary response and, as a consequence, the adaptation towards the fittest life strategy. Although there is a separation between these two fields of knowledge, ecological dynamics influence evolutionary dynamics and the other way around. Studies that mix Ecology and Evolution are becoming more common, but few or none of them takes disturbance in consideration. Here, we use an individual-based model to generate contexts in which adaptation and competitive exclusion might act apart and together in order to understand how disturbance determines life strategies that occur in communities under ecological, evolutionary and eco-evolutionary dynamics. In the model, life strategy is an inheritable character defined for a trade-off between longevity and fecundity. Simulations from the evolutionary context were composed by one population under mutation acting, simulations from the ecological context by various species without mutation and simulations from the eco-evolutionary context by various species with mutation occurrence. We observed that disturbance was positively correlated with fecund individuals preponderance in all contexts but that disturbance effect on life strategy diversity varied between the different contexts. In the evolutionary and the eco-evolutionary contexts, life strategy diversity increased with disturbance raise, while in the ecological context diversity decreased. This result evidences the mutation role as a source of new life strategy variants when there is a high renovation of individuals given by raised mortality. Only in the eco-evolutionary context there was an interspecific heterogeneity peak on intermediate levels of disturbance. In this scenario, species reproductive isolation, in contrast to populations panmixy, allows species to differ in relation to its life strategies. In parallel to this, the constant input of new life strategy variants by mutation prevents the definite extinction of life strategies from the system. Therefore, when disturbance level is intermediate, productive species as well as long-lived ones are able to coexist. Given that the different contexts resulted in varied patterns of life strategies\' relative frequency, this study evidences the importance of studying disturbance effect on communities structure and dynamics unifying processes that are typically separated between Ecology and Evolution fields

A ocorrência de distúrbios impacta a diversidade de estratégias de vida em comunidades e a evolução de estratégias de vida em populações. Na Ecologia, o distúrbio é estudado enquanto fator ambiental que altera a disponibilidade de recursos e a abundância das populações, ocasionando a exclusão competitiva de espécies menos favorecidas a depender da intensidade e da frequência de sua ocorrência. Na Biologia Evolutiva, o distúrbio é avaliado enquanto pressão que, dependendo de sua regularidade no ambiente, determina a intensidade da resposta evolutiva das espécies e, assim, a adaptação a estratégias de vida de maior aptidão. Ainda que haja separação entre as duas áreas, a dinâmica ecológica influencia a dinâmica evolutiva e vice-versa. Estudos que integram Ecologia e Evolução têm sido cada vez mais recorrentes, no entanto, poucos ou nenhum consideram o distúrbio. Neste trabalho, utilizamos um modelo baseado em indivíduo para criar cenários nos quais os processos de adaptação e exclusão competitiva de espécies possam ocorrer, tanto conjunta quanto isoladamente, a fim de entender como o distúrbio determina as estratégias de vida presentes em comunidades sob dinâmicas ecológicas, evolutivas e eco-evolutivas. No modelo, as estratégias de vida são atributos herdáveis definidos por um trade-off entre longevidade e fecundidade. O cenário evolutivo foi composto por populações (apenas uma espécie) com mutação; o cenário ecológico, por diversas espécies sem mutação e o cenário eco-evolutivo, por diversas espécies com mutação. Observamos que o distúrbio esteve positivamente relacionado com a predominância de indivíduos fecundos em todos os cenários, mas o efeito do distúrbio sobre a diversidade de estratégias variou. Nos cenários evolutivo e eco-evolutivo, a diversidade de estratégias aumentou com a intensificação do distúrbio, enquanto no cenário ecológico a diversidade caiu. Isso indica a importância da mutação como fonte de novas variantes da estratégia quando há alta renovação de indivíduos da comunidade, condicionada pela mortalidade elevada. Apenas no cenário eco-evolutivo houve um pico de heterogeneidade de estratégias em níveis intermediários de distúrbio. Neste cenário, o isolamento reprodutivo das espécies, em contraposição à pan-mixia que ocorre dentro das populações, permite que as espécies difiram em relação à sua estratégia de vida média. Em paralelo, a entrada constante de variantes de estratégias por mutação previne a extinção definitiva das estratégias do sistema. Assim, quando o nível de distúrbio é intermediário, tanto espécies mais fecundas quanto espécies mais longevas conseguem coexistir na comunidade. Dado que os diferentes cenários resultaram em padrões distintos de frequência relativa de estratégias de vida, este trabalho evidencia a importância de estudarmos o efeito do distúrbio na estrutura e na dinâmica de comunidades unindo processos que são tipicamente estudados de forma isolada pela Ecologia e pela Biologia Evolutiva / Disturbance events impact life strategy diversity in communities and life strategy evolution in populations. In the field of Ecology, disturbance occurrence is studied while an environmental factor that alters resource availability and populations abundance, causing competitive exclusion of less favorable life strategies depending on disturbance frequency and intensity. In the field of Evolutionary Biology, disturbance is evaluated as a pressure, depending on its spatial and temporal regularity, that determines the intensity of species\' evolutionary response and, as a consequence, the adaptation towards the fittest life strategy. Although there is a separation between these two fields of knowledge, ecological dynamics influence evolutionary dynamics and the other way around. Studies that mix Ecology and Evolution are becoming more common, but few or none of them takes disturbance in consideration. Here, we use an individual-based model to generate contexts in which adaptation and competitive exclusion might act apart and together in order to understand how disturbance determines life strategies that occur in communities under ecological, evolutionary and eco-evolutionary dynamics. In the model, life strategy is an inheritable character defined for a trade-off between longevity and fecundity. Simulations from the evolutionary context were composed by one population under mutation acting, simulations from the ecological context by various species without mutation and simulations from the eco-evolutionary context by various species with mutation occurrence. We observed that disturbance was positively correlated with fecund individuals preponderance in all contexts but that disturbance effect on life strategy diversity varied between the different contexts. In the evolutionary and the eco-evolutionary contexts, life strategy diversity increased with disturbance raise, while in the ecological context diversity decreased. This result evidences the mutation role as a source of new life strategy variants when there is a high renovation of individuals given by raised mortality. Only in the eco-evolutionary context there was an interspecific heterogeneity peak on intermediate levels of disturbance. In this scenario, species reproductive isolation, in contrast to populations panmixy, allows species to differ in relation to its life strategies. In parallel to this, the constant input of new life strategy variants by mutation prevents the definite extinction of life strategies from the system. Therefore, when disturbance level is intermediate, productive species as well as long-lived ones are able to coexist. Given that the different contexts resulted in varied patterns of life strategies\' relative frequency, this study evidences the importance of studying disturbance effect on communities structure and dynamics unifying processes that are typically separated between Ecology and Evolution fields

Cette thèse a pour objet la modélisation individu-centrée des systèmes sociaux. Une première partie orientée aide à la décision présente un modèle d’évolution des populations rurales fortement inspiré des données. Une seconde partie, plus théorique, étudie divers mécanismes permettant à un individu d’accepter ou de résister à une influence sociale. Nous proposons tout d’abord un modèle individu-centré de la dynamique des municipalités rurales européennes, implémenté pour le département du Cantal. Nous proposons un nouvel algorithme de génération des populations initiales ne nécessitant pas d’échantillon de population (approche classique). Nous concevons et paramétrons un modèle de la dynamique de l’individu face au marché du travail basé sur les données de la « European Labour Force Survey ». Il inclut des heuristiques originales de transition d’états tel qu’actifs, inactifs, chômeurs, … prenant en compte l’âge, la profession et le secteur d’activité de l’individu. Nous déterminons les dynamiques non fondés sur des données individuelles en testant la capacité de dynamiques simples à produire des résultats proches des données agrégées disponibles. Est ainsi conçu un modèle de mobilité résidentielle, expliquant partiellement la migration et intégrant décision de déménager et choix d’une nouvelle résidence. La seconde partie de la thèse étudie les effets collectifs de différents mécanismes permettant aux individus de résister à ou d’accepter une influence sociale. Un premier mécanisme étudié est un filtre cognitif impliquant qu’un individu ne reçoit pas une information incongruente ou peu importante. Les individus « filtreurs » exhibent le biais de primauté car leur attitude n’est déterminée que par les premiers éléments reçus et se montrent négatifs alors que le message diffusé par un media est neutre. Le taux d’individus négatifs dans la population est accru ou diminuer par l’échange direct d’information entre les individus. Un second mécanisme est un rejet de la tentative d’influence qui mène l’individu à différencier davantage son attitude de celle de son interlocuteur. Il intervient lorsque l’individu éprouve un inconfort lié au fait qu’il est à la fois en accord et en désaccord avec son interlocuteur. Le couplage de ce rejet à un mécanisme d’attraction entre individus en accord entraîne un nombre moindre de groupes d’opinion différentes à l’échelle de la population (ie par rapport au nombre de groupes obtenus avec le seul mécanisme d’attraction). / This thesis is dedicated to individual-based modeling of social systems. While the first part is very practical, decision-support oriented, presenting a model which studies the evolution of a rural population, the second part is more theoretical, interested in various mechanisms allowing individual to accept or resist to social influence. Firstly, we propose an individual-based model of the European rural municipalities implemented for the French Cantal département. We use a new sample-free algorithm for generating the initial population, while classical methods require an initial sample. We design and parameterize the individual activity dynamics with data from the European Labour Force Survey database. The individual dynamics includes an original heuristic for labour statuses and employments changes, based on individual age, profession and activity sector when she is occupied. The last part of the model deals with dynamics that we have not been able to derive from data, mainly the demographic dynamics. Based on the Occam razor principle, we test very simple dynamics and choose them on their capacity to lead to model results close to reference data. In particular, we propose a simple residential mobility model, partly ruling the emigration, which integrates decision to move and location choice. Secondly, we study the collective effects of various mechanisms leading individuals to resist or accept social influence. A first mechanism leads individuals to neglect some features of an object if they are not important enough or incongruent. These individuals exhibit the primacy bias because their attitudes are determined by the first accepted feature. We show that this bias increases when individuals directly exchange about features compared to when they only get the features from the media, in a random order. The second mechanism is a rejection reaction that we suppose occurring because of the discomfort taking place when individuals are close on one dimension of attitude and far on another dimension. The main effect of this rejection mechanism is to lead to a lower number of clusters than with the attraction mechanism alone.

Steelhead populations support an economically valuable fishery in the Great Lakes region. Development of the region, resulting in land use changes and the introduction of hydropower, has affected the riverine habitat used by steelhead. I have developed an individual-based model of steelhead in the Manistee River, Michigan that simulates the long-term production of steelhead from the river. The model begins each year with a spawning population that produces redds for that year and then follows the offspring from each redd as individuals until they smolt one, two, or three years after spawning. Simulations run for ten-year periods. The simulated individuals are subjected to mortality from predation, starvation, and temperature extremes. Predation is a length-based mortality and is thereby affected by growth. Growth is determined by an individual's foraging success and bioenergetics. I conducted simulation experiments to examine the effect of changes in spawning numbers, temperature, and flow regime, on the number of individuals smolting in the river each year. Simulations reveal that the current flow regime and colder water temperatures are most beneficial for steelhead production and increasing the number of spawners does not increase steelhead production. The results also suggest that the young-of-the-year (YOY) stages have the greatest impact on steelhead production because the model showed no indication that steelhead life stages older than the YOY could compensate for density-related losses that occurred during the first year.

Movement patterns and space use by mature fishes are critical in determining the effectiveness of marine reserves in conserving spawning stock biomass and/or providing biomass to adjacent fisheries through 'spillover'. Home range sizes, activity patterns, site fidelity and habitat preferences were determined for acoustically-tagged snappers and groupers using a rigorously-calibrated array of omnidirectional hydroacoustic receivers deployed in the diverse coral reef environments of a no-take marine reserve (NTMR) network in the Dry Tortugas, Florida. An individual-based localizing tendency model of reef fish movement was parameterized from fine-scale acoustic telemetry data and integrated into a Spatial Management Performance Assessment (SMPA) simulation model for reef fish populations developed to quantitatively evaluate performance of no-take marine reserves in the Dry Tortugas, Florida. Spatially-explicit SMPA models were parameterized for three overfished stocks in the lucrative snapper-grouper fishery: red grouper (Epinephelus morio), black grouper (Mycteroperca bonaci), and mutton snapper (Lutjanus analis). SMPA models were used to evaluate the impacts of a variety of life histories, movement strategies and speeds, and management regulations upon long-term stock sustainability, as measured by annual changes in spawning potential ratio (SPR), and long-term stock productivity, as measured by annual changes in fisheries yield-in-weight per recruit (Yw/R). Under assumptions of constant regional fishing pressure, constant recruitment, and 'realistic' fish movement, SMPA simulation runs from initial conditions in 2000 suggested that by 2014, the Tortugas NTMR network should function to restore red grouper populations to 30% SPR, a Federal management benchmark for sustainability. Mutton snapper were the most mobile of the species investigated; if mutton snapper movements are ignored, their population is predicted to attain 30% SPR by 2014, but given 'realistic' mobility, they may not attain this target by 2021 without additional protections. Black grouper are currently fished at over 9 times sustainable levels. SMPA simulations suggest coupling an increase in minimum size at capture of 20 - 25 cm with NTMR implementation would result in substantial short term losses in yield, but would restore both black grouper and mutton snapper populations to 30% SPR by 2021 and lead to increased long-term yields. Although marine reserve sites are often chosen opportunistically, these findings strongly suggest that reserve designs (e.g. proper sizes and configurations) must take into account the scales and patterns of movement exhibited by the exploited stocks they are intended to protect. These modeling efforts also suggested reserves are not a panacea; in order to promote sustainability for severely depleted stocks, they must be accompanied by an overall reduction in fishing capacity. Although important questions remain concerning the movements of reef fish in response to habitat and density dependent processes, our analyses of realistic reef fish behaviors suggest that the NTMRs of the Dry Tortugas promote substantial gains in SPR, promoting long-term stock sustainability and enhanced egg production. Increased rates of movement diminish these benefits, but may also mitigate short-term losses in yield associated with NTMR establishment.

This thesis aims at a better mechanistic understanding of animal communities. Therefore, an allometry- and individual-based model has been developed which was used to simulate mammal and bird communities in heterogeneous landscapes, and to to better understand their response to landscape changes (habitat loss and fragmentation). / Diese Doktorarbeit strebt ein besseres mechanistisches Verständnis von Tiergemeinschaften an. Dafür wurde ein allometrie- und individuen-basiertes Modell entwickelt und dazu benutzt, Säugetier- und Vogelgemeinschaften in heterogenen Landschaften zu simulieren, und ihre Reaktion auf Landschaftsveränderungen (Habitatverlust und -fragmentierung) besser zu verstehen.