No description available.

It is widely recognized that livestock industries are vulnerable to intentional or accidental introductions of Foreign Animal Diseases (FADs). Combating disease is difficult because of unknown wildlife-livestock interactions. Feral hogs (Sus scrofa) could harbor and shed disease in areas used by domestic livestock such as cattle (Bos taurus). Extent of risk logically depends on spatio-temporal interactions between species. I used Global Positioning System (GPS) collars on cattle and hogs in combination with a Geographic Information Systems (GIS) for detailed analysis on movement patterns of these 2 species on a ranch in southwestern Texas, USA. Motion-triggered video recorders were also utilized to determine interspecific activity patterns. I tested hypotheses that spatio-temporal distributions of domestic cattle and feral hogs on rangeland overlap and that interspecific contact occurs. If these posits are true, it is possible that introduced pathogens like foot-and-mouth disease (FMD) could be transmitted from feral hogs to cattle. Using a rate of 1 GPS fix/15 min (96 fixes/day), I found that spatial distribution of individual hogs and cattle overlapped on both the 95% and 50% kernel area use among 4 seasons. Both cows and feral hogs used Clay Flat, Clay Loam, and Rolling Hardland more so than other range sites. During Summer 2004, riparian zones were the most used feature, identified at 14% (2,760/19,365) of cattle and 70% (445/632) of hog fixes. Other than brush strips, cattle and feral hogs primarily interacted at riparian zones, fencelines, and roads. There were no direct interspecific contacts evident from GPS data, but 3 cases were recorded from video data. Indirect interspecific contacts that may be sufficient for disease transmission occurred much more frequently (GPS = 3.35 indirect contacts/day, video = cows follow hogs: 0.69 indirect contacts/day and hogs follow cows: 0.54 indirect contacts/day). Research results suggested that both species often travel along the same roads and fencelines to water and food sources, especially during extreme heat and low-precipitation conditions. This research provides basic information needed to improve models for management of FAD outbreaks in the U.S., based on specific knowledge of landscape usage and movement patterns of feral hogs and cattle.

This thesis focuses on the spread of organisms in both ecological and epidemiological contexts. In most of the studies presented, displacement is modeled with a spatial kernel function, which is characterized by scale and shape. These are measured by the net squared displacement (or kernel variance) and kurtosis, respectively. If organisms disperse by the assumptions of a random walk or correlated random walk, a Gaussian shaped kernel is expected. Empirical studies often report deviations from this, and commonly leptokurtic distributions are found, often as a result of heterogeneity in the dispersal process. In the studies presented in two of the included papers, the importance of the kernel shape is tested, by using a family of kernels where the shape and scale can be separated effectively. Both studies utilize spectral density approaches for modeling the spatial environment. It is concluded that the shape is not important when studying the population distribution in a habitat/matrix context. The shape is however important when looking at the invasion of organisms in a patchy environment, when the arrangement of patches deviates from randomly distributed. The introduced method for generating patch distribution is also compared to empirical distributions of patches (farms and old trees). Here it is concluded that the assumptions used for modeling of the spatial environment are consistent with the observed patterns. These assumptions include fractal properties such that the same aggregational patterns are found at different scales. In a series of papers, movements of animals are considered as vectors for between-herd disease spread. The studies are based on data found in databases held by the Swedish Board of Agricultural (SJV), consisting of reported movements, as well as farm location and characteristics. The first study focuses on the distance related probability of contacts between herds. In the following papers, the analysis is expanded to include production type and herd size. Movement data of pigs (and cattle in Paper I) are analyzed with Bayesian models, implemented with Markov Chain Monte Carlo (MCMC). This is a flexible approach that allows for parameter estimations of complex models, and at the same time includes parameter uncertainty. In Paper IV, the effects of the included factors are investigated. It is shown that all three factors (herd size, production type structure and distance related probability of contacts) are expected to influence disease spread dynamics, however the production type structure is found to be the most important factor. This emphasizes the value of keeping such information in central databases. The models presented can be used as support for risk analysis and disease tracing. However, data reliability is always a problem, and implementation may be improved with better quality data. The thesis also shows that utilizing spatial kernels for description of the spatial spread of organisms is an appropriate approach. However, these kernels must be flexible and flawed assumptions about the shape may lead to erroneous conclusions. Hence, the joint distribution of kernel shape and scale should be estimated. The flexibility of Bayesian analysis, implemented with MCMC techniques, is a good approach for this, and further allows for implementation of more complex models where other factors may be included.

No description available.

A movimentação de animais em uma rede de fazendas e o espalhamento de algumas doenças animais estão intrinsecamente relacionados. Assim, compreender a dinâmica do espalhamento de doenças infecciosas nestas redes é um instrumento importante no controle dessas doenças. Usando as informações sobre as movimentações de bovinos no estado de Mato Grosso, Brasil, em 2007, reconstruiu-se a rede de trânsito e a rede de proximidade geográfica entre os estabelecimentos desse estado, além de redes hipotéticas seguindo os modelos de rede Molloy-Reed, Kalisky, Método A e Método B, onde simulou-se, usando diferentes configurações do modelo SLIRS, o espalhamento de doenças com parâmetros hipotéticos e reais (brucelose e febre aftosa). Além disso, simulou-se o controle do espalhamento dessas doenças considerando o controle por imunização e por restrição, com e sem rearranjo das movimentações após a restrição, selecionando os estabelecimentos a serem protegidos de forma aleatória, baseando-se no grau de movimentação dos animais e utilizando o conceito do paradoxo da amizade. Dentre os resultados, destacam-se que apesar dos padrões das curvas de prevalência nas redes hipotéticas serem semelhantes aos da rede real, os valores observados foram maiores nas redes hipotéticas, indicando que utilizá-las no planejamento de políticas de controle de doenças no lugar da rede real pode levar a um maior uso de recursos do que seria necessário. Além disso, no controle das doenças tanto com parâmetros hipotéticos quanto com parâmetros reais, nas simulações usando apenas a rede de trânsito dos animais, observou-se uma redução mais efetiva da prevalência ao se selecionar os estabelecimentos com maior grau total do que a da seleção aleatória, enquanto que nas simulações que consideraram a rede de proximidade geográfica dos estabelecimentos, a redução na prevalência das estratégias que selecionaram estabelecimentos específicos foram semelhantes aos da seleção aleatória. Sobre o efeito do rearranjo das movimentações, observou-se que este pode facilitar o espalhamento de doenças na rede, mesmo nas situações em que se aplica alguma estratégia de controle. Espera-se que os resultados das simulações matemáticas possam contribuir para a discussão do impacto relativo entre as estratégias de controle mencionadas e que futuramente possam auxiliar nas atividades dos órgãos responsáveis pela vigilância epidemiológica e no desenvolvimento de políticas de prevenção e controle de doenças em animais. / The animals’ movements in a farms network and the spread of some animal diseases are intrinsically related. Therefore, comprehending the dynamics of the spreading of infectious diseases in these networks is an important tool in controlling these diseases. Using the information about the bovine movements from the State of Mato Grosso, Brazil, in 2007, we rebuilt the network of animal movements and the geographic proximity network between the premises of this state, in addition to hypothetical networks following the network models Molloy-Reed, Kalisky, Method A and Method B, where we simulated, using different configurations of the model SLIRS, the spread of diseases with hypothetical parameters e real ones (brucellosis and foot and mouth disease). Moreover, we simulated the control of these diseases spreading, considering the control by immunization and by restriction, with and without the rearrangement of the movements after the restriction, selecting the premises to be protected randomly, based on the degree of animal’s movements and using the concept of the friendship paradox. Among the results, stands out that although the pattern of the prevalence curves in the hypothetical networks were similar to the ones in the real network, the observed values were higher in the hypothetical networks, indicating that using them in the planning of policies to control diseases in place of the real network might lead to a greater expense of resources than it would be necessary. Furthermore, in the control of the diseases both with hypothetical parameters as well as with real parameters, in the simulations using only the animal’s movements network, it was observed a more effective reduction of the prevalence when selecting the premises with the highest total degree than the random selection, while in the simulations that considered the network of geographic proximity of the premises, the reduction in the prevalence of the strategies that selected specific premises were similar to the random selection. On the effect of rearranging the movements, it was observed that it may facilitate the spread of diseases in the network even in situations where some control strategy is used. We hope that the results of the mathematical simulations may contribute to the discussion of the relative impact of the mentioned control strategies and that in the future they may assist in the activities of agencies responsible for disease surveillance and in the development of policies to prevent and control diseases in animals.

A dinâmica de movimentação de animais em uma rede de propriedades rurais e o espalhamento de algumas doenças animais estão intrinsecamente relacionados. Assim, compreender a dinâmica do espalhamento de doenças infecciosas nestas redes é um instrumento importante no controle destas. Neste projeto, foram implementados algoritmos para gerar redes de movimentação de animais hipotéticas e reconstruiu-se a rede de movimentações de bovinos do Estado do Mato Grosso, 2007, Brasil. Foram feitas diversas simulações a fim de verificar o espalhamento de doenças agudas e crônicas nessas redes. Diferentes dinâmicas de espalhamento de doenças infecciosas foram observadas em redes com a mesma distribuição de graus e diferentes estruturas topológicas. Espera-se que os resultados das simulações matemáticas possam auxiliar nas atividades dos órgãos responsáveis pela vigilância epidemiológica e incentivar outros Estados a seguirem o exemplo do Estado do Mato Grosso, a construírem bancos de dados que possam ser analisados utilizando a metodologia de redes. / The animals\' movements in a farms network and the spread of some animal diseases are intrinsically related. Therefore, comprehending the dynamics of the spreading of infectious diseases in these networks is an important tool in controlling these diseases. In this project, we have implemented algorithms to generate hypothetical networks of animals\' movements and rebuilt the network of bovine movements from the State of Mato Grosso, 2007, Brazil. We made several simulations in order to check the spreading of acute and chronic disease in these networks. Different dynamics of infectious disease spreading were observed in networks with the same degree distribution and different topological structure. We hope that the results of the mathematical simulations may assist in the activities of agencies responsible for disease surveillance and encourage other States to follow the example of the State of Mato Grosso, to build databases that can be analyzed using the methodology of networks.

A dinâmica de movimentação de animais em uma rede de propriedades rurais e o espalhamento de algumas doenças animais estão intrinsecamente relacionados. Assim, compreender a dinâmica do espalhamento de doenças infecciosas nestas redes é um instrumento importante no controle destas. Neste projeto, foram implementados algoritmos para gerar redes de movimentação de animais hipotéticas e reconstruiu-se a rede de movimentações de bovinos do Estado do Mato Grosso, 2007, Brasil. Foram feitas diversas simulações a fim de verificar o espalhamento de doenças agudas e crônicas nessas redes. Diferentes dinâmicas de espalhamento de doenças infecciosas foram observadas em redes com a mesma distribuição de graus e diferentes estruturas topológicas. Espera-se que os resultados das simulações matemáticas possam auxiliar nas atividades dos órgãos responsáveis pela vigilância epidemiológica e incentivar outros Estados a seguirem o exemplo do Estado do Mato Grosso, a construírem bancos de dados que possam ser analisados utilizando a metodologia de redes. / The animals\' movements in a farms network and the spread of some animal diseases are intrinsically related. Therefore, comprehending the dynamics of the spreading of infectious diseases in these networks is an important tool in controlling these diseases. In this project, we have implemented algorithms to generate hypothetical networks of animals\' movements and rebuilt the network of bovine movements from the State of Mato Grosso, 2007, Brazil. We made several simulations in order to check the spreading of acute and chronic disease in these networks. Different dynamics of infectious disease spreading were observed in networks with the same degree distribution and different topological structure. We hope that the results of the mathematical simulations may assist in the activities of agencies responsible for disease surveillance and encourage other States to follow the example of the State of Mato Grosso, to build databases that can be analyzed using the methodology of networks.

A movimentação de animais em uma rede de fazendas e o espalhamento de algumas doenças animais estão intrinsecamente relacionados. Assim, compreender a dinâmica do espalhamento de doenças infecciosas nestas redes é um instrumento importante no controle dessas doenças. Usando as informações sobre as movimentações de bovinos no estado de Mato Grosso, Brasil, em 2007, reconstruiu-se a rede de trânsito e a rede de proximidade geográfica entre os estabelecimentos desse estado, além de redes hipotéticas seguindo os modelos de rede Molloy-Reed, Kalisky, Método A e Método B, onde simulou-se, usando diferentes configurações do modelo SLIRS, o espalhamento de doenças com parâmetros hipotéticos e reais (brucelose e febre aftosa). Além disso, simulou-se o controle do espalhamento dessas doenças considerando o controle por imunização e por restrição, com e sem rearranjo das movimentações após a restrição, selecionando os estabelecimentos a serem protegidos de forma aleatória, baseando-se no grau de movimentação dos animais e utilizando o conceito do paradoxo da amizade. Dentre os resultados, destacam-se que apesar dos padrões das curvas de prevalência nas redes hipotéticas serem semelhantes aos da rede real, os valores observados foram maiores nas redes hipotéticas, indicando que utilizá-las no planejamento de políticas de controle de doenças no lugar da rede real pode levar a um maior uso de recursos do que seria necessário. Além disso, no controle das doenças tanto com parâmetros hipotéticos quanto com parâmetros reais, nas simulações usando apenas a rede de trânsito dos animais, observou-se uma redução mais efetiva da prevalência ao se selecionar os estabelecimentos com maior grau total do que a da seleção aleatória, enquanto que nas simulações que consideraram a rede de proximidade geográfica dos estabelecimentos, a redução na prevalência das estratégias que selecionaram estabelecimentos específicos foram semelhantes aos da seleção aleatória. Sobre o efeito do rearranjo das movimentações, observou-se que este pode facilitar o espalhamento de doenças na rede, mesmo nas situações em que se aplica alguma estratégia de controle. Espera-se que os resultados das simulações matemáticas possam contribuir para a discussão do impacto relativo entre as estratégias de controle mencionadas e que futuramente possam auxiliar nas atividades dos órgãos responsáveis pela vigilância epidemiológica e no desenvolvimento de políticas de prevenção e controle de doenças em animais. / The animals’ movements in a farms network and the spread of some animal diseases are intrinsically related. Therefore, comprehending the dynamics of the spreading of infectious diseases in these networks is an important tool in controlling these diseases. Using the information about the bovine movements from the State of Mato Grosso, Brazil, in 2007, we rebuilt the network of animal movements and the geographic proximity network between the premises of this state, in addition to hypothetical networks following the network models Molloy-Reed, Kalisky, Method A and Method B, where we simulated, using different configurations of the model SLIRS, the spread of diseases with hypothetical parameters e real ones (brucellosis and foot and mouth disease). Moreover, we simulated the control of these diseases spreading, considering the control by immunization and by restriction, with and without the rearrangement of the movements after the restriction, selecting the premises to be protected randomly, based on the degree of animal’s movements and using the concept of the friendship paradox. Among the results, stands out that although the pattern of the prevalence curves in the hypothetical networks were similar to the ones in the real network, the observed values were higher in the hypothetical networks, indicating that using them in the planning of policies to control diseases in place of the real network might lead to a greater expense of resources than it would be necessary. Furthermore, in the control of the diseases both with hypothetical parameters as well as with real parameters, in the simulations using only the animal’s movements network, it was observed a more effective reduction of the prevalence when selecting the premises with the highest total degree than the random selection, while in the simulations that considered the network of geographic proximity of the premises, the reduction in the prevalence of the strategies that selected specific premises were similar to the random selection. On the effect of rearranging the movements, it was observed that it may facilitate the spread of diseases in the network even in situations where some control strategy is used. We hope that the results of the mathematical simulations may contribute to the discussion of the relative impact of the mentioned control strategies and that in the future they may assist in the activities of agencies responsible for disease surveillance and in the development of policies to prevent and control diseases in animals.

In this paper, we discuss methods for developing a stochastic model which incorporates behavior differences in the predation movements of Anelosimus studiosus (a subsocial spider). Stochastic models for animal movement and, in particular, spider predation movement have been developed previously; however, this paper focuses on the development and implementation of the necessary mathematical and statistical methods required to expand such a model in order to capture a variety of distinct behaviors. A least squares optimization algorithm is used for parameter estimation to fit a single stochastic model to an individual spider during predation resulting in unique parameter values for each spider. Similarities and variations between parameter values across the spiders are analyzed and used to estimate probability distributions for the variable parameter values. An aggregate stochastic model is then created which incorporates the individual dynamics. The comparison between the optimal individual models to the aggregate model indicate the methodology and algorithm developed in this paper are appropriate for simulating a range of individualistic behaviors.

Le caribou forestier est une espèce menacée au Canada, la principale hypothèse au déclin des populations étant l’intensification de la prédation provoquée par les perturbations anthropiques du paysage. Afin de faire face à cette situation, il est nécessaire d’étudier et comprendre l’impact de l’environnement sur les interactions prédateur-proies entre le caribou et le loup, ainsi qu’avec l’orignal, qui est sa principale proie alternative. Pour cela, cette thèse présente la conception d’un modèle centré sur l’individu des déplacements de ces trois espèces en fonction de leur environnement, dont résulteront les interactions prédateur-proies. Afin de permettre l’application de ce modèle sur de longues périodes, et donc pour un environnement changeant, une méthodologie a été développée, qui s’articule atour de deux aspects principaux. Tout d’abord, la notion de niveaux d’émergence est introduite, permettant d’ordonner les comportements observables du système selon leurs interdépendances, afin de choisir comme trait du modèle un com- portement correspondant au domaine d’applicabilité visé. Ordonner les comportements selon leurs niveaux d’émergence permet également d’identifier la redondance entre les patrons, qui peut être à l’origine d’un phénomène de sur-apprentissage lorsqu’ils sont utilisés lors de la calibration. Dans un second temps, un nouveau protocole pour la calibration et la validation du ou des traits choisis à l’aide des niveaux d’émergence, nommé réplication de système basé sur l’individu (Individual Based System Replication - IBSRtion) est également présenté. Ce protocole met l’emphase sur la modélisation directe, contrairement au principal protocole existant, la modélisation orientée patrons (Pattern Oriented Modelling - POM), et permet une approche empirique en générant artificiellement des données non disponibles ou ne pouvant être récoltées par des études de terrains. IBSRtion a également l’avantage de pouvoir être intégrée dans POM, afin de contribuer à la création d’une méthodologie universelle pour la conception de modèles centrés sur l’individu. Le processus de conception de ce modèle aura entre autre permis de faire une synthèse des connaissances et d’identifier certaines lacunes. Une étude visant à palier le manque de connaissances satisfaisantes sur les réponses comportementales à court-terme des proies face au risque de prédation a notamment permis d’observer que celles-ci sont une combinaison de comportements chroniques et éphémères, et que les mécanismes qui en sont à l’origine sont complexes et non-linéaires. Le résultat de ce travail est un modèle complexe utilisant de nombreux sous-modèles, et calibré de façon empirique, applicable à une grande variété d’environnements. Ce modèle a permis de tester l’impact de l’enfeuillement sur les relations prédateur-proies. Des simulations ont été effectuées pour différentes quantités d’enfeuillement, suivant deux configurations spatiales différentes. Les résultats de simulation suggèrent que des plans d’aménagement considérant également l’habitat de l’orignal pourraient être bénéfiques pour le caribou forestier, car ils permettraient d’améliorer la ségrégation spatiale entre les deux espèces, et donc entre le caribou et le loup. En le couplant avec un module de naissances et de morts naturelles ainsi qu’un modèle d’évolution du paysage, ce modèle permettra par la suite d’évaluer l’impact de plans d’aménagement forestier sur la viabilité des populations de caribou forestier. / Forest-dwelling woodland caribou are considered threatened in Canada. The main hypothesis to the decrease of populations is the intensification of predation provoked by anthropogenic perturbations in the landscape. To deal with this situation, it is necessary to study and to understand the impact of the environment on the predator-prey interactions between the caribou and the wolf, and with the moose, its main alternative prey. In this perspective, this thesis presents the design of an individual-based model of displacements of these three species with respect to their environment, from which the predator-prey interactions will result. To allow for the application of this model for long periods of time, i.e. for changing environments, a methodology has been developed, which is based on two key points. First, the notion of levels of emergence is introduced, allowing to order the different observable comportments of the system according to their inter-dependencies, to help with choosing a trait of the model corresponding to the intended domain of applicability. Ordering the comportments according to their levels of emergence also permits to identify redundancy between patterns, which can lead to over-fitting when they are used for calibration. Second, a new methodology for calibration and validation of the trait(s) chosen by means of the levels of emergence framework is also presented, named Individual Based System Replication (IBSRtion). This protocol emphasizes forward modelling, contrary to the main existing methodology, Pattern Oriented Modelling (POM), and allows to use an empirical approach by artificially generating data that are unavailable or that cannot be obtained by means of field studies. IBSRtion can also be integrated into POM, to contribute to the establish- ment of a universal methodology for the design of individual based models. The design process of this model allowed for a synthesis of existing knowledge and to point out some gaps. More specifically, a study conducted to deal with the lack of sufficient information on the short-term response of prey to predation risk allowed to observe that their behavioural responses to prior presence of predators are a combination of chronic and ephemeral behaviours, and that the mechanisms that produce them are complex and non-linear. The outcome of this work is a complex model, using many sub-models, and calibrated in an empirical fashion, that can be applied to a wide variety of environments. This model allowed to test the impact of the encroachment of deciduous trees on predator-prey relations. Simulations have been run for different quantities of encroachment, according to two different spatial configurations. Simulation results suggest that management plans taking into account the moose’s habitat might benefit woodland caribou, because they could increase spatial segregation between the two species, and thus between caribou and wolf. Coupling this model with a module of birth and natural death, along with a model of landscape transformation, would allow the assessment of the impact of different forest management plans on the viability of woodland caribou populations.