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La maladie de Newcastle (MN) et l'influenza aviaire (IA) sont des maladies virales d'importances majeures. L'aviculture malgache est dominée par de petits élevages familiaux. Plusieurs facteurs de risque d'IA et de MN décrits dans la littérature sont présents à Madagascar. Les objectifs de cette thèse sont de déterminer les facteurs de risque associés à la transmission des virus de la MN et de l'IA ; d'évaluer leur niveau de circulation et leur incidence clinique ; d'étudier le rôle des circuits de commercialisation des volailles dans leur diffusion et de proposer des mesures de surveillance adaptées.Les sites d'étude étaient Antananarivo et son pourtour, et le Lac Alaotra. Une étude exploratoire des facteurs de risque a été effectuée, suivie d'une.surveillance épidémiologique événementielle et d'une épidémiologie participative pour estimer l'incidence clinique des maladies. Le rôle des circuits commerciaux a été évalué par des méthodes d'analyse de réseaux sociaux.La circulation des 2 virus était plus importante au Lac Alaotra, caractérisé par les rizières, les eaux de surface et les palmipèdes. Les élevages de basse-cour et les élevages de poulets à haut niveau relatif de protection sanitaire étaient les plus à risque à la MN Antananarivo. Leurs profils de facteurs de risque étaient l'absence de mesure de biosécurité et un contact avec plusieurs marchés pour le premier ; et une densité élevée, les visites des auxiliaires d'élevage et des collecteurs d'œufs et un contact avec d'autres acteurs pour le second. Il n'y a pas de circulation d'IAH, la MN est la maladie dominante avec un taux de mortalité de 44%. Le rôle du circuit de commercialisation a été confirmé. Les villages ayant les plus fortes connexions commerciales étaient les plus exposés à la MN mais constituaient aussi des super-diffuseurs de virus. L'association de plusieurs méthodes de surveillance a été discutée pour en améliorer la sensibilité, la faisabilité pratique et l'efficacité. / Newcastle disease (ND) and avian influenza (AI) are major poultry viral diseases. Poultry production in Madagascar is dominated by smallholder family system. Several risk factors for both diseases described in the literature are present in Madagascar: The objectives of this thesis were to determine the risk factors associated with transmission of AI and ND viruses; evaluate the intensity of their transmission and their clinical incidence; study the role of poultry trade network in their spread and suggest surveillance adapted to local conditions.Study sites were: Antananarivo and its surrounding and the Lake Alaotra. An exploratory study of risk factors was carried out. Passive surveillance and participatory surveys were combined to assess the incidence and clinical impact of AI and ND. The role of poultry-trade network was assessed using social network analysis methods. Higher circulating level for both viruses was observed in Lake Alaotra which is characterized by large paddy fields and surface water, and a high density of domestic waterfowl. At the farm level, backyard chicken and chicken farms with some biosecurity awareness were associated with higher risk of ND in Antananarivo. Risk factors associated with them were lack of biosecurity measures and contact with many markets for the former, and a high density of poultry, high exposition to the visits of animal health workers, egg collectors and multiple interactions with other poultry stakeholders for the second. There was no evidence of HPAI circulation The major infection was ND with an overall mortality rate of 44%, within observed outbreaks. The role of poultry trade in the spread of these viruses was confirmed. Villages with the highest commercial connections were the most exposed to ND. They were also super-spreaders of these viruses. The relevance of the specific combination of several methods of surveillance was discussed to improve their sensitivity, practical implementation, and effectiveness.

L’Influenza Aviaire Hautement Pathogène H5N1 (IAHP à H5N1) a été déclaré en Thaïlande lors de plusieurs vagues épidémiques puis lors de cas sporadiques entre 2004 et 2008, et le risque persiste encore en Thaïlande. La plupart des foyers confirmés d’IAHP à H5N1 en Thaïlande ont eu lieu dans les populations de volailles de basse-cour. Les poulets de basse-cour sont élevés pour de nombreuses raisons, y compris pour un revenu supplémentaire. Ce commerce est géré informellement par les collecteurs de volailles qui peuvent être classés en collecteur-abatteur (TS), sous-collecteur (HT) et collecteur de collecteurs (TT). Ces collecteurs se déplacent entre villages avec les mêmes véhicules et matériel non nettoyés. Nous avons mesuré leurs activités commerciales dans l'espace et le temps. Nous avons développé un modèle spatial dynamique compartimental et stochastique de la filière de poulet de basse-cour dans une province. Nos résultats indiquent que ces échanges commerciaux peuvent contribuer à la propagation d’IAHP à H5N1 grâce au chevauchement des zones de collecte et aux distances parcourues. Des variations temporelles ont été observées lors de certaines grandes fêtes rituelles tel le Nouvel An chinois. Nous avons développé un modèle SIR couplé au modèle de la filière de poulets. Nous avons supposé que la maladie peut se propager par deux moyens : localement entre villages voisins et par les échanges commerciaux. Nous avons utilisé ce modèle infectieux de base pour tester plusieurs mesures de contrôle connexes. Nos résultats suggèrent que lors d’un foyer une interdiction totale et rapide de tous les échanges de volailles devrait être mise en oeuvre ainsi qu’une campagne de désinfection. / Highly pathogenic avian influenza H5N1 (HPAI H5N1) was recognized in Thailand by multiple epidemic waves and some sporadic cases between 2004 and 2008 but the risk of disease remerging in Thailand still remains up to present. Most of HPAI H5N1 confirmed outbreaks in Thailand occurred in backyard chicken populations. Backyard chickens are reared for many purposes including for additional cash income. Backyard chicken trade is informally managed by poultry traders which can be categorized into trader–slaughterhouse (TS), household trader (HT) and trader of trader (TT). These traders roam around different villages with the same unclean vehicle and facilities. Thus, their trade patterns in space and time are necessary to be elaborately studied. In our study, we developed a spatial compartmental stochastic dynamic model of backyard chicken trade network in a province of Thailand. Our model results indicated that the structure of poultry networks may contribute to HPAI H5N1 spread through overlapped catchment areas and long distance trades. Also, temporal variations of live poultry movements were observed during some major ritual festivals especially Chinese New Year. Subsequently, we developed an SIR model upon the dynamic model of backyard chicken trade network. It was assumed in this study that the disease can spread by two means: local spread to neighboring uninfected villages and spread by poultry traders. Then, we used this baseline infectious model to test multiple related control measures. Our ultimate results suggested that a complete ban of all poultry traders should be promptly implemented with poultry area disinfection campaign once the outbreak occurs.

The stratification of bird species along elevational gradients is widely reported, with montane bird communities typically characterized by distinctive species occurring in relatively small and isolated populations; as such, these species are the subject of considerable interest to ecologists and conservationists. The stratification of species along elevation is largely attributed to compressed climatic zonation. Recent evidence that bird species are shifting up in elevation has fueled speculation that these species are tracking their climactic niches in response to climate change. However, there is also evidence plant communities are shifting in elevation, presenting a potential additional mechanism explaining changes observed in the bird community. Uncertainty as to the degree to which climate directly influences bird abundance versus the degree to which climate indirectly influences bird abundance via habitat composition and structure represents a key impediment to understanding the ecology of these species in montane environments. To address this question I measured species abundance, habitat characteristics, and temperature at 150 survey points located along 15 elevational transects in the Presidential Mountains of New Hampshire in the summers of 2014 and 2015. I used N-mixture models to correct for imperfect detection of species and structural equation models, incorporating abundance, habitat, temperature, and precipitation derived from a downscaled regional dataset to assign variation to the direct and indirect effects of climate upon birds. Analysis of 21 species revealed species-specific patterns on how climate exerts direct effects and indirect effects mediated by forest composition and structure on bird abundance. This work represents an important contribution to the ecological understanding of the pathways by which climate influences bird abundance. Finding that 62% of species experience both direct and indirect effects of climate, with 62% experiencing stronger direct than indirect effects, these results underscore the vulnerability of these species to climate change. With 81% of species found to experience indirect effects of climate via forests, these findings indicate great conservation value of maintaining forest habitat amidst climate change. Overall, this information will facilitate the refinement of predictive models of the abundance of montane bird species and represents an approach that will advance future investigations of climate effects in the Northern Appalachians and other systems.

Avian leukosis virus (ALV)-induced osteopetrosis is a proliferative disorder of the bone affecting the growth and differentiation of osteoblasts. Osteopetrosis is a polyclonal disease in which cells of the bone contain, on average, multiple viral DNA copies. Osteopetrotic bone is also characterized by the accumulation of unintegrated viral DNA, suggesting an atypical life cycle of the virus in the infected osteoblasts. To better understand virus-host interactions in the induction of osteopetrosis by ALVs, infected chick osteoblast cultures and osteopetrotic bone were examined for aspects of the virus life cycle and effects of infection on osteoblast function. Levels of infection and virus expression were compared in cultured osteoblasts and osteopetrotic bone. Osteopetrotic bone contained higher levels of viral DNA and correspondingly higher levels of viral proteins than infected osteoblast cultures, suggesting a higher viral load in the diseased bone. A significant level of mature Gag protein was present in the bone, suggesting the accumulation of mature virus particles in the diseased bone. It is possible that the accumulation of virus could facilitate the high levels of infection observed in the diseased bone. The mechanism by which unintegrated viral DNA persisted in osteopetrotic bone was investigated by examining the susceptibility of infected osteoblasts to superinfection. The results indicated that, in culture, infected osteoblasts were able to establish interference to superinfection. This suggests that the persistence of unintegrated viral DNA in osteopetrotic bone may not result from the continuing infection of productively infected osteoblasts. The effect of virus infection on osteoblast function was examined in the diseased bone and in osteoblast cultures. In infected chickens, osteoblast activity, as evidenced by the expression of osteoblast phenotypic markers, was increased only in chickens developing severe osteopetrosis. In culture, virus infection had no apparent effect on either the proliferation or differentiation of osteoblasts. This indicates that infection was itself not sufficient to perturb osteoblast function. Furthermore, it suggested that additional components of the bone may be required for ALV infection to induce the abnormal activity of osteoblasts observed in osteopetrosis.

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<div>Wildlife diseases are an increasingly growing concern for public health managers, conservation biologists, and society at large. These diseases may be zoonotic -- infective wildlife are able to spread pathogens to human populations. Animal or plant species of conservation concern may also be threatened with extinction or extirpation due to the spread of novel pathogens into their native ranges. In this thesis, I develop some mathematical methods for understanding the dynamics of vector-borne diseases in wildlife populations which include several elements of host and vector biology. </div><div><br></div><div>We consider systems where a vector-borne pathogen is transmitted to a host population wherein individuals either die to disease or recover, remaining chronically infective. Both ordinary differential equations (ODE) and individual based (IBM) models of such systems are formulated then applied to a specific system of wildlife disease: avian malaria in Hawaiian honeycreeper populations -- where some species endure disease-induced mortality rates exceeding 90\%. The ODE model predicts that conventional management methods cannot fully stop pathogen transmission.</div><div><br></div><div>Vector dispersal and reproductive biology may also play a large role in the transmission of vector-borne diseases in forested environments. Using an IBM which models dispersal and mosquito reproductive biology, we predict that reducing larval habitat at low elevations is much more effective than at higher elevations. The ODE model is extended to include distinct populations of sensitive and tolerant hosts. We find that the form which interaction between the hosts takes has a significant impact on model predictions.</div>

Altitudinal gradients constitute a powerful test system for understanding distribution of species around the globe. Tropical mountains are quite rich in species even after controlling for environmental productivity, and are ideally suited for studying patterns of species distributions because they have had sufficient time for species to produce a response to environmental changes that affect their life histories. In this thesis, I investigate basic ecological mechanisms potentially behind avian distribution patterns along an altitudinal gradient in West-Central Africa. I used data collected with four methodological approaches (point counts, mist netting, random walks and artificial nest experiments) along an altitudinal gradient on Mt. Cameroon from October 2011 to September 2013. This work is focused on two interrelated themes: selection pressures on life histories (Chapters 1, 2, 3 & 4), and avian assemblage structures (Chapters 5 & 6). In the General Introduction, I present an overview of the study area with conservation implications of the study and my study objectives. In Chapters 1, 2 & 3, I investigate how selection pressures, i.e., nest predation and parasitism by haematozoa, affect bird assemblages. I used artificial nest experiments to assess nest predation rates in Chapters 1 & 2, and my...

(EN) Research in interactions between the nervous and immune systems is focused mainly on mammals, while in other vertebrates, including birds, it remains neglected. Two types of cannabinoid receptors interconnect the nervous and immune systems: CB1, which is in mammals involved in regulation of neural processes, and CB2, which is in mammals involved in regulation of immune processes. However, little is presently known about the roles of these receptors in nervous and especially immune processes in birds. Therefore, in this work I focus on the expression of cannabinoid receptors in cognitively advanced bird species (parrots, passerines) during induced sterile peritoneal inflammation. Unlike passerines, parrots appear to lack the gene for CB2, which may affect the inflammation regulation. I have revealed no changes in the expression of these receptors during peritoneal inflammation neither in parrots, nor in songbirds. Nevertheless, the increase in expression of the proinflammatory cytokine IL- 1β in the brain in parrots confirms the importance of neuroimmune interaction and mutual influences along the gut-brain axis. This work suggests that even in birds, the central nervous system is affected by inflammation through the gut-brain axis. The expression of cannabinoid receptors does not change much...

I assessed fish community data collected by the Oklahoma Conservation Commission from 82 minimally impaired wadeable reference streams in eastern Oklahoma to determine whether existing aquatic ecoregions provide the best framework for spatial classification for the development of biological assessment methods and biocriteria. I used indirect ordination and classification to identify groups of sites that support similar fish communities. Although correspondence was observed between fish assemblages and three montane ecoregions, the classification system must be refined and expanded to include major drainage basins and physical habitat attributes for some areas to adequately partition variance in key measures of biological integrity. Results from canonical correspondence analysis indicated that substrate size and habitat type were the primary physical habitat variables that influenced the fish species composition and community structure.