Dendrocolaptes platyrostris é uma espécie de ave florestal associada às matas de galeria do corredor de vegetação aberta da América do sul (D. p. intermedius) e à Floresta Atlântica (D. p. platyrostris). Em um trabalho anterior, foi observada estrutura genética populacional associada às subespécies, além de dois clados dentro da Floresta Atlântica e evidências de expansão na população do sul, o que é compatível com o modelo Carnaval-Moritz. Utilizando approximate Bayesian computation, o presente trabalho avaliou a diversidade genética de dois marcadores nucleares e um marcador mitocondrial dessa espécie com o objetivo de comparar os resultados obtidos anteriormente com os obtidos utilizando uma estratégia multi-locus e considerando variação coalescente. Os resultados obtidos sugerem uma relação de politomia entre as populações que se separaram durante o último período interglacial, mas expandiram após o último máximo glacial. Este resultado é consistente com o modelo de Carnaval-Moritz, o qual sugere que as populações sofreram alterações demográficas devido às alterações climáticas ocorridas nestes períodos. Trabalhos futuros incluindo outros marcadores e modelos que incluam estabilidade em algumas populações e expansão em outras são necessários para avaliar o presente resultado / Dendrocolaptes platyrostris is a forest specialist bird associated to gallery forests of the open vegetation corridor of South America (D. p. intermedius) and to the Atlantic forest (D. p. platyrostris). A previous study showed a population genetic structure associated with the subspecies, two clades within the Atlantic forest, and evidence of population expansion in the south, which is compatible with Carnaval- Moritz\'s model. The present study evaluated the genetic diversity of two nuclear and one mitochondrial markers of this species using approximate Bayesian computation, in order to compare the results previously obtained with those based on a multi-locus strategy and considering the coalescent variation. The results suggest a polytomic relationship among the populations that split during the last interglacial period and expanded after the last glacial maximum. This result is consistent with the model of Carnaval-Moritz, which suggests that populations have undergone demographic changes due to climatic changes that occurred in these periods. Future studies including other markers and models that include stability in some populations and expansion in others are needed to evaluate the present result

Neste trabalho apresentaremos dois problemas do contexto de controle estatístico da qualidade: monitoramento \"on-line\'\' de qualidade e environmental stress screening, analisados pela óptica bayesiana. Apresentaremos os problemas dos modelos bayesianos relativos a sua aplicação e, os reanalisamos com o auxílio do ABC o que nos fornece resultados de uma maneira mais rápida, e assim possibilita análises diferenciadas e a previsão novas observações. / In this work we will present two problems in the context of statistical quality control: on line quality monitoring and environmental stress screening, analyzed from the Bayesian perspective. We will present problems of the Bayesian models related to their application, and also we reanalyze the problems with the assistance of ABC methods which provides results in a faster way, and so enabling differentiated analyzes and new observations forecast.

Neste trabalho apresentaremos dois problemas do contexto de controle estatístico da qualidade: monitoramento \"on-line\'\' de qualidade e environmental stress screening, analisados pela óptica bayesiana. Apresentaremos os problemas dos modelos bayesianos relativos a sua aplicação e, os reanalisamos com o auxílio do ABC o que nos fornece resultados de uma maneira mais rápida, e assim possibilita análises diferenciadas e a previsão novas observações. / In this work we will present two problems in the context of statistical quality control: on line quality monitoring and environmental stress screening, analyzed from the Bayesian perspective. We will present problems of the Bayesian models related to their application, and also we reanalyze the problems with the assistance of ABC methods which provides results in a faster way, and so enabling differentiated analyzes and new observations forecast.

Dendrocolaptes platyrostris é uma espécie de ave florestal associada às matas de galeria do corredor de vegetação aberta da América do sul (D. p. intermedius) e à Floresta Atlântica (D. p. platyrostris). Em um trabalho anterior, foi observada estrutura genética populacional associada às subespécies, além de dois clados dentro da Floresta Atlântica e evidências de expansão na população do sul, o que é compatível com o modelo Carnaval-Moritz. Utilizando approximate Bayesian computation, o presente trabalho avaliou a diversidade genética de dois marcadores nucleares e um marcador mitocondrial dessa espécie com o objetivo de comparar os resultados obtidos anteriormente com os obtidos utilizando uma estratégia multi-locus e considerando variação coalescente. Os resultados obtidos sugerem uma relação de politomia entre as populações que se separaram durante o último período interglacial, mas expandiram após o último máximo glacial. Este resultado é consistente com o modelo de Carnaval-Moritz, o qual sugere que as populações sofreram alterações demográficas devido às alterações climáticas ocorridas nestes períodos. Trabalhos futuros incluindo outros marcadores e modelos que incluam estabilidade em algumas populações e expansão em outras são necessários para avaliar o presente resultado / Dendrocolaptes platyrostris is a forest specialist bird associated to gallery forests of the open vegetation corridor of South America (D. p. intermedius) and to the Atlantic forest (D. p. platyrostris). A previous study showed a population genetic structure associated with the subspecies, two clades within the Atlantic forest, and evidence of population expansion in the south, which is compatible with Carnaval- Moritz\'s model. The present study evaluated the genetic diversity of two nuclear and one mitochondrial markers of this species using approximate Bayesian computation, in order to compare the results previously obtained with those based on a multi-locus strategy and considering the coalescent variation. The results suggest a polytomic relationship among the populations that split during the last interglacial period and expanded after the last glacial maximum. This result is consistent with the model of Carnaval-Moritz, which suggests that populations have undergone demographic changes due to climatic changes that occurred in these periods. Future studies including other markers and models that include stability in some populations and expansion in others are needed to evaluate the present result

Population genetic analyses can provide information about both neutral and selective evolutionary processes shaping genetic variation. In this thesis, extensive population genetic methods were used to make inferences about genetic drift and selection in spruce species. In paper I we studied four species from the Qinghai-Tibetan Plateau (QTP): Picea likiangensis, P. purpurea, P. wilsonii and P. schrenkiana. Big differences in estimates of genetic diversity and Ne were observed in the more restricted species, P. schrenkiana, and the other more widely distributed species. Furthermore, P. purpurea appears to be a hybrid between P. likiangensis and P. wilsonii. In paper II we used Approximate Bayesian Computation (ABC) to find that the data support a drastic reduction of Ne in Taiwan spruce around 300-500 kya, in line with evidence from the pollen records. The split from P. wilsonii was dated to between 4-8 mya, around the time that Taiwan was formed. These analyses relied on a small sample size, and so in Paper III we investigated the impact of small datasets on the power to distinguish between models in ABC. We found that when genetic diversity is low there is little power to distinguish between simple coalescent models and this can determine the number of samples and loci required. In paper IV we studied the relative importance of genetic drift and selection in four spruce species with differing Ne: P. abies, P. glauca, P. jezoensis and P. breweriana. P. breweriana, which has a low Ne, exhibits a low fraction of adaptive substitutions, while P. abies has high Ne and a high fraction of adaptive substitutions. The other two spruce, however, do not support this suggesting other factors a more important. In paper V we find that several SNPs correlate with both a key adaptive trait (budset) and latitude. The expression of one in particular (PoFTL2) correlates with budset and was previously indentified in P. abies. These studies have helped characterise the importance of different population genetic processes in shaping genetic variation in spruce species and has laid some solid groundwork for future studies of spruce.

<p>Agent-based models (ABMs) are computational models used to simulate the behaviors, </p><p>actionsand interactions of agents within a system. The individual agents </p><p>each have their own set of assigned attributes and rules, which determine</p><p>their behavior within the ABM system. These rules can be</p><p>deterministic or probabilistic, allowing for a great deal of</p><p>flexibility. ABMs allow us to</p><p>observe how the behaviors of the individual agents affect the system</p><p>as a whole and if any emergent structure develops within the</p><p>system. Examining rule sets in conjunction with corresponding emergent</p><p>structure shows how small-scale changes can</p><p>affect large-scale outcomes within the system. Thus, we can better</p><p>understand and predict the development and evolution of systems of</p><p>interest. </p><p>ABMs have become ubiquitous---they used in business</p><p>(virtual auctions to select electronic ads for display), atomospheric</p><p>science (weather forecasting), and public health (to model epidemics).</p><p>But there is limited understanding of the statistical properties of</p><p>ABMs. Specifically, there are no formal procedures</p><p>for calculating confidence intervals on predictions, nor for</p><p>assessing goodness-of-fit, nor for testing whether a specific</p><p>parameter (rule) is needed in an ABM.</p><p>Motivated by important challenges of this sort, </p><p>this dissertation focuses on developing methodology for uncertainty</p><p>quantification and statistical inference in a likelihood-free context</p><p>for ABMs. </p><p>Chapter 2 of the thesis develops theory related to ABMs, </p><p>including procedures for model validation, assessing model </p><p>equivalence and measuring model complexity. </p><p>Chapters 3 and 4 of the thesis focuses on two approaches </p><p>for performing likelihood-free inference involving ABMs, </p><p>which is necessary because of the intractability of the </p><p>likelihood function due to the variety of input rules and </p><p>the complexity of outputs.</p><p>Chapter 3 explores the use of </p><p>Gaussian Process emulators in conjunction with ABMs to perform </p><p>statistical inference. This draws upon a wealth of research on emulators, </p><p>which find smooth functions on lower-dimensional Euclidean spaces that approximate</p><p>the ABM. Emulator methods combine observed data with output from ABM</p><p>simulations, using these</p><p>to fit and calibrate Gaussian-process approximations. </p><p>Chapter 4 discusses Approximate Bayesian Computation for ABM inference, </p><p>the goal of which is to obtain approximation of the posterior distribution </p><p>of some set of parameters given some observed data. </p><p>The final chapters of the thesis demonstrates the approaches </p><p>for inference in two applications. Chapter 5 presents application models the spread </p><p>of HIV based on detailed data on a social network of men who have sex with</p><p>men (MSM) in southern India. Use of an ABM</p><p>will allow us to determine which social/economic/policy </p><p>factors contribute to thetransmission of the disease. </p><p>We aim to estimate the effect that proposed medical interventions will</p><p>have on the spread of HIV in this community. </p><p>Chapter 6 examines the function of a heroin market </p><p>in the Denver, Colorado metropolitan area. Extending an ABM </p><p>developed from ethnographic research, we explore a procedure </p><p>for reducing the model, as well as estimating posterior </p><p>distributions of important quantities based on simulations.</p> / Dissertation

No description available.

Les hêtraies-sapinières-pessières de montagne paraissent particulièrement menacées par le réchauffement climatique. Pour appréhender la dynamique future de ces forêts et adapter la sylviculture à ces nouvelles conditions, il est important de mieux connaître les facteurs environnementaux impactant la démographie de ces espèces. Nous avons abordé cette problématique en combinant des données historiques de gestion, le modèle de dynamique forestière Samsara2 et une méthode de calibration basée sur le Calcul Bayésien Approché. Nous avons ainsi pu étudier conjointement les différents processus démographiques dans ces forêts. Nos analyses montrent que la démographie forestière peut varier fortement entre les parcelles et que le climat n'est pas toujours déterminant pour expliquer ces variations. Ainsi, malgré les changements climatiques attendus, la gestion irrégulière pratiquée actuellement devrait permettre de maintenir les services rendus par les peuplements mélangés situés en conditions mésiques. / The spruce-fir-beech mountain forests could be particularly threatened by the global warming. To better understand the future dynamics of these forests and adapt the silviculture to these new conditions, a better knowledge of the environmental factors affecting the species demograhics is needed. We studied this issue by combining a historical management data set, the forest dynamics model Samsara2 and a calibration method based on Approximate Bayesian Computation. We were able thus to study jointly the different demographic process in these forests. Our analysis show that the forest demographics can strongly vary between stands and that climate is not always determining to explain these variations. The unven-aged management currently applied seem adapted for the mixed stands located in mesic conditions, but the pure spruce forests and the low elevation stands could be highly impacted.

Les réseaux de gènes régulateurs représentent un ensemble de gènes qui interagissent, directement ou indirectement, les uns avec les autres ainsi qu'avec d'autres produits cellulaires. Comme ces interactions réglementent le taux de transcription des gènes et la production subséquente de protéines fonctionnelles, l'identification de ces réseaux peut conduire à une meilleure compréhension des systèmes biologiques complexes. Les technologies telles que les puces à ADN (microarrays) et le séquençage à ultra-haut débit (RNA sequencing) permettent une étude simultanée de l'expression des milliers de gènes chez un organisme, soit le transcriptome. En mesurant l'expression des gènes au cours du temps, il est possible d'inférer (soit "reverse-engineer") la structure des réseaux biologiques qui s'impliquent pendant un processus cellulaire particulier. Cependant, ces réseaux sont en général très compliqués et difficilement élucidés, surtout vu le grand nombre de gènes considérés et le peu de répliques biologiques disponibles dans la plupart des données expérimentales.<br /> <br /> Dans ce travail, nous proposons deux méthodes pour l'identification des réseaux de gènes régulateurs qui se servent des réseaux Bayésiens dynamiques et des modèles linéaires. Dans la première méthode, nous développons un algorithme dans un cadre bayésien pour les modèles linéaires espace-état (state-space model). Les hyperparamètres sont estimés avec une procédure bayésienne empirique et une adaptation de l'algorithme espérance-maximisation. Dans la deuxième approche, nous développons une extension d'une méthode de Approximate Bayesian Computation basé sur une procédure de Monte Carlo par chaînes de Markov pour l'inférence des réseaux biologiques. Cette méthode échantillonne des lois approximatives a posteriori des interactions gène-à-gène et fournit des informations sur l'identifiabilité et le robustesse des structures sous-réseaux. La performance des deux approches est étudié via un ensemble de simulations, et les deux sont appliqués aux données transcriptomiques.

Genetic variation is a prerequisite for the viability and evolution of species. Information on population genetic patterns on spatial and temporal scales is therefore important for effective management and for protection of biodiversity. However, incorporation of genetics into management has been difficult, even though the need has been stressed for decades. In this thesis population genetic patterns in continuous environments are described, compared among species, and related to conservation management. The model systems are moose (Alces alces) in Sweden and multiple species in the Baltic Sea, with particular focus on the Northern pike (Esox lucius). The spatial scope of the studies is large, and much focus is dedicated towards comprehensive sampling over large geographic areas. The moose population in Sweden is shown to be divided into two major subpopulations, a northern and a southern one. Both subpopulations show genetic signals of major population bottlenecks, which coincide with known population reductions due to high hunting pressure (Paper I). The Northern pike in the Baltic Sea shows relatively weak, but temporally stable population genetic structure. An isolation by distance pattern suggests that gene flow primarily takes place among neighboring populations, either over shortest waterway distance or along the mainland coast, with island populations acting as stepping stones (Paper III). In a comparative study of seven Baltic Sea species no shared genetic patterns were found, either in terms of genetic divergence among or genetic diversity within geographic regions. These results complicate the incorporation of genetic data into management, because it suggests that no generalization can be made among species in the Baltic Sea, but that species-specific management is needed (Paper II). Over the last 50 years, 61 species in the Baltic Sea have been studied with respect to spatial genetic patterns. For over 20 of these species information of direct relevance for management is available. Relevant information is synthesized into management recommendations (Paper IV). This thesis provides vital information on spatial and temporal genetic structure for a number of ecologically and socio-economically important species. It shows that such information is important to consider species by species and that both local and metapopulation approaches are needed to effectively manage genetic diversity in e.g. moose and pike. Further, it identifies for which organisms in the Baltic Sea genetic information exists, how it can be used, and where important information is lacking. In order to successfully make use of genetic data in management, effective communication channels between academia and policy-makers are needed. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>