Many of the earth’s ecosystems are experiencing large species losses due to human impacts such as habitat destruction and fragmentation, climate change, species invasions, pollution, and overfishing. Due to the complex interactions between species in food webs the extinction of one species could lead to a cascade of further extinctions and hence cause dramatic changes in species composition and ecosystem processes. The complexity of ecological systems makes it difficult to study them empirically. The systems often consist of large species numbers with lots of interactions between species. Investigating ecological communities within a theoretical approach, using mathematical models and computer simulations, is an alternative or a complement to experimental studies. This thesis is a collection of theoretical studies. We use model food webs in order to explore how biodiversity (species number) affects the response of communities to species loss (Paper I-III) and to environmental variability (Paper IV). In paper I and II we investigate the risk of secondary extinctions following deletion of one species. It is shown that resistance against additional species extinctions increases with redundancy (number of species per functional group) (Paper I) in the absence of competition between basal species but decreases with redundancy in the presence of competition between basal species (Paper II). It is further shown that food webs with low redundancy run the risk of losing a greater proportion of species following a species deletion in a deterministic environment but when demographic stochasticity is included the benefits of redundancy are largely lost (Paper II). This finding implies that in the construction of nature reserves the advantages of redundancy for conservation of communities may be lost if the reserves are small in size. Additionally, food webs show higher risks of further extinctions after the loss of basal species and herbivores than after the loss of top predators (Paper I and II). Secondary extinctions caused by a primary extinction and mediated through direct and indirect effects, are likely to occur with a time delay since the manifestation of indirect effects can take long time to appear. In paper III we show that the loss of a top predator leads to a significantly earlier onset of secondary extinctions in model communities than does the loss of a species from other trophic levels. If local secondary extinctions occur early they are less likely to be balanced by immigration of species from local communities nearby implying that secondary extinctions caused by the loss of top predators are less likely to be balanced by dispersal than secondary extinctions caused by the loss of other species. As top predators are vulnerable to human-induced disturbances on ecosystems in the first place, our results suggest that conservation of top predators should be a priority. Moreover, in most cases time to secondary extinction is shown to increase with species richness indicating the decay of ecological communities to be slower in species-rich than in species-poor communities. Apart from the human-induced disturbances that often force species towards extinction the environment is also, to a smaller or larger extent, varying over time in a natural way. Such environmental stochasticity influences the dynamics of populations. In paper IV we compare the responses of food webs of different sizes to environmental stochasticity. Species-rich webs are found to be more sensitive to environmental stochasticity. Particularly, species-rich webs lose a greater proportion of species than species-poor webs and they also begin losing species faster than species-poor webs. However, once one species is lost time to final extinction is longer in species-rich webs than in species-poor webs. We also find that the results differ depending on whether species respond similarly to environmental fluctuations or whether they are totally uncorrelated in their response. For a given species richness, communities with uncorrelated species responses run a considerable higher risk of losing a fixed proportion of species compared with communities with correlated species responses.

The variability of the postsynaptic response following a presynaptic action potential arises from: i) the neurotransmitter release being probabilistic and ii) channels in the postsynaptic cell involved in the response to neurotransmitter release, having stochastic properties. Spike timing dependent plasticity (STDP) is a form of plasticity that exhibits LTP or LTD depending on the precise order and timing of the firing of the synaptic cells. STDP plays a role in fundamental tasks such as learning and memory, thus understanding and characterizing the effect variability in synaptic transmission has on STDP is essential. To that end a model incorporating both forms of variability was constructed. It was shown that ion channel stochasticity increased the magnitude of maximal potentiation, increased the window of potentiation and severely reduced the post-LTP associated LTD in the STDP curves. The variability due to short term plasticity decreased the magnitude of maximal potentiation.

The variability of the postsynaptic response following a presynaptic action potential arises from: i) the neurotransmitter release being probabilistic and ii) channels in the postsynaptic cell involved in the response to neurotransmitter release, having stochastic properties. Spike timing dependent plasticity (STDP) is a form of plasticity that exhibits LTP or LTD depending on the precise order and timing of the firing of the synaptic cells. STDP plays a role in fundamental tasks such as learning and memory, thus understanding and characterizing the effect variability in synaptic transmission has on STDP is essential. To that end a model incorporating both forms of variability was constructed. It was shown that ion channel stochasticity increased the magnitude of maximal potentiation, increased the window of potentiation and severely reduced the post-LTP associated LTD in the STDP curves. The variability due to short term plasticity decreased the magnitude of maximal potentiation.

La course à la miniaturisation des dispositifs oblige les industriels a développé sans cesse de nouvelles technologies de gravure afin de contourner les limites imposées par les procédés plasmas continus CW à haute densité. Parmi ces nouvelles technologies on trouve, les plasmas pulsés en impulsion courtes introduits depuis une dizaine d’année et le procédé de gravure cyclée développé très récemment par Applied Materials. Ces deux types de procédés de gravure présentent la caractéristique d’avoir un faible flux d’ions. Au premier abord, cette faible densité d’ions énergétiques permet la diminution des défauts induits par les ions. Cependant, un problème se pose lorsque le nombre d’ions impactant la surface devient trop faible (moins de 1 ions/site atomique/s). Ce travail de thèse se concentre donc ici sur l’étude de l’impact de la stochasticité du bombardement ionique sur l’état de la surface dans les deux procédés de gravure utilisés. Dans un premier temps, nous avons focalisé notre travail sur l’interaction entre les plasmas pulsés de chlore puis d’HBr et le silicium. A faible rapport de cycle, une très forte rugosité de surface a été observée sans lien avec un phénomène de micro-masquage. Des diagnostics plasma ont révélés que la présence d’un très faible flux d’ions énergétique couplé avec forte réactivité chimique engendre une forte augmentation du taux de gravure créant ainsi la rugosité de surface. Dans un second temps, l’étude du plasma capacitif d’hydrogène utilisé pour la modification du SiN durant le procédé de gravure cyclée a montré après retrait de la couche modifiée en plasma délocalisé, la présence d’une rugosité de surface au sommet des espaceurs nitrure qui n’est pas acceptable pour l’application du « simplified quadruple patterning ». Une étude paramétrique de l’état de surface a permis de mettre en évidence l’impact direct de la faible quantité d’ions H+ reçue par le matériau et la rugosité observée. La stochasticité du bombardement ionique implique donc une modification inhomogène du SiN qui est révélée lors de la phase de retrait et amplifiée au cours des cycles générant une rugosité de surface.Mots-clés : Microélectronique, procédés de gravure, plasma, stochasticité, ions. / The microelectronics industry is more and more challenged by the miniaturization of devices thus constantly constrained to develop new plasma etching technologies and to overcome limits imposed by CW plasma processes. Among, these new technologies, there are pulsed plasmas and the cycled etching process developed by Applied Materials. A characteristic of these processes is to work with very low flux of ions. However, a problem arises when the number of ions impacting the surface becomes too small (less than 1 ion/atomic site/second). Thus this work focuses on the study of the impact of the stochasticity of ion bombardment on the surface state in two etching processes. In a first part of our work, we studied the interaction between pulsed plasmas of chlorine and silicon. Similarly the effect of pulsed plasmas of HBr was also investigated. At a low duty cycle, a very high surface roughness was observed, unrelated to a micro-masking phenomenon. Under these experimental conditions, plasma diagnostics were carried out to measure the flux of energetic ions and the flux of neutrals. In this way, we highlighted that a very low flux of energetic ions and a high ratio neutrals/ions lead to high chemical reactivity. It results in the creation of a strong surface roughness. In a second part of our work, we studied the modification of SiN layers during the cyclic etching process using capacitive hydrogen plasma. After removal of the modified layer in remote plasma, we brought out the presence of a surface roughness at the top of the nitride spacer. Our parametric study of the surface state highlighted the correlation between the low fluence of hydrogen ions received by the material and the surface roughness. Thus, the stochasticity of ion bombardment implies an inhomogeneous modification of the SiN which is revealed by the remote plasma and amplified during the cycles. In this situation, an important surface roughness is generated. These results are consistent with simulation study in molecular dynamics. Therefore we demonstrated that the number of ions impacting on the surface (ion stochastic effect) appears as being a very limiting parameter in the pulsed plasma processes as well in some CCP processes.Key words: Microelectronics, etching processes, plasma, stochasticity, ions.

Abstract Plants in riparian environments have to tolerate disturbances like floods and erosion. In the absence of disturbances, habitats will gradually become unfavorable for early-successional species. This can have fundamental consequences not only for adaptation at the individual level, but also for the viability of local populations as well as for the persistence of the species on a regional scale. Silene tatarica is a rare perennial plant exposed to annual floods of the Oulanka River. After sand burial most plants formed vertical rhizomes and new meristems by bud ramification. The special anatomical features of these fleshy underground structures seemed to allow the plants to be very resilient against fast-flowing water. Seed structure may enhance long-distance dispersal by water. Selection gradients for plant height were positive at the individual and group levels, but for the number of stems they were in opposition, as selection at the group level favored a smaller number of stems. This can be associated with pollination and herbivory, since taller and larger plants often attract more pollinators and mammalian herbivores. At the local level, population growth was most sensitive to the survival and growth of juvenile individuals. The populations showed different fates, and according to stochastic simulations some of them will disappear in the near future. Their colonization and extinction rates varied between the years, but their balance over the study period was positive. Small patches had the highest risk of extinction and recolonization of extinct patches was very rare. Elasticity analysis indicated that the survival of patches made a much greater contribution to patch dynamics than did the production of new patches. The short-term dynamics of S. tatarica depend primarily on local dynamics but, in the long run, the species will track the availability of habitat, and its persistence will depend on successful colonizations. The amount of suitable habitat depends on river disturbance. Conservation of this species requires the creation of new suitable open sites for colonization, a dispersal process leading to successful colonizations, and favorable habitats for survival. These conditions can be maintained either by natural processes of river disturbance or by active conservation management.

The Monte Carlo tree search-algorithm (MCTS) has been proven successful when applied to combinatorial games, a term applied to sequential games with perfect information. As the focus for MCTS has tended to lean towards combinatorial games, general MCTS-strategies for other types of board games are hard to find. On another front, board games under the name of “Eurogames” have become increasingly popular in the last decade. These games introduce yet another set of challenges for game-playing agents on top of what combinatorial games already offer. Since its initial conception, a large number of enhancements to the MCTS-algorithm has been proposed. Seeing that eurogames share much of the same game-mechanics with each other, MCTS-enhancements proving effective for one game could potentially be aimed towards eurogames in general. In this paper, alterations to the expansion phase, the playout phase and the backpropagation phase are made to the standard MCTS-algorithm for agents playing the game of Carcassonne. To detect how enhancements are affected by chance events, both a deterministic and a stochastic version of the game is examined. It can be concluded that a reward policy relying solely on in-game score outperforms the conventional wins-against-losses policy. Concerning playouts, the Early Playout Termination enhancement only yields better results when the number of MCTS-iterations are somewhat restricted. Lastly, delayed node expansion is shown to be preferable over that of conventional node expansion. None of the enhancements showed any increasing or declining performance with regard to chance events. Additional experiments on other eurogames are needed to reaffirm any findings. Moreover, subsequent studies which introduce modifications to the examined enhancements is proposed as a measure to further increase agent performance. / Monte Carlo tree search-algoritmen (MCTS) har visat sig framgångsrik när den tillämpats på "combinatorial games", en term som används för sekventiella spel med perfekt information. Eftersom fokusområdet för MCTS har tenderat att luta mot "combinatorial games", är det svårt att hitta allmänna MCTS-strategier för andra typer av brädspel. På en annan front har brädspel under namnet "Eurogames" blivit allt populärare under det senaste decenniet. Dessa spel introducerar ännu en uppsättning utmaningar för agenter utöver vad "combinatorial games" redan erbjuder. Sedan dess begynnande så har ett stort antal förbättringar av MCTS-algoritmen föreslagits. Med tanke på att eurogames delar mycket av samma spelmekanik med varandra kan MCTS-förbättringar som visar sig vara effektiva för ett spel potentiellt riktas mot eurogames i allmänhet. I denna studie görs förändringar av expansionsfasen, playout-fasen och backpropagation-fasen i standard MCTS-algoritmen för agenter som spelar spelet Carcassonne. För att upptäcka hur förbättringar påverkas av slumpmässiga händelser undersöks både en deterministisk och en stokastisk version av spelet. Man kan dra slutsatsen att en belöningspolicy som enbart förlitar sig på poäng i spelet överträffar konventionell vinst-mot-förlust-policy. När det gäller "playouts" så bidrar Early Playout Termination-tillägget endast med bättre resultat när antalet MCTS-iterationer är något begränsat. Slutligen kan det visas att fördröjd expansion av noder att föredra framför konventionell expansion. Ingen av förbättringarna visade någon ökande eller minskande prestanda med avseende på slumpmässiga händelser. Ytterligare experiment på andra eurogames behövs för att bekräfta eventuella fynd. Dessutom föreslås efterföljande studier som introducerar modifieringar av de undersökta förbättringarna som ett mått för att ytterligare öka agentens prestanda.

The concept of regulation in ecosystems has been given considerable attention in the ecological literature, but no formal treatment has been offered. This study proposes a rigorous definition of regulation which is derived from the mathematics of information and communication theory. A theoretical, mathematical equivalent of the definition is also offered which implies serious limitations as to the value of most traditional laboratory population studies and deterministic population models in understanding regulation in ecosystems. The empirical validity of this theoretical equivalence is tested through use of a competition model of two diatoms. Other observations concerning the relationship between environmental variability and regulation are also reported.

Communities are a critical link that impact how species-level population dynamics translate into ecosystem functions, and thus, understanding community assembly is an important goal of ecology. Variation in the relative importance of the four processes of drift, selection, speciation, and dispersal likely govern much of the variation that is observed in community structure across landscapes. Microbial communities provide critical functions across an array of environments, but only recently have technological advances in DNA sequencing allowed us to study these communities with higher resolution. My dissertation research has investigated community assembly in host-associated microbial communities, with a focus on understanding how stochasticity in dispersal that leads to priority affects can impact bacterial community assembly in amphibian embryos. In chapter 1, I experimentally show that priority effects resulting from stochastic dispersal can be observed in the microbiome of newly-hatched hourglass treefrog (Dendropsophus ebraccatus) tadpoles. Changes in microbiome composition due to priority effects could be observed in a simple two bacteria system and when the inoculation by the initial bacteria is followed by a more diverse community inoculum. Outcomes of my two taxa system in co-culture do not strictly mirror those observed in treefrog embryos, highlighting that priority effect outcomes are context dependent. Additionally, these results provide support that priority effects do not benefit all bacterial species equally and the magnitude of these effects will be dependent on the traits of individual colonists. In chapter 2 I demonstrate that priority effects are not unique to the hourglass treefrog system but can be observed in spring peeper (Pseudacris crucifer) tadpoles as well. This study demonstrates the applicability of priority effects in increasing the abundance of target probiotic taxa; a benefit to amphibian populations facing threats by a lethal fungal pathogen. By treating embryos with a priority inoculation of Janthinobacterium lividum, a bacterial species known to inhibit fungal pathogen growth, I increased the relative abundance of J. lividum on newly hatched tadpoles. I also provide evidence that closely-related species of bacteria can effectively co-exist regardless of priority inoculation. An understanding of variation in the amphibian microbiome across life stages in the wild is required to better understand the long-term impacts of priority effects in embryos. My final chapter, therefore, examined compositional changes in the microbiomes of locally occurring amphibians in Virginia across the egg, tadpole, and juvenile developmental stages. In this study, I show characterize the initial egg microbiome across amphibian species and demonstrate that egg microbiomes, are distinct between species but are more similar across species than tadpole or juvenile microbiomes. Additionally, I show that minor differences in host environment can lead to differences in the microbiome structure of conspecific tadpoles. Overall, my dissertation empirically demonstrates the role of dispersal, and more specifically priority effects, in the assembly of the vertebrate microbiome. / Doctor of Philosophy / An ecological community is a set of species that occur at a given site. Communities have been a fundamental focus of ecological research, as communities serve to link the population dynamics of individual species to ecosystem level processes provided by species. Microbial communities, in particular, are of interest because of the wide range of important functions they provide across a variety of systems, yet relatively little is known about how these communities initially come together and are maintained. This is particularly true for the microbial communities that live in and on plants and animals, which are called "host-associated" communities. Host-associated microbial communities contribute many important functions to their hosts, including guiding host development, assisting with nutrient assimilation, and providing disease resistance. Four processes are thought to govern how ecological communities assemble across landscapes at local sites or habitat patches: selection, dispersal, speciation, and drift. Variation in the relative importance of these processes is thought to drive the variation in community composition across sites, or in the case of host-associated microbial communities, across hosts. Selection occurs at a local level when environmental variables or the presence of other species impact where a species occurs. Dispersal of individuals among habitat patches can also impact what species occur at a local site, and speciation gives rise to new species in communities over time. Drift is the stochastic, or random, element of species abundance that is driven by variation in the birth and death rates of a population at a site. I have investigated the assembly of host-associated microbial communities using amphibians as a study system. In chapter 1, I experimentally demonstrate that stochasticity in dispersal that impacts which species arrive first to a site (priority effects) can be observed in the host-associated bacterial communities of newly-hatched treefrog (Dendropsophus ebraccatus) tadpoles. This can be observed in a simplified system where only two bacterial species are used, and also when a single bacterial species arrives and is followed by a more diverse community of bacteria. However, not every bacterial species is able to take advantage of priority, and these results seem to be context dependent, as the outcomes in treefrog embryos do not exactly mirror the outcomes when the bacteria are grown in a nutrient broth together. In chapter 2, I show that priority effects are not unique to the hourglass treefrog system; priority effects can also be observed in spring peeper (Pseudacris crucifer) tadpoles. In this study, I also demonstrated that we may be able to apply our knowledge of priority effects to benefit amphibian populations threatened by a potentially lethal fungal pathogen by manipulating the abundances of bacteria on the skin during development. Priority treatment of embryos with Janthinobacterium lividum, a bacterial species known for its ability to inhibit growth of this fungal pathogen, resulted in increased relative abundance of J. lividum in the tadpoles following hatching. Additionally, I found that even closely-related bacterial species can have differing abilities to take advantage of priority effects and can co-exist on tadpoles. To determine long-term impacts of priority effects in embryos requires an understanding of the variation associated with amphibians in the wild across different life stages. My final chapter, therefore, focused on examining changes in the bacterial communities associated with locally occurring amphibians in Virginia across the egg, tadpole, and juvenile stages of development. Specifically, I characterize the initial communities associated with eggs across different species, including predicted associations with algal symbionts, and examine patterns of host-associated communities among species and across development. Overall, my dissertation showcases the role that dispersal, but more specifically priority effects, can play in the development of the vertebrate microbiome.

No description available.

<p>Elucidating the mechanisms structuring communities has been a challenge for community ecology since its beginnings. One theory argues that assembly rules structure communities by means of deterministic mechanisms arising from biological interactions. Another view maintains that patterns seen in community composition and species abundance result from stochastic processes such as migration and extinction. The dilemma has yet not been resolved unambiguously. The main issue is that communities shaped by deterministic mechanisms can produce stochastic patterns via priority effects. The main goal of this study was to determine whether assembly rules structure communities. My strategy was to minimize priority effects by controlling timing of colonization. To do this I used a null community by combining communities of 17 rock pools. This null community was later divided among experimental communities. I conducted three experiments: (1) Experimental communities were exposed to the same external conditions. (2) Communities were exposed to different environments, disturbance, dispersal and habitat heterogeneity. (3) Replicated null communities were connected to allow inter-replicate dispersal. After 4 months, communities (experiment 1) formed alternative states, suggesting the lack of assembly rules control in community structure. The second experiment showed that adding factors results in more alternative states. The increasing number of alternative states among replicate communities indicates that diversified environment and migration are needed to reproduce qualitative patterns observed in nature. The last experiment (3) showed that patterns observed among connected replicate communities resemble patterns that emerged in the presence of biological interactions in unconnected communities. Similarity of patterns between connected and unconnected groups of communities suggest that local biological interactions can be sufficient to structure communities to a considerable degree. Nevertheless, the regional processes appear necessary in their role of supplying species for local communities.</p> / Doctor of Philosophy (PhD)