Dissertations / Theses on the topic 'Population outbreak'

The sequencing of highly virulent Escherichia coli O104:H4 strains isolated during the outbreak of bloody diarrhea and hemolytic uremic syndrome in Europe in 2011 revealed a genome that contained a Shiga toxin encoding prophage and a plasmid encoding enteroaggregative fimbriae. Here, we present the draft genome sequence of a strain isolated in Sweden from a patient who had travelled to Tunisia in 2010 (E112/10) and was found to differ from the outbreak strains by only 38 SNPs in non-repetitive regions, 16 of which were mapped to the branch to the outbreak strain. We identified putatively adaptive mutations in genes for transporters, outer surface proteins and enzymes involved in the metabolism of carbohydrates. A comparative analysis with other historical strains showed that E112/10 contained Shiga toxin prophage genes of the same genotype as the outbreak strain, while these genes have been replaced by a different genotype in two otherwise very closely related strains isolated in the Republic of Georgia in 2009. We also present the genome sequences of two enteroaggregative E. coli strains affiliated with phylogroup A (C43/90 and C48/93) that contain the agg genes for the AAF/I-type fimbriae characteristic of the outbreak population. Interestingly, C43/90 also contained a tet/mer antibiotic resistance island that was nearly identical in sequence to that of the outbreak strain, while the corresponding island in the Georgian strains was most similar to E. coli strains of other serotypes. We conclude that the pan-genome of the outbreak population is shared with strains of the A phylogroup and that its evolutionary history is littered with gene replacement events, including most recently independent acquisitions of antibiotic resistance genes in the outbreak strains and its nearest neighbors. The results are summarized in a refined evolutionary model for the emergence of the O104:H4 outbreak population.

Dissertação de Mestrado Integrado em Medicina Veterinária
Bovine theileriosis is a tick-borne disease caused by one or more haemoprotozoan parasites of the genus Theileria. In the past, Theileria infection in cattle in Australia was largely asymptomatic and recognized to be associated with Theileria buffeli. However, in the recent years, outbreaks of theileriosis have occurred in beef and dairy cattle in subtropical climatic regions (New South Wales) of Australia. There is also one published report of a recent theileriosis outbreak on a beef farm near Seymour in the south-eastern state of Victoria. In order to gain an improved insight into the genetic composition of Theileria populations following this outbreak, we undertook herein an integrated PCR-coupled mutation scanning-sequencing-phylogenetic analysis of sequence variation in part of the major piroplasm surface protein (MPSP) gene within and among samples from cattle involved in the outbreak. Theileria DNA was detected in 89.4% of 94 cattle on the Seymour farm; the genetic analysis showed that the ikeda and chitose genotypes representing the Theileria orientalis complex were detected in 75% and 4.8% of 84 infected cattle, respectively, and that mixed populations of these two genotypes were found in 20.2% of infected cattle. Given unpublished reports of a significant increase in the number of outbreaks in Victoria, future investigations should focus sharply on elucidating the epidemiology of Theileria to subvert the economic impact on the cattle industry in this state. Although used here to explore genetic variation within the T. orientalis complex in Australia, a mutation scanning-based approach has broad applicability to other species of Theileria in other countries.
RESUMO - ANÁLISE GENÉTICA DE POPULAÇÕES DE THEILERIA ORIENTALIS, EM BOVINOS, APÓS UM SURTO DE THEILERIOSE EM VITORIA, AUSTRÁLIA - A teileriose é uma doença transmitida por carraças e causada por hemoprotozoários pertencentes a uma ou mais espécies do género Theileria. Historicamente, a infecção de gado na Austrália, com este parasita, é considerada assintomática e associada especificamente à espécie Theileria buffeli. Contudo, nos últimos anos, surtos de teileriose têm ocorrido tanto em explorações de carne como de leite em regiões de clima subtropical da Austrália (Nova Gales do Sul). Recentemente foi publicado um relatório, correspondente a um surto de teileriose perto de Seymour, Victoria, um estado a sudeste do país. A fim de obter uma melhor compreensão sobre a composição genética das populações de Theileria envolvidas neste surto, foi levado a cabo um sistema de análise integrada de PCR - análise de mutações – sequenciação– filogenia, das variações existentes na sequência de parte do gene codificador da principal proteína de superfície do piroplasma (major piroplasm surface protein – MPSP), dentro e entre diferentes amostras provenientes de animais residentes na exploração envolvida no surto. O ADN do parasita foi detectado em 89,4% de 94 bovinos testados, na exploração de Seymour e a subsequente análise genética mostrou que os genótipos Ikeda e Chitose, representativos do complexo formado por diferentes estirpes pertencentes à espécie Theileria orientalis, foram detectados em 75% e 4,8% de 84 animais infectados, respectivamente, e que populações mistas compostas por ambos os genótipos foram detectadas em 20,2% desses mesmos animais. Dado que, relatórios não publicados apontam para um aumento significativo do número de surtos de teileriose em Victoria, futuras investigações deverão centrar-se fortemente na elucidação da epidemiologia deste parasita, a fim de avaliar o impacto económico que este poderá ter sobre a indústria bovina neste Estado. Ademais, apesar de usados neste estudo para explorar a variação genética das populações de T. orientalis na Austrália, uma abordagem baseada na análise de mutações tem ampla aplicabilidade para outras espécies de Theileria presentes em outros países.

Thesis (M.S.)--University of Florida, 2000.
Title from first page of PDF file. Document formatted into pages; contains viii, 66 p.; also contains graphics. Abstract copied from student-submitted information. Vita. Includes bibliographical references (p. 57-65).

Pseudomonas aeruginosa est un pathogène d’origine environnementale capable de croître et de persister dans les systèmes de distribution d’eau et la plomberie. A l’hôpital, la fréquence des infections et épidémies associées aux soins dues à P. aeruginosa soulève de nombreuses questions quant à son cycle de transmission à l’homme dans l’environnement hospitalier. La situation épidémiologique du Centre Hospitalier Régional Universitaire de Montpellier a permis d’établir une collection de 730 souches de P. aeruginosa isolées durant une période de 9 ans. Cette collection est représentative des différentes niches environnementales et de deux périodes épidémiologiques marquées. Les souches cliniques impliquées dans des phénomènes épidémiques et des infections graves ont aussi été collectées. L’analyse génétique et phénétique de cette collection a pour objectif de mieux comprendre la structure, la dynamique et la persistance des populations de P. aeruginosa dans divers réservoirs environnementaux hospitaliers ainsi que les relations entre les réservoirs environnementaux et le succès épidémiologique des populations de P. aeruginosa.L’analyse intégrée des données obtenues dans les trois parties de cette étude convergent vers les résultats principaux suivants. Les réservoirs environnementaux médico-technologiques présentent une forte dynamique avec des phénomènes d’émergence clonale en relation avec les traitements réalisés sur les réseaux. A l’échelle d’un hôpital, le réservoir environnemental est directement impliqué dans les phénomènes épidémiques. La rupture du cycle homme/environnement par des barrières physiques conduit à un changement de situation épidémiologique avec une limitation de l’importance et de la fréquence des épidémies clonales. De plus, les souches les plus ubiquitaires et les plus persistantes dans l’environnement correspondent aux génotypes à fort risque épidémique local et mondial ou clones EHR (Epidemic High Risk). La structure de population de P. aeruginosa au sein de l’hôpital est similaire à celle de la population mondiale ou à celle décrite dans d’autres études : une structure épidémique avec la recombinaison qui a un effet prépondérant sur l’émergence des lignées. Le clone EHR majoritaire ST308 est plus résistant aux antibiotiques que les clones prévalants dans l’hôpital mais non impliqués dans des épidémies. Toutefois, la caractérisation de 46 souches du clone EHR majoritaire, ST308, montre une extrême variabilité au sein du génotype avec, en particulier, des comportements divers en termes de résistance aux antibiotiques. La forte capacité de formation de biofilm et la faible motilité décrites dans la littérature comme caractéristique des clones EHR ne sont pas observées dans cette étude. Notre principale hypothèse est que le succès épidémique du clone EHR ST308 dans l’hôpital est lié à sa diversité intraclonale plutôt qu’à un caractère particulier partagé par toutes les souches EHR.Ce travail apporte des arguments forts en faveur de l’implication des réservoirs environnementaux hospitaliers dans les épidémies d’infections associées aux soins dues à P. aeruginosa. Dans le but de mieux contrôler ces épidémies, les résultats de cette étude incitent à la surveillance des clones EHR de P. aeruginosa quel que soit leur profil de résistance aux antibiotiques et à mettre en place des mesures barrières entre l’environnement hydrique et le patient dès qu’un réservoir environnemental d’EHR se constitue.Mots clés : Pseudomonas aeruginosa, infections associées aux soins, épidémie, environnement, réseau d’eau, structure de population, clone à haut risque épidémique, résistance aux antibiotiques, biofilm, motilité, variabilité intraclonale, adaptation
Pseudomonas aeruginosa is an environmental pathogen that growths in water and plumbing systems. In hospital, the rate of healthcare associated infections (HAIs) and outbreaks caused by P. aeruginosa raised questions about the cycle of its transmission to human beings in the hospital environment. P. aeruginosa epidemiology at the Montpellier Academic Hospital allowed to collect 730 strains isolated over a 9-years period. This collection is representative of various environmental niches and two marked epidemiological periods. Clinical strains involved in outbreak events and serious infections were also included in the study. Genetic and phenetic analysis were performed with the aim to understand structure, dynamics and persistence of P. aeruginosa populations in various hospital reservoirs as well as the relationships between environmental reservoirs and epidemic success of P. aeruginosa.The experimental study, organized in 3 parts, produced the following major results. Medical and technological reservoirs of P. aeruginosa are highly dynamic and clonal emergence occurs in these systems, particularly in relation with networks decontamination by biocides. At the hospital scale, environmental reservoirs are directly involved in outbreak events. Physical barriers between water and patients cut the cycle of transmission from environment to human and markedly changed the epidemiology with a decrease of outbreaks in frequency and incidence. Moreover, the most ubiquitary strains that also persists in environment correspond to Epidemic High Risk (EHR) clones that succeed locally and globally. Population structure of P. aeruginosa within the hospital is similar to the worldwide population or to more local populations previously described: an epidemic structure with a background of recombinations involved in lineages emergence. The major EHR clone ST308 is more resistant to antibiotics than other prevalent clones not involved in outbreaks. However, the study of 46 strains in ST308 showed extreme within genotype variability, particularly various behaviours against antimicrobial agents. Increased ability to form biofilm and decreased motility have been described in literature as specific traits of EHR clones but it is not observed in this study. Our main hypothesis is that epidemic success of EHR clone ST308 in the hospital was linked to its diversity and versatility rather than to specific characters shared by all EHR strains.This study provides strong arguments in favour of the involvement of P. aeruginosa environmental reservoirs in HAI outbreaks. For a better control of these outbreaks, a surveillance of EHR clones of P. aeruginosa should be implemented independently to their antibiotic resistance. Moreover, barriers between environment and patient should be established as soon as an environmental reservoir of EHR clone is detected.Key words : Pseudomonas aeruginosa, Healthcare Associated Infections, outbreak, environment, water network, population structure, epidemic high risk clone, resistance to antibiotics, biofilm, motility, intraclonal variation, adaptation

Para examinar como o nível de diversidade genética de Plasmodium vivax em uma comunidade varia no tempo e no espaço, investigamos a dinâmica de polimorfismos do parasito durante as primeiras fases de ocupação de um assentamento agrícola na Região Amazônica brasileira. A caracterização por microssatélites de 84 isolados de P. vivax, colhidos ao longo de três anos, revelou uma diversidade genética de moderada a alta (heterozigosidade esperada média, 0,699), com uma grande proporção (78,5%) de infecções por múltiplos clones (IMC), mas também um forte desequilíbrio de ligação (DL) consistente com um raro cruzamento entre os haplótipos. Observamos uma pequena influência temporal na diversidade genética dos haplótipos do parasito e nenhum padrão de distribuição espacial dos mesmos. Em amostras consecutivas colhidas de um mesmo indivíduo observou-se uma intensa renovação de haplótipos ao longo do tempo. Um único haplótipo foi compartilhado por três indivíduos cujas amostras foram colhidas durante um surto; todos os outros 81 haplótipos foram recuperados apenas uma vez. A menor diversidade parasitária, com a menor proporção de IMC e um DL mais intenso, foi observada no momento do surto, fornecendo um claro exemplo de uma estrutura populacional epidêmica de um patógeno humano. Todos os parâmetros populacionais retornaram aos valores prévios ao surto durantes os últimos anos de estudo, apesar da queda concomitante na transmissão de malária. Sugerimos que a genotipagem do parasito pode ser útil para monitorar a propagação de novas linhagens do parasito associadas a surtos em áreas que se aproximam da eliminação da malária.
To examine how community-level genetic diversity of the malaria parasite Plasmodium vivax varies across time and space, we investigated the dynamics of parasite polymorphisms during the early phases of occupation of a frontier settlement in the Amazon Basin of Brazil. Microsatellite characterization of 84 isolates of P. vivax sampled over 3 years revealed a moderate to high genetic diversity (mean expected heterozygosity, 0.699), with a large proportion (78.5%) of multiple-clone infections (MCI), but also a strong multilocus linkage disequilibrium (LD) consistent with rare outcrossing. Little temporal and no spatial clustering was observed in the distribution of parasite haplotypes. A single microsatellite haplotype was shared by 3 parasites collected during an outbreak; all other 81 haplotypes were recovered only once. The lowest parasite diversity, with the smallest proportion of MCI and the strongest LD, was observed at the time of the outbreak, providing a clear example of epidemic population structure in a human pathogen. Population genetic parameters returned to preoutbreak values during last 2 years of study, despite the concomitant decline in malaria incidence. We suggest that parasite genotyping can be useful for tracking the spread of new parasite strains associated with outbreaks in areas approaching malaria elimination.

Chez les scolytes (Curculionidae : Scolytinae) réalisant des pullulations éruptives, les processus conditionnant l’intensité et la durée des pullulations sont généralement mal connus. Nous avons étudié trois facteurs susceptibles de moduler les pullulations d’Ips sexdentatus (Börner) : la compétition intraspécifique, les ennemis naturels et la température. Les densités de colonisation et le seuil critique de densité d’attaques sur arbres ont été estimés lors d’une pullulation, et les effets de ces densités sur la productivité et la fitness des insectes ont été mesurés en laboratoire. L’entomofaune associée au scolyte a été étudiée dans des peuplements de pins présentant différents niveaux de dégâts de l’insecte. Les effets thermiques ont été estimés via des élevages à différentes températures. Les densités de colonisation sur arbres, ou celle correspondant à la valeur du seuil critique, ont fortement affecté la productivité et la fitness d’I. sexdentatus. L’entomofaune associée était peu sensible aux niveaux de population du scolyte, dont la productivité a cependant été réduite par la durée d’exposition aux ennemis naturels. L’estimation des besoins thermiques de l’espèce a permis de calculer qu’un réchauffement de 1°C augmenterait les effectifs et permettrait l’apparition d’une troisième génération annuelle, tout en réduisant la fitness des insectes. La compétition intraspécifique serait un facteur critique de régulation des pullulations d’I. sexdentatus alors que les ennemis naturels joueraient un rôle plus secondaire. Une élévation de température pourrait aggraver les pullulations mais aussi réduire la fitness des insectes et augmenter la compétition intraspécifique
For eruptive bark beetles (Curculionidae: Scolytinae), the processes affecting the intensity and duration of outbreaks are generally poorly known. We have investigated three factors that may affect the population dynamics of Ips sexdentatus (Börner), namely the intraspecific competition, the natural enemies and the temperature. Colonization densities and the critical threshold of attack densities on trees have been estimated during an outbreak. How such densities affected the productivity and fitness of the beetles has been evaluated under laboratory conditions. The insect community associated with the bark beetle has been characterized in pine stands exhibiting different damage levels. To assess the thermal effects, the insects have been reared at different temperatures. Colonization densities on trees, or equivalent to the critical threshold of attacks, dramatically affected both the productivity and fitness of I. sexdentatus. The associated fauna was loosely related to the population levels of the bark beetle, although the duration of the exposure to the natural enemies affected its productivity. The assessment of thermal requirements allowed calculating that an average warming of 1°C during the activity period would increase the population levels and number of generations per year, but also decrease the beetles’ fitness. Intraspecific competition is probably a critical regulating factor for I. sexdentatus, while natural enemies would rather play a secondary role. A temperature increase could aggravate the outbreaks, but this could be counterbalanced by a fitness reduction and an increase of intraspecific competition

La surveillance épidémiologique est le recueil systématique et continu d’informations sur l’état de santé des populations, leur analyse, leur interprétation et leur diffusion à tous les décideurs ayant besoin d’être informés. Un de ses objectifs est la détection des événements inhabituels, i.e. des épidémies, nécessitant la mise en place rapide de contre-mesures. Les objectifs de ce travail de thèse sont : (i) d’évaluer les principales méthodes statistiques de détection publiées et communément employées dans différents systèmes de surveillance épidémiologique, (ii) de proposer une nouvelle approche reposant sur la combinaison optimale de méthodes de détection statistique des épidémies et (iii) de développer une nouvelle méthode statistique d’analyse étiologique d’une épidémie à partir des données de surveillance épidémiologique collectées en routine par le système.Pour atteindre ces objectifs, nous évaluons les principales méthodes statistiques de la littérature, à partir d’un jeu publié de données simulées. Puis nous proposons une approche originale pour la détection des épidémies sur le principe de la combinaison de méthodes sélectionnées lors de l’étape précédente. Les performances de cette approche sont comparées aux précédentes selon la méthodologie utiliséeà la première étape. Enfin, nous proposons une méthode d’analyse étiologique d’une épidémie à partir des données de surveillance en employant des modèles statistiques adaptés aux séries chronologiques
Public health surveillance is the ongoing, systematic collection, analysis, interpretation, and dissemination of data for use in public health action to reduce morbidity and mortality of health-related events and to improve health. One of its objectives is the detection of unusualevents, i.e. outbreaks, requiring the rapid implementation of countermeasures.The objectives of this work are: (i) to evaluate the main published statistical methods for outbreak detection commonly implemented in different public health surveillance systems, (ii) to propose a new approach based on the optimal combination of statistical methods foroutbreak detection and benchmark it to other methods; and (iii) develop a new statistical method for the etiological analysis of an outbreak from public health surveillance data routinely collected by the system. To achieve these objectives, as a first step, we evaluate the main statistical methods, from a published set of simulated public health surveillance data. Statistical methods have been evaluated for an operational purpose: for all simulated time series, we used the tuning parameters recommended by their authors for each algorithm when available. We propose sensitivity and specificity metrics suitable for these tools. Then we propose an original approach for outbreak detection based on combination of methods selected in the previous step. The performance of this approach is compared to the previous ones according to the methodology implemented in the first step.Finally, we propose a method for the etiological analysis of an outbreak from surveillance data by using statistical models suitable for time series analysis

ABSTRACT OBJECTIVES: The objectives of this project are to review current literature regarding conjunctivitis including the pathogens that cause conjunctivitis, how to diagnose and differentiate between viral and bacterial conjunctivitis, and the different modalities to treating the disease with limited resources in rural communities. Then examine an outbreak of viral hemorrhagic conjunctivitis in rural Belize in October of 2017. This includes examining data collected by ETSU Family Medicine Department during health outreach clinics regarding diagnosis made, treatment provided, and comparing this information to a survey collected about social determinants of health. Finally, discuss the importance of disseminating public health education regarding how to limit the spread of contagious infections to a rural population with limited health literacy and access to resources. METHODS: In October of 2017 East Tennessee State University (ETSU) Quillen College of Medicine medical students, primary care physicians, and residents traveled to rural Belize to provide free primary care. The clinics consisted of seeing patients at both an established clinic in Roaring Creek, Belize and at remote health clinics in even more rural locations. Many of the patients who presented to the clinics had similar complaints of itchy, red, and productive eyes. Quantitative data was recorded from patient charts regarding their presenting symptoms, diagnosis, and the treatment. The data was organized utilizing microsoft excel and evaluated using SPSS and measures of central tendency. Qualitative data was also collected from interactions with patients and newspaper articles published in Belize about the conjunctivitis outbreak. RESULTS: The results showed that a total of 431 patients received care and 52% of them were diagnosed with conjunctivitis. 46.9% of the patients were determined to have viral conjunctivitis, while 2.8% of them had bacterial conjunctivitis. It was discovered that many patients utilized one reusable cloth to wipe their children's eyes repeatedly thus spreading the disease across and throughout the rural communities. It was found through careful conversations with patients that they were putting urine and breast milk into their eyes in hopes that it would help their pink eye. The Belize Ministry of Health Reported that there were 5,343 cases of pink eye countrywide, with a viral strain being more predominant than bacterial. CONCLUSION: In conclusion, extremely contagious diseases like conjunctivitis are dangerous in rural developing countries because of lack of education about hygiene and limited resources necessary to contain such diseases. While medication is not effective for viral conjunctivitis, it can have devastating consequences (e.g blindness) if a superinfection is not caught early in the course. Education can be the best medicine especially in cases of viral diseases. Patients were also provided with resources to wash their hands often, sterilized water to flush their eyes, and single use towels. A lesson on conjunctivitis, its complications, and how to prevent the spread of the disease was aired on public television. This reports provides examples of both practice creative ways to spread health literacy in rural populations with limited access to resources.

Les insectes forestiers évoluent dans des écosystèmes particuliers caractérisés par leur longévité et leurs dimensions spatiales. Certains insectes forestiers, en particulier les défoliateurs, montrent des patterns de pullulations cycliques, parfois associés à un développement spatial précis. Zeiraphera diniana présente deux caractéristiques intéressantes (1) une temporelle et (2) une spatiale : (1) une très forte régularité dans la périodicité de ses pullulations observée depuis plus d’un millénaire. Les densités de population fluctuant drastiquement tous les 8 à 10 ans dans les Alpes, provoquant des défoliations impressionnantes sur de grandes surfaces forestières (2) le développement spatial du pic de pullulation suit un pattern de “traveling waves” avec une initiation toujours située dans une région Française appelée Briançonnais. En tant que première étude sur la génétique des populations de la tordeuse du mélèze à l’échelle de son aire de pullulation, cette thèse donne des éléments descriptifs sur les caractéristiques génétiques spatiales, avec une vision phylogéographique et historique. De plus, cette étude propose un regard sur la dynamique des populations complexe de cet insecte, en testant les prédictions génétiques correspondent aux modèles et hypothèses de dynamique existants
Forest insects evolve in particular ecosystems characterized by their longevity and their spatial dimensions. Some populations of forest insects, in particular defoliators, exhibit a pattern of cyclic outbreaks that can be associated with particular spatial development. Zeiraphera diniana exhibits two interesting characteristics, a (1) temporal one and a (2) spatial one : (1) really high regularity in outbreak periodicity observed for more than a thousand years. Population densities fluctuate dramatically with outbreaks every 8 to 10 years in the Alps, causing spectacular defoliation of large stands of larch forests (2) the outbreak spatial development follows a travelling wave pattern always initiated from an area located in a French area called Briançonnais. As the first study on population genetics of the larch budmoth all over its outbreak range, this PhD gives descriptive elements on the spatial genetic characteristics of the insect, with an insight in its phylogeography and past history. This study furthermore gives a spatio-temporal insight in the complex population dynamics observed, by testing genetic predictions corresponding to existing population dynamics models and hypotheses

Quantitative trait loci (QTL) mapping in outbred populations faces some challenges unique to the divergent genetic background and complex pedigree relationships. Motivated by a dairy cattle half-sib data set from a grand daughter design, we present in this dissertation a series of endeavors to address various challenges along the analysis flow of QTL mapping. A first step is to infer the haplotypes in sires based on the observed genotypes in sires and his offspring. Our method was shown to outperform peer methods with greater robustness and accuracy yet with fast speed performance. Then in light of adapting the multiple interval mapping method to within-family QTL analysis, we extended the modeling framework by allowing for heteroscedastic residual variances and upgraded the Windows QTL Cartographer accordingly. The advantageous post-analysis result parsing from Windows QTL Cartographer and more importantly, the improved analysis outputs due to more powerful maximum likelihood-based mixture modeling than the least squares regression manifest our efforts in delivering better methodology via practically user friendly software. We further developed a mixed model approach for the purpose of QTL mapping across multiple families that was aimed at modeling QTL effects as both the fixed effect across families and the random effect within families. Our mixed model was shown to encompass similar or higher statistical testing performance on QTL variation than the widely used variance component modeling approach, yet still allowing permutations for obtaining chromosome-wide or genome-wide significance threshold. What's more, the flexibility of our mixed model in constructing alternative hypotheses testing on either fixed or random QTL effects or both was shown to offer interesting insight into the varying sources of signal that would not be unveiled by least squares regression or variance component methods. In concluding our comprehensive approach to QTL linkage mapping in dairy cattle populations, we continue to explore methods of fine mapping by combining both the linkage disequilibrium and linkage information and prospective method improvements are being sought.

The subject of this thesis is the study of a system of multiple simultaneously spreading diseases, or strains of diseases, in a structured host population. The disease spread is modelled using the well-studied SEIR compartmental model; host population structure is imposed through the use of random graphs, in which each host individual is explicitly connected to a predetermined set of other individuals. Two different graph structures are used: Zipf power-law distributed graphs, in which individuals vary greatly in their number of contacts; and Poisson distributed graphs, in which there is very little variation in the number of contacts. Three separate explorations are undertaken. In the first, the extent to which two SEIR processes will overlap due to chance is examined in the case where they do not affect each other's ability to spread. The overlap is found to increase with increased heterogeneity in the number of contacts, all things equal. Introducing differences in infection probability or a delay between introducing the two strains produces more complex dynamics. I then extend the model to allow strains to modify each other's transmissibility. This is found to lead to modest changes in the size of the outbreak of affected strains, and larger effects on the size of the overlap. The extent of the effect is found to depend strongly on the order in which the strains are introduced to the population. Zipf graphs experience somewhat larger reductions in outbreak size and less reduction of overlap size, but overall the two graphs experience similar effects. This is due to the reduced effect of modification in key high-degree vertices in the Zipf graph being offset by higher local clustering. Finally, I introduce recombination and competition by replacement into the model from the first project. The number of recombinant strains that arise is found to be either very low or very high, with chance governing which occurs. Recombinant strains in Zipf distributed graphs have a significant chance of failing to spread, but not in Poisson distributed graphs. Replacement competition in the presence of a growing number of strains is found to both increase the chance of a strain failing to spread, and to reduce the overall size of outbreaks. This effect is equal in both graph types.

Association based tests are designed to capitalize on evolutionaryforces and population history in order to localize genes affecting thetraits of interest to within very small regions. In the case-controltest, a sample of affected individuals (the cases) and a matched setof unaffected individuals (the controls) are collected, and markerallele frequency differences between the two groups are compared. Ifa significant difference between allele frequencies is found, it isdetermined that there is an association between the marker and adisease susceptibility locus. One shortcoming of this test is that ifthe cases and controls are not well matched, or if the controls arechosen from different subpopulations than the cases, spuriousassociations may be detected within the samples which do not reflectactual population values. Additionally, it is possible that genotypeinformation on a set of controls is simply not available. We explorethe relationship between Hardy-Weinberg disequilibrium among affectedindividuals at a marker locus and linkage disequilibrium between themarker and a disease susceptibility locus and show that there is aconnection between these disequilibrium measures which may be usefulfor detecting association using affected individuals only. As part ofthis work, we introduce two summary disequilibrium terms, one allelicand one genotypic, which appear as factors in variousassociation-based measures. Following up on several suggestive equations which led to the summarydisequilibrium terms, we examine the relationship between phenotypeand marker genotypes through the perspective of classical quantitativegenetics. Within this framework, we show that in a randomly matingpopulation there is a simple connection between the additive effectsof a marker locus and the additive effects of an associated traitlocus. An equivalent relationship holds between the dominancedeviations at the marker and the dominance deviations at the traitlocus. These relationships are captured by the summary disequilibriumterms introduced earlier. Using these results, we characterize the genetic properties that lociaffecting a quantitative trait must express in order for common testsof association to be able to detect them. We examine the case-controltest and the basic form of the transmission/disequilibrium test (TDT),and show that by focusing on alleles rather than on genotypes, thesetests are sensitive mainly to additive genetic effects at thesusceptibility loci. We offer several illustrations of theeffectiveness of these tests in detecting association under variousgenetic models.

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A aplicação de análises de “Quantitative Trait Loci” (QTL) em populações exogâmicas é desafiadora porque pressuposições simplificadoras não podem ser aplicadas (por exemplo, os alelos QTL não podem ser assumidos fixados em diferentes famílias, o número de alelos QTL segregantes não é conhecido a priori, não há desequilíbrio de ligação entre um dado alelo marcador e um dado alelo QTL). Quando o efeito genotípico do QTL é assumido aleatório no modelo de análise, a matriz de covariância gamética deve ser calculada para a realização das análises em populações exogâmicas. A acurácia dessa matriz é importante para a obtenção de estimativas confiáveis da posição ou efeito do QTL em análises de mapeamento, ou de valores genotípicos em avaliação genética assistida por marcadores. O objetivo do primeiro estudo foi avaliar diferente estratégias já implementadas em programas computacionais (SO- LAR, LOKI, ESIP e MATVEC) para calcular a matriz de coeficientes Idênticos por Descendência (IBD), que é necessária para o mapeamento de QTL em populações exogâmicas. SOLAR utiliza um método baseado em regressão linear, LOKI e ESIP são ambos baseados em “reverse peeling” e o amostrador implementado em MAT VEC amostra indicadores de segregação. Um pedigree com estrutura F2 típica foi simulado com uma família F2 pequena (2 indivíduos) ou grande (20 indivíduos) e marcadores flanqueadores localizados a 2 cM, 5 cM ou 10 cM de distância um do outro, com o QTL localizado no meio do intervalo. A habilidade dessas estratégias em lidar com informações de marcadores perdidas foi avaliada assumindo um dos pais da geração F2 com ou sem informação de marcador. SOLAR nao estimou os coeficientes IBD corretamente para a maior parte das situações simuladas, enquanto que LOKI apre- sentou problemas quando o tamanho da família F2 era grande. ESIP e o amostrador em MATVEC apresentaram bom desempenho em todas as situacões simuladas, com estimativas de coeficientes IBD próximas aos coeficientes verdadeiros. Portanto, ESIP e MATVEC são os softwares mais indicados quando analises genéticas são realizadas em pedigrees com estruturas complexas. O objetivo do segundo estudo foi avaliar o efeito da utilização de uma melhor aproximação da inversa da matriz de covariância gamética para a avaliação genética de grandes populações de animais domésticos. Algoritmos eficientes, baseados no rastreamento dos alelos QTL de um indivíduo em relação aos de seus avós (Probabilidade de Descendência de um QTL - PDQ), podem ser usados para construir a inversa da matriz de covariância gamética diretamente. Mas essa inversa é uma aproximação quando há informação incompleta de marcador. Também, o calculo exato de PDQºs torna-se difícil quando a informação de marcador é incompleta. Nesse estudo, a inversa da matriz de covariãncia gamética para uma pop- ulação exogãmica simulada foi calculada usando o algoritmo eficiente, mas as PDQ's foram calculadas usando um algoritmo Monte Carlo Cadeia de Markov (MCMC). Essa inversa foi utilizada para predizer o valor genético dos indivíduos através de BLUP assistido por marcadores (MABLUP). O efeito dos cálculos de PDQ usando o algoritmo MCMC sobre a acurãcia da MABLUP foi avaliado com base na resposta a seleção realizada, calculada para o pedigree simulado. Os resultados mostraram que quando as PDQ’S foram estimadas usando MCMC a perda em resposta devido ao uso da inversa aproximada pode ser reduzida em aproximadamente 20%, enquanto que em estudos anteriores essa redução foi de 50%. Ainda, quando quatro marcadores bi-alélicos foram utilizados a resposta para MABLUP foi maior e a perda em re- sposta devido a marcadores com informação perdida foi menor, quando comparadas a situação onde apenas dois marcadores bi-alélicos foram utilizados.
The application of Quantitative Trait Loci (QTL) analyses in outbred population is challenging because simplified assumptions do not hold for these populations (e.g., the QTL alleles cannot be assumed fixed in different families, the number of QTL alleles segregating is not known a priori, there is not gametic phase disequilibrium between a given genetic marker allele and a QTL allele). When the QTL genotypic effect is assumed random, the gametic covariance matrix must be calculated to per- form QTL analyses in outbred populations. The accuracy of this matrix is important to obtain reliable estimates of QTL position or effect when applying QTL mapping, or QTL genotypic values when applying Marker Assisted Genetic Evaluation. The objective of the first study was to evaluate the different strategies already imple- mented in softwares (SOLAR, LOKI, ESIP and MATVEC) to calculate the matrix of identical by descent (IBD) coefficients, which is required for QTL mapping anal- ysis in outbred populations. SOLAR uses a regression method, LOKI and ESIP are both based on reverse peeling, and the MAT VEC sampler samples segregation in- dicators. A typical F2 pedigree was simulated with a small (2 offspring) or a large (20 offspring) F2 family, and the flanking markers were simulated 2 CM, 5 CM, or 10 CM apart, with the QTL located in the middle. The ability of these strategies to deal with missing genetic marker information was evaluated assuming one of the F2 parents with or without marker information. SOLAR failed to estimate the correct coefficients at almost all situations simulated, while LOKI showed problems when a large family was present in the pedigree. ESIP and MATVEC sampler performed well at all situations, providing IBD coefficients closed to the true ones. Therefore, ESIP and MATVEC are more indicated when genetic analysis are carried out on complex pedigree structures. The objective of the second study was to evaluate the effect of using a better approximation of the inverse of the gametic covariance matrix on the genetic evaluation of large livestock populations. Efficient algorithms, based on trac- ing the QTL alleles of an individual to its grandmother or grandfather (probability of descent a QTL - PDQ’s), can be used to construct the inverse of the gametic covari- ance matrix directly. But this inverse is an approximation when incomplete marker information is available. Also, computing the exact PDQ’s becomes difficult when marker information is incomplete. In this study, the inverse of the gametic covariance matrix for a simulated outbred pedigree was calculated using the efficient algorithm, but the PDQ’s were calculated using a Markov chain Monte Carlo (MCMC) algo- rithm. This inverse was used to calculate the predicted genetic value of individuals through Marker Assisted Best Linear Unbiased Prediction (MABLUP). The effect of PDQ calculations using the MCMC algorithm on MABLUP accuracy was evaluated based on the realized response to selection for the simulated pedigree. The results showed that by estimating the PDQ’s by MCMC the loss in response because of using an approximate inverse could be reduced to about 20%, while in previous studies this reduction was of 50%. Further, response to MABLUP was greater when four bi-allelic markers were used, and the loss in response due to missing markers was smaller in the case with four markers compared to when only two bi-allelic markers were used.
Tese importada do Alexandria

Bien que considérées comme étant sous contrôle durant la seconde partie du 20ième siècle avec la découverte des antimicrobiens, les maladies infectieuses demeurent une menace bien réelle pour l’humanité. Quelque soit l’état de connaissance que nous avons sur ces maladies, toutes demeurent imprédictibles. Afin de lutter contre ce phénomène, de nombreuses stratégies de surveillance ont été développées amenant à la mise en place de divers outils informatiques de surveillance épidémiologique visant à détecter et identifier, le plus précocement possible, des événements anormaux. L’objectif initial de notre travail a consisté à mettre en place, au sein de l’Institut Hospitalo-Universitaire Méditerranée Infection et à partir du logiciel Microsoft Excel, deux nouveaux outils informatiques de surveillance épidémiologique visant à identifier, de façon hebdomadaire et automatisée, des événements anormaux sur la base des données de microbiologie clinique issues du laboratoire du Centre Hospitalo-Universitaire Timone à l’Assistance Publique- Hôpitaux de Marseille (AP-HM). Une fois cette étape achevée, nous avons par la suite travaillé au développement d’une structure de surveillance complète intégrant l’investigation et la validation des alarmes émises par les systèmes de surveillance créés, l’émission d’alertes à l’Agence Régionale de Santé (ARS) de la région Provence-Alpes Côte d’Azur (PACA), la valorisation des cas d’événements anormaux confirmés par des publications scientifiques, ainsi que la mise en place de rétro-informations et de bulletins épidémiologiques hebdomadaires visant à informer les acteurs locaux de la surveillance épidémiologique des maladies infectieuses
Although considered under control in the second half of the 20th century with the discovery of antimicrobials, infectious diseases remain a serious threat to humanity. Regardless of the state of knowledge we possess on these diseases, all remained unpredictable. To fight this phenomenon, many monitoring strategies have been developed leading to the implementation of various epidemiological surveillance computer programs to detect and identify, as soon as possible, abnormal events including epidemic phenomena. The initial objective of our work was to implement, within the Hospitalo-Universitaire Méditerranée Infection and based on the Microsoft Excel software, two new automated computer-based programs for the weekly automated epidemiological surveillance of abnormal epidemic events using clinical microbiological data from the Timone teaching hospital of of Assistance Publique- Hôpitaux de Marseille (AP-HM). Once completed, we then worked to develop a comprehensive monitoring structure incorporating the investigation and the validation of alarms emitted by the established surveillance systems, the transmission of alerts to the Regional Health Agency (ARS) of the Provence-Alpes Côte d'Azur (PACA), the public dissemination of confirmed abnormal events by publishing scientific articles, and the implementation of feedback and weekly epidemiological bulletins to inform local infectious diseases epidemiological surveillance actors

Les pullulations de « papillon cendre » du genre Hylesia, appartenant à la famille des Saturniidae, constituent un problème récurrent de santé publique en Guyane et au Venezuela. En effet, pour protéger ses oeufs des prédateurs, la femelle possède des soies détachables extrêmement urticantes qu’elle est susceptible de libérer dans l’atmosphère. L’augmentation des sources de lumière artificielle depuis la fin du 19ème siècle liée à l’urbanisation croissante attire ces papillons nocturnes vers les villes et les villages, où la libération des soies urticantes est susceptible d’affecter l’Homme en générant une douloureuse affection de peau, la « papillonite ». Malgré les enjeux sociaux et économiques liés à la présence récurrente de ces papillons en zones urbaines, leur biologie et leur écologie reste peu connue. Les pullulations de « papillon cendre » attribuées à l’espèce H. metabus constituent un problème récurrent de santé publique en Guyane et au Venezuela. La définition de méthodes spécifiques de régulation des populations s’avère donc très urgente mais nécessitait au préalable de vérifier que seule l’espèce H. metabus est impliquée dans ces épisodes d’urtication et de préciser la structure des populations de ces insectes. Il était également important de préciser les mécanismes de reconnaissance des partenaires sexuels chez cette même espèce. Ces questions ont été les objectifs principaux de cette thèse. L’utilisation d’outils moléculaires a permis de montrer que seule l’espèce Hylesia metabus était impliquée dans les récents épisodes d’urtication en Guyane et au Venezuela. L’étude a également démontré que les populations guyanaises de cette espèce se distinguaient au plan génétique des populations du Vénézuela, et surtout qu’elles se structuraient en 2 sousensembles génétiques distincts entre la côte et l’intérieur de la Guyane. Tous les insectes collectés durant les épisodes de pullulation appartenaient au sous-ensemble côtier. Une approche basée sur l’étude du comportement de reproduction a été utilisée afin de préciser la temporalité d’émission de la phéromone sexuelle et ouvre de nouvelles perspectives pour l’identification de cette phéromone
The genus Hylesia (Lepidoptera Saturniidae) are moths of human health importance in Venezula and French Guiana, inducing epidemic outbreaks of lepidopterism, a puriginous dermatitis caused by the urticating properties of the females’ abdominal setae. Adult female releases extremely urticating setae in the surrounding air, causing itchy dermatitis known as ‘papillonite’. Hylesia are attracted by artificial light source which are increasing since the end of the 19th century due to urbanization resulting in serious invasion event in towns and villages. Despite of the impact on human health, many aspects of the biology and their ecology remain unclear. The definition of specific methods of population regulation is thus very urgent but it was necessary first of all to verify that only the species H. metabus is involved in these episodes of urtication and to specify the population structure of these insects. It was also important to clarify the mechanisms for recognizing sexual partners in this same species. These questions were the mainobjectives of this thesis.The use of molecular tools has shown that a single species, Hylesia metabus, was involved in recent episodes ofurtication in Guyana and Venezuela. The study also demonstrated that the Guyanese populations of this species aregenetically distinct from the Venezuelan populations, and especially that they are structured in 2 distinct genetic subgroupsbetween the coast and the interior of French Guiana. All insects collected during outbreaks belonged to thecoastal subset. An approach based on the study of reproductive behavior has been used to clarify the temporality ofemission of the sex pheromone and opens new perspectives for the identification of this pheromone

Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第10913号
農博第1419号
新制||農||891(附属図書館)
学位論文||H16||N3924(農学部図書室)
UT51-2004-G760
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 佐々木 義之, 教授 守屋 和幸, 教授 広岡 博之
学位規則第4条第1項該当

Les maladies infectieuses posent un problème majeur de santé publique à travers le monde. En effet, les maladies infectieuses étaient la cause en 2004 de près de 15 millions de décès, que ce soit pour des pathogènes émergents, des pathogènes connus de l’homme depuis de nombreuses années ou encore des pathogènes ré-émergents (Estimation 2004 de l’OMS). Ce nombre a diminué. Cette évolution à la baisse touche la plupart des maladies infectieuses, mais une augmentation reste du domaine du possible comme l’a démontré la récente épidémie d’Ebola. Pour lutter contre ces maladies infectieuses, de nombreux outils de surveillance épidémiologique ont vu le jour à travers le monde. Ces systèmes ont pour but de détecter et d’identifier le plus précocement possible des évènements épidémiques favorisant l’alerte auprès des autorités compétentes et la mise en place de contre-mesures. L’objectif de notre travail a été de construire et de développer un système de surveillance épidémiologique à partir des données de laboratoire de microbiologie de la région Provence-Alpes Côte d’Azur (PACA). Ce système doit nous permettre d’identifier de possibles évènements anormaux de façon hebdomadaire à partir des données des différents laboratoires participants. Le système de surveillance nous a par la suite permis de déclarer plusieurs alertes auprès de l’Agence Régionale de Santé (ARS) PACA, de valoriser notre travail par des publications et enfin de valoriser le travail des laboratoires en leur transmettant une rétro-information contenant les principales alarmes de la semaine
Infectious diseases are a major public health problem worldwide. Indeed, infectious diseases were the cause in 2004 to nearly 15 million deaths, whether for emerging pathogens, pathogens known to man for many years or even re-emerging pathogens (2004 Estimation of WHO). It has fallen since we moved, for example, 1.27 million cases of malaria in 2004 to 854,600 in 2013. This downward trend affecting most infectious diseases, but an increase is still the realm of possibility as the demonstrated by the recent outbreak of Ebola.To fight against these infectious diseases, many epidemiological surveillance tools have emerged worldwide. These systems are designed to detect and identify as early as possible of possible epidemic events to promote the warning to the competent authorities and the establishment of counter-measures. The objective of our work was to build and develop an epidemiological surveillance system from the microbiology laboratory data of the Provence-Alpes Côte d'Azur (PACA). This system should enable us to identify possible abnormal events weekly data from the different participating laboratories. The monitoring system has enabled us later to declare several warnings from the Regional Health Agency (ARS) PACA, enhance our work through publications and finally to promote the work of laboratories by providing them a feedback containing the main alarms of the week.The development and automation of the system through the creation of an IT platform developed within the Mediterranean Institute University Hospital Infection (IHU) and by increasing the number of participants and the extension of this system to other regions in France or other countries

Introduction. La détection précoce des infections par un système de surveillance efficace permet de mettre en œuvre des mesures de prévention et de contrôle adaptées. L’objectif de cette thèse était d’évaluer les performances d’un système de détection automatique, type syndromique, des patients à risque épidémique à partir des données du dossier médical informatisé des urgences. Population d’étude. 101001 patients ayant consulté aux urgences du groupement Nord des Hospices Civils de Lyon, entre le 01/06/2007 et le 31/03/2011, dont 10895 patients hospitalisés dans l’établissement à l’issue de la consultation. Méthode. Trois étapes ont été nécessaires. 1) Évaluation de la faisabilité d’utiliser les données structurées et textuelles, à l’aide d’une application de traitement automatisé des données textuelles. 2) Construction et évaluation d’algorithmes de repérage, pour les syndromes respiratoire, cutané et gastro-intestinal, de patients avec une infection à risque épidémique à partir des données du dossier médical informatisé des urgences. 3) Évaluation des données du dossier médical des urgences pour la détection d’épidémies communautaires de grippe, comparées aux données régionales de surveillance de la grippe. Résultats et Discussion. Cette thèse a montré que qu’il est possible de repérer des patients à risque épidémique avec une balance raisonnable entre la sensibilité et la spécificité pour des syndromes respiratoires et cutanés. Les algorithmes pour des syndromes gastro-intestinaux n'étaient pas assez spécifiques pour une utilisation de routine. Les données d’urgences ont permis aussi de détecter les épidémies communautaires dès le début de l’épidémie locale
Introduction. The early detection of the infections by an effective surveillance system allows implementing adapted measures of prevention and control. The objective of this thesis was to estimate the performances of an automatic system syndromic-like to detect the patients with potentially transmissible infectious diseases from the emergency department computerized medical record data. Study population. 101,001 adults, who were admitted to the emergency department and hospitalised of the North Hospital In University Hospital of Lyon, between 01/06/2007 and 30/03/2011. Method. Three steps were necessary. 1) Evaluation of the feasibility to use the structured and textual data with an application which automatically extracts and encodes information found in narrative reports. 2) Different algorithms were built for the detection of patients with infectious respiratory, cutaneous or gastrointestinal syndromes, and assessed. 3) Evaluation of the data of the electronic medical record of emergency department for the detection of flu community epidemics, compared with regional surveillance networks for flu. Results and discussion. This thesis showed that it is possible to detect patients with potentially transmissible infectious diseases with reasonable balance between sensitivity and specificity for respiratory and cutaneous syndromes. The algorithms for gastrointestinal syndromes were not specific enough for their routine use. Emergency department data enabled the detection of community outbreaks for flu

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In the genetic mapping in outbred populations not always it is possible to determine the linkage phase of the alleles. Thus, heterozygous individuals are discarded from these analyses due to the lack of information, once it is not possible, through their genotype, to distinguish the origin of their parental alleles. In this way, the main objective of this work was to propose the endosperm genotyping as a strategy to identify the allelic origin of those heterozygotes individuals. Initially, fragments from the endosperm representing 10, 25 and 50% of the corn seeds weight were extracted and the seeds were submitted to the germination test. The results suggest that the elimination of up to 50% of the endosperm did not affected the seed germination. The methodology of semiquantitative PCR was optimized to differentiate doses of the alleles in the mixtures of DNA derived from leaves of two maize inbred lines (L3 and L1113- 01). It was represented different allelic proportions observed in the endosperm of their reciprocal crosses, based on the maximum amount of endosperm that could be used for DNA extraction. SSR markers were generated by semiquantitative PCR technique and the amplified fragments were evaluated in both agarose gels treated with ethidium bromide and poliacrylamide gels using fluorescently labeled primers. Gel resolution using agarose did not allow the differentiation of the mixtures of parental DNAs. However, through the regression analysis and comparison of the band intensity corresponding to the same allele in the different mixtures, the initial concentration of each one of the alleles could be inferred. The requirement of an allelic pattern limited the use of this technique to QTL analysis in populations where at least one of the genitors is known. Although the resolution of poliacrylamide gels using fluorescent markers was more efficient in the endosperm genotyping, once it was allowed to differentiate the maternal origin of reciprocal hybrids seed´s. So, the strategy of endosperm genotyping using fluorescent SSR primer amplified by semiquantitative PCR allowed the determination of allelic origin in the heterozygous offspring derived from outbred populations, including these individuals in the QTL detection, and consequently, increasing the precision of this analysis.
No mapeamento genético e detecção de QTLs em populações exogâmicas nem sempre é possível a determinação da fase de ligação dos alelos. Assim, indivíduos heterozigotos são descartados dessas análises por serem não informativos, uma vez que não é possível, por meio do seu genótipo, distinguir a origem de seus alelos em relação aos dois genitores. Dessa forma, o objetivo principal deste trabalho foi propor a genotipagem do endosperma para identificar a origem alélica dos indivíduos heterozigotos. Inicialmente, fragmentos do endosperma representando 10, 25 e 50% do peso das sementes de milho foram retirados, sendo as sementes submetidas ao teste de germinação. Observou-se que a remoção de até 50% do endosperma não afetou a taxa de germinação das sementes. A metodologia de PCR semiquantitativo foi otimizada para diferenciar doses dos alelos nas misturas de DNA foliar de duas linhagens de milho (L3 e L1113-01), representando as diferentes proporções alélicas observadas no tecido endospermático dos seus cruzamentos recíprocos, tendo como base a quantidade máxima de endosperma que podia ser utilizada na extração do DNA. Marcadores SSR foram gerados pela técnica de PCR semiquantitativo, e os fragmentos amplificados foram avaliados tanto em gel de agarose tratado com brometo de etídio quanto em gel de poliacrilamida, usando-se primers fluorescentes. A resolução do gel de agarose não possibilitou a diferenciação das misturas dos DNAs parentais. No entanto, por meio da análise de regressão e da comparação da intensidade da banda correspondente a um mesmo alelo nas diferentes misturas, pôde-se inferir a concentração inicial de cada um dos alelos. A necessidade de um padrão de alelos limitou o uso dessa técnica nas análises de QTLs em populações nas quais pelo menos um dos genitores é conhecido. Já a resolução do gel de poliacrilamida utilizando marcadores fluorescentes foi mais eficiente na genotipagem de endospermas, uma vez que possibilitou a diferenciação da origem materna das sementes dos híbridos recíprocos. Assim, a estratégia de genotipagem do endosperma utilizando primers SSR fluorescentes amplificados pela técnica de PCR semiquantitativo possibilitou a determinação da origem dos alelos dos descendentes heterozigotos derivados de populações exogâmicas, permitindo a inclusão destes na detecção de QTLs e, conseqüentemente, aumentando a precisão das análises.

Cryptococcus gattii has been actively emerging and adapting to the climates and environment in western North America, bringing with it life-threatening disease to humans and animals. Through systematic investigations of the dynamics of this pathogen in the United States, by studying outbreaks and individual cases, our studies have aimed to increase the understanding of the expansion, emergence, pathogenicity, molecular epidemiology, population structure, and speciation dynamics of this organism that had previously been largely restricted to tropical and sub-tropical climates of the world.

Molecular sequence typing has revealed that there are four distinct C. gattii molecular types (VGI-VGIV). A major focus of our efforts to examine this pathogen in the United States surrounds the unprecedented C. gattii outbreak that emerged in British Columbia, Canada in 1999 and has since expanded throughout the Pacific Northwest region of the United States (Chapters 2, 3). This outbreak has resulted in a large number of infections in both humans and animals, including a high percentage of otherwise healthy individuals. The outbreak isolates are primarily molecular type VGIIa (the major genotype), VGIIb (the minor genotype), or VGIIc, a novel genotype that emerged in Oregon in approximately 2005.

The North American Pacific Northwest harbors one of the highest incidences of C. gattii infections. In an expansion of molecular epidemiology and population analysis of both MLST and VNTR markers, we show that the VGIIc group is clonal and hypothesize it arose recently. The VGIIa/c outbreak lineages are sexually fertile and studies support ongoing recombination in the global VGII population. This illustrates two hallmarks of emerging outbreaks: high clonality and the emergence of novel genotypes via recombination. In macrophage and murine infections, the novel VGIIc genotype and VGIIa/major isolates from the United States are highly virulent compared to similar non-outbreak VGIIa/major-related isolates. Molecular analysis distinguishes clonal expansion of the VGIIa/major outbreak genotype from related but distinguishable less-virulent genotypes isolated from other geographic regions. Our evidence documents emerging hypervirulent genotypes in the United States that may expand further and provides insight into the possible molecular and geographic origins of the outbreak.

While the outbreak is a significant public health concern, an overlooked but considerable disease burden attributable to C. gattii among HIV/AIDS patients in Southern California has also occurred (chapter 4). In our studies, we examined the molecular epidemiology, population structure, and virulence attributes of C. gattii isolates collected from a cohort of HIV/AIDS patients in Los Angeles County, California. We show that these isolates consist almost exclusively of VGIII molecular type (>93%), in contrast to the vast majority of VGII molecular type isolates found in the outbreak region. Based on molecular phylogenetic analysis, the global VGIII population structure can be divided into two groups, VGIIIa and VGIIIb. We show that isolates from the Californian patients are virulent in murine and macrophage models of infection, with VGIIIa significantly more virulent than VGIIIb. Several VGIII isolates are highly fertile and able to produce large numbers of spores that may serve as infectious propagules. Based on molecular analysis, the a and α VGIII MAT locus alleles are largely syntenic with limited rearrangements compared to the known VGI (a/α) and VGII (α) MAT loci, but each has unique characteristics including a distinct deletion flanking the 5' VGIII MAT a alleles. Fingerprinting analyses of the MAT locus shows that the α allele is more heterogeneous than the aallele. Our studies indicate that C. gattii VGIII is endemic in Southern California, with other isolates originating from the neighboring regions of Mexico, and in some rarer cases from Oregon and Washington state. Given that >1,000,000 cases of cryptococcal infection and >620,000 attributable mortalities occur annually in the context of the global AIDS pandemic, our findings suggest a significant burden of C. gattii infection in AIDS patients may be unrecognized, with potential prognostic and therapeutic implications. These results signify the need to classify pathogenic Cryptococcus cases and highlight possible host differences among the C. gattii molecular types, influencing infection of immunocompetent (VGI/VGII) vs. immunocompromised (VGIII/VGIV) hosts.

In 2007, the first confirmed case of Cryptococcus gattii was reported in the state of North Carolina, USA (chapter 5). An otherwise healthy HIV- male patient presented with a large upper thigh cryptococcoma in February, which was surgically removed and the patient was started on long-term high-dose fluconazole treatment. In May of 2007, the patient presented to the emergency room with seizures. Magnetic resonance imaging revealed two large CNS lesions found to be cryptococcomas based on brain biopsy. Prior chest CT imaging had revealed small lung nodules indicating that C. gattii spores or desiccated yeast were likely inhaled into the lungs and dissemination occurred to both the leg and CNS. The patient's travel history included a visit throughout the San Francisco, California region in September-October of 2006, consistent with acquisition during this time period. Cultures from both the leg and brain biopsies were subjected to analysis. Both isolates were C. gattii, VGI molecular type. Based on molecular studies and virulence in a heterologous host model, the leg and brain isolates are identical, but the two differed in mating fertility. Two clinical isolates, one from a transplant recipient in San Francisco and the other from Australia, were identical to the North Carolina isolate at all markers tested. Closely related isolates that differ at only one or a few noncoding markers are present in the Australian environment. Our findings support a model in which C. gattii VGI was transferred from Australia to California, possibly though an association with its common host plant E. camaldulensis, and the patient was exposed in San Francisco and returned to present with disease in North Carolina.

To elucidate the speciation dynamics between molecular types VGII and VGIII and what influence nuclear and mitochondrial genomes have on intracellular proliferation and hyoervirulence, we conducted a comprehensive analysis of progeny sets between these molecular types, including progeny sets of VGIIa x VGIIIα and VGIIα x VGIIIa crosses (chapter 6). Our analysis reveals that spore viability is exceedingly low, supporting that these are distinct species. We also found that the mitochondrial genome of virulent strains may be necessary but not fully sufficient to confer virulence characteristics. These studies show that each molecular type is likely a distinct species, which was further supported by high levels of diploid or aneuploid progeny, and also shed light into the possible control that both the mitochondrial and nuclear genomes may play in hypervirulence of C. gattii outbreak genotypes. Future analyses of both the regions regulating the virulence and also the generation of progeny sets between other species will further address the roles of both speciation and virulence evolution in C. gattii.

Overall, the studies documented in this dissertation have increased the understanding of molecular epidemiology, population structures, fertility, phenotypic characteristics, virulence characterizations, and speciation of this expanding and emerging fungal pathogen in the United States. This dissertation adds a foundation to the studies of C. gattii in the United States and enables future research to be conducted in several critical areas to better understand and ultimately influence surveillance, prognosis, and treatment of patients and animals in future years.

Dissertation

Forest tent caterpillar (Malacosoma disstria Hübner; FTC), a major defoliator of aspen trees, occupies both aspen and mixedwood forest stands in Alberta’s boreal forest. Forest stand composition could influence the spatial pattern of FTC outbreaks if mortality from natural enemies differs between stand types. I conducted field experiments to determine whether predator- or parasitoid-caused mortality of FTC differed between aspen and mixedwood forest stands and developed a spatial population model to determine the effects of variation in generalist predation on the spread of an FTC outbreak, including the effects of potential predator-caused Allee effects. Generalist predation on FTC was higher in aspen stands than in mixedwood stands, and the spatial model suggests that these observed differences may be sufficiently large to impact FTC outbreak spread rates. Forest stand composition may contribute to the spatial pattern of FTC outbreaks through variation in the impacts of predators on FTC populations.
Ecology

Communities are linked by dispersers that arrive from neighboring habitats and sustain emerging populations. Differences in recruitment establish dissimilarities in composition and diversity among communities and alter levels of connectivity. In heterogeneous habitats, source populations provide propagules to neighboring sinks, which rely on incoming recruits to sustain populations. However, recruitment is not static, and changing environmental conditions that alter habitats can shift population growth and community structure. In this thesis, I evaluate whether changing environmental conditions, such as habitat loss and future climate change, drive shifts in community assembly and population growth. Using marine peracarids as a model system, I examined the effects of isolation on community assemblage trajectories in seagrass beds and explored the effects of elevated temperature and CO₂ on population growth and quality of amphipods that inhabit temperate reef ecosystems. Here, I show that the identity and abundance of recruits leads to local (α) and between-community (β) diversity differences and that the state of communities is dependent on incoming source recruits. Isolation from sources elicits different responses within and among species, which minimizes differences among communities and shifts species abundances. Furthermore, I show how environmental conditions (i.e. elevated temperature and CO₂), that enhance resource availability in sinks, can boost reproductive output and population growth of an amphipod species (Cymadusa pemptos). My test of the hypothesis that future climate conditions enhances sexual characters, reducing variation in mating success and boosting population growth, suggests that future climate might relax constraints on mechanisms of reproduction. As future climate conditions drive population outbreaks, growing establishment of artificial structures that are increasingly used as habitats provide amphipods with alternative settlement space. Together, these studies highlight the importance of examining population growth and community assembly in spatially structured systems. Sources and sinks that are undergoing shifts in abundance and quality of habitats drive change in the density and distribution of mobile species, and when favorable conditions align, such as greater resource availability and reduced competition and predation, populations can boom. However, the potential for population growth depends on how individuals distribute across spatially structured habitats. Since the identity and abundance of incoming recruits drives sink population growth and community structure, it is essential to understand the effect each species’ dispersing stage (i.e. male, female and juvenile) and resource requirements have on sink development.
Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 2017

This dissertation is concerned with effects dispersal and forest structure on forest insect population dynamics, and with identifying generating processes by comparing observed patterns to model predictions. In chapter 2, we investigated effects of changing forest landscape patterns on integro-difference models of host-parasitoid population dynamics. We demonstrated that removing habitat can increase herbivore density when herbivores don't disperse far, and parasitoids disperse further, due to differences in dispersal success between trophic levels. This is a novel potential explanation for why forest fragmentation increases the duration of forest tent caterpillar outbreaks. To better understand spatial model behaviour, we proposed a new local variation of the dispersal success approximation. The approximation successfully predicts effects of habitat loss and fragmentation on realistically complex landscapes, except when outbreak cycle amplitude is very large. Local dispersal success is useful in part because parameters can be estimated from widely available habitat data. In chapter 3, we investigated how well a discretized integro-difference model of mountain pine beetle population dynamics predicted the occurrence of new infestations in British Columbia. We found that a model with a large dispersal kernel, and high emigration from new, low severity infestations yielded the best predictions. However, we do not believe this to be convincing evidence that many beetles disperse from new, low severity infestations. Rather, we argued that differences in habitat quality, detection errors, and Moran effects can all confound dispersal patterns, making it difficult to infer dispersal parameters from observed infestation patterns. Nonetheless, predicting infestation risk is useful, and large kernels improve predictions. In chapter 4, we used generalized linear mixed models to characterize spatial and temporal variation in the propensity of jack pine trees to produce pollen cones, and account for confounding effects on the relationship between pollen cone production and previous defoliation by jack pine budworm. We found effects of stand age, and synchronous variation in pollen cone production among years. Accounting for background patterns in pollen cone production clarified that pollen cone production declines in with previous defoliation, as expected.

Emerging infectious diseases are a serious threat to wildlife, but not all populations or species have the same response to outbreaks. In some cases, diseases shift from being epizootic to enzootic, allowing populations to recover, but both the causes of recoveries and the long-term consequences of disease outbreaks remain poorly understood. My PhD aimed to further our knowledge of these important topics by using a frog assemblage in the Australian Wet Tropics as a model system for understanding recoveries from disease outbreaks. This region was impacted by an outbreak of the fungal disease chytridiomycosis (caused by the pathogen Batrachochytrium dendrobatidis [Bd]) in the late 1980s and early 1990s, during which high elevation populations of several frog species declined or disappeared, while low elevation populations remained stable. Following the outbreak, some species recovered at upland sites, but the patterns of both declines and recoveries vary among species. Litoria dayi disappeared from upland sites and has never recovered. Litoria nannotis disappeared from upland sites and has largely recovered. Litoria serrata declined at upland sites and has recovered, and Litoria wilcoxii did not decline substantially at any elevation. These different histories with the disease presented a great opportunity for studying the factors that allowed some species to recover, while apparently precluding recovery in others, and my thesis examined both population genetics and microbiomes of frogs in this system. My primary goals were to examine the long-term consequences of the outbreak (e.g., fragmentation, inbreeding, loss of diversity) and test several hypotheses for the differences in the history of declines and recoveries among species (e.g., differences in dispersal abilities, a lack of adaptive potential due to lost diversity, differences in microbiomes). I used single nucleotide polymorphisms to examine connectivity patterns, test for a loss of diversity, and test for Bd-driven selection. I examined low elevation populations of L. nannotis, L. serrata, and L. dayi that survived the outbreak, and compared them to recovered upland populations of L. nannotis and L. serrata. I sampled L. dayi at three national parks and L. nannotis and L. serrata at two national parks. All three species showed high levels of connectivity within a given park, and there was no structuring along streams, suggesting that all three species have good dispersal abilities. No inbreeding was present in any species, and all species showed high genetic diversity levels north of Paluma Range National Park. At Paluma, however, both L. nannotis and L. serrata had reduced genetic diversity, and diversity levels followed a west–east pattern, with higher diversity on the western half of the park (L. dayi does not occur at Paluma). These diversity patterns matched habitat patterns, with higher diversity in wetter areas with larger sections of rainforest, suggesting that the size and quality of refuge habitat may play an important role in the retention of genetic diversity during a disease outbreak. I did not find consistent evidence of selection in L. nannotis, but there was consistency among outlier testes for L. dayi. These tests could not conclusively demonstrate that L. dayi was undergoing diseaseinduced selection, but they were suggestive. Prior to analysing the microbiomes of the frog species, it was necessary to test or develop several microbiome methodologies. First, microbiome data often need to be normalized prior to analysis, and many methods are available, but several of the most popular methods use variance standardizing techniques that can distort ecological data. Therefore, I compared six methods (rarefaction, proportions, upper quartile, CSS, edgeRTMM, and DESeq-VS) using both a published data set and simulations. My results showed that upper quartile, CSS, edgeR-TMM, and DESeq-VS failed to fully standardize reads, and inflated minor differences among rare micro-organisms while suppressing large differences among common micro-organisms, thus distorting community comparisons. In contrast, using proportions or rarefaction produced accurate results, with proportions outperforming rarefaction. Another common issue with microbiome studies is the ubiquitous presence of bacterial contamination. This problem has been widely documented, but no method of accurately removing contaminate reads exists. Therefore, I developed an algorithm for identifying and removing contaminate reads, wrote an R package (microDecon) to implement it, and tested it using two large simulations, a published data set, and a sequencing experiment. All tests showed that microDecon was highly accurate and improved the results in 98.1% of cases. Having tested and developed these methods, I was able to apply them to the microbiomes of frog populations. Multiple laboratory studies have documented beneficial effects of bacteria for amphibian hosts during Bd infections, and several field studies have suggested that microbiomes may play important roles in infection dynamics. Nearly all of this research has focused on bacteria, while the fungal microbiomes of amphibians remain largely unexplored. Therefore, I examined both the fungal and bacterial microbiomes of L. dayi, L. nannotis, L. serrata, and L. wilcoxii to make one of the first comparisons of bacteria and fungi in frog populations and test the hypothesis that differences in microbiomes could explain the differences in patterns of declines and recoveries in the Wet Tropics frog assemblage. I also used qPCR to examine Bd infection prevalence and intensity. Bacterial microbiomes generally had higher operational taxonomic unit (OTU) richness but lower evenness than the fungal microbiomes. Bacterial microbiomes also tended to be less variable within groups of samples (e.g., frog species), resulting in stronger clustering in ordination plots. Nevertheless, fungal and bacterial Bray-Curtis dissimilarities were positively correlated within frog species (i.e., two individuals with similar fungal microbiomes tended to also have similar bacterial microbiomes). Fungal and bacterial richness were also correlated. This is a somewhat novel result that suggests that either one microbiome is driving the other, or both are being affected similarly by environmental variables. Results for associations with Bd were mixed. I did not find associations between Bd and beta-diversity for fungi or bacteria. Also, the relative abundance of bacteria that are inhibitory to Bd (based on previous culturing studies) did not follow the expected patterns of association with Bd. Litoria dayi had the highest relative abundance of inhibitory bacteria despite having never recovered from the outbreak, while L. wilcoxii (which never declined) had a low relative abundance of inhibitory bacteria. Additionally, for L. dayi and L. wilcoxii there were significant positive associations between the relative abundance of inhibitory bacteria and Bd infection intensity. In contrast, OTU richness showed negative associations with Bd infection intensity for both fungi and bacteria. Additionally, for both fungi and bacteria, L. dayi had the lowest OTU richness of any frog species. These results are consistent with a protective effect of OTU richness and suggest that a lack of richness in L. dayi has played a role in its inability to recover from the outbreak. In summary, I found that having large areas of high-quality lowland habitat is likely important for allowing populations to retain genetic diversity during an outbreak, and they should be a focus of conservation efforts. Additionally, neither differences in genetic diversity nor differences in dispersal abilities could explain why L. dayi has been unable to recover from population declines. There was some evidence that L. dayi is in the process of adapting, but this was not conclusive. The microbiome data did not show significant associations between Bd and either total community composition or the relative abundance of inhibitory bacteria, but there were associations with the OTU richness of both fungal and bacterial microbiomes, suggesting that richness may be an important factor in infection dynamics.

Wood bison (Bison bison athabascae) conservation in Northern Canada is negatively affected by diseases that kill these animals, such as anthrax caused by the bacterium Bacillus anthracis. Although this disease is considered ancient and was identified more than 2000 years ago in Egypt, little is still known about this disease in wild bison, such as why adult males are often predominantly affected and if the reason there are mortalities in some years and not in others is due to environmental, pathogen, or host factors. The overall objective of this thesis was to use descriptive and serological epidemiology to provide evidence needed to enhance our understanding of anthrax in wild wood bison. The first chapter explored the 2012 anthrax outbreak in bison of the Mackenzie bison population using descriptive epidemiology. Field crews discovered 451 bison carcasses during the outbreak. The carcasses were found between late June and early August, and it was estimated that the epidemic peaked between July 13-19 based on the date carcasses were found and the estimated length of time the animal had been deceased. A unique feature of this outbreak compared with the two previous outbreaks in the same population, as well as outbreaks in other wild wood bison herds, is that numerous calves, yearlings and adult females died rather than mostly adult males. Three separate geographic regions were identified by a field wildlife veterinarian, and examined for differences in outbreak characteristics. One region had proportionally more male carcasses than the others, and one had more calf deaths. Lack of complete data made it difficult to ascertain if the outbreak truly started in one of these regions before the others, or if it began simultaneously in all three. The second component of this project used serological epidemiology of anthrax in the Mackenzie bison population to gain an understanding of wood bison exposure to the bacterium. Serological samples were collected through various sources between 1986 and 2009, and later tested for anti-PA antibodies. Of the 278 samples tested, 191 (69%) were positive, indicating previous exposure to B. anthracis. Of the samples with a recorded gender, approximately 18.2% of those from females and 35.5% from males tested positive. The dataset spanned only one anthrax outbreak year in this population of animals, and the year with the highest proportion of positive samples was the year following this known epidemic (1994, 90% positive submissions). Adults had a higher prevalence of being seropositive than any of the other age categories, for both sexes. This research has revealed that in some outbreak years, all age classes and both genders of bison are affected by anthrax unlike in most outbreaks where predominantly adult males succumb to disease. Furthermore, bison are likely exposed to B. anthracis in non-outbreak years, indicating that they either experience subclinical disease or recover from clinical disease.

Population outbreaks of crown-of-thorns starfish (Acanthaster planei L.) represent one of the most significant, but also least understood processes affecting coral reef communities. Limited understanding of crown-of-thorns outbreaks is due, at least in part, to a critical lack of data on the structure and dynamics of A. planci populations. Therefore, this study examined fine-scale (within reef) patterns in the size structure, distribution, and abundance of starfish populations, during an outbreak of A. planci in the northern Great Barrier Reef. The outbreak resulted from steady and prolonged increase in starfish densities, over a three year period. Furthermore, starfish populations comprised individuals from at least four different year classes, suggesting that the outbreak was caused by progressive accumulation of starfish from multiple recruitment events. Overall densities of A. planci increased to 1.0 starfish per 200m ² (±0.1 SE), in January 1997, and then remained fairly constant until June 1998, after which time starfish densities declined rapidly. During the outbreak, densities of A. planci varied greatly among locations (separated by 0.5-8km), and also between reef zones (<5m apart). Densities of A. planci were consistently highest at locations in sheltered back reef habitats, but considerable numbers of starfish were also recorded at depth (>7 metres) in some exposed locations. Fine-scale patterns in the distribution and abundance of A. planci were partly attributable to spatial variation in wave exposure (whereby starfish avoid turbulent environments), but also resulted from spatial patterns established at settlement. Outbreak populations of A. planci caused substantial coral mortality, and also significantly altered the structure of coral communities. Scleractinian coral cover declined by 32%, from a mean of 32.2% cover (± 1.1SE) in October 1996 down to 21.9% cover (± 1.2SE) in January 1999. The impacts of A. planci were however, very patchy. At the most severely affected locations (in sheltered back reef habitats) coral cover declined by 72% between 1996 and 1999, whereas at several other locations (e.g., lagoonal habitats) there was no observable change in scleractinian coral cover. Crown-of-thorns starfish also had varying impacts among different coral species, caused by significant selectivity in their patterns of feeding. In general, starfish had a disproportionate impact on fast growing branching corals (e.g. Acropora spp. and pocilloporids), tending to avoid slow growing massive corals (e.g., Diploastrea spp., Porites spp.). Crown-of-thorns starfish are well adapted to feed on a wide range of different coral prey, and it is not known why they consistently target a restricted suite of different coral species. Herein, I tested the role of coral symbionts in structuring the feeding preferences of A. planci, for common branching coral species (Acropora spp. and pocilloporids). To test the role of coral symbionts, this study compared feeding preferences of A. planci for six different coral species, with and without their usual complement of coral symbionts. Crown-of-thorns starfish had a clearly defined hierarchy of preference for the six different corals when they contained symbionts (Acropora gemmifera > A. nasuta = A. lorzpes > Seriatopora hystrix > Pocillopora damicornis > Stylophora pistillata). In contrast, when coral symbionts were removed, starfish readily consumed all six corals and did not exhibit any significant selectivity. For the six coral species tested, it is clear that coral symbionts (and particularly trapeziid crabs) do have a marked influence on the feeding preferences of crown-of-thorns starfish. However, despite the protection provided by coral symbionts, Acropora and pocilloporid corals were among the first corals eaten by field populations of A. planci. Therefore, other factors (e.g., the size, morphology, chemical defence and/ or nutritional value of corals) may be more important in determining overall feeding preferences of A. planci (across a broader range of different coral species). Clearly, crown-of-thorns starfish have a major impact on coral communities, but impacts of starfish outbreaks may also extend to a wider range of reef associated organisms, such as coral reef fishes. Despite a close association between reef fishes and benthic habitats, there has been little consideration for how disturbances to benthic reef habitats (particularly, extensive reductions in coral cover) affect coral reef fishes. It is likely that impacts will be most pronounced in those fish species which exhibit a direct reliance on scleractinian corals, such as coral feeding butterflyfishes. This study examined long-term changes in the distribution and abundance of butterflyfishes throughout the course of a crown-of-thorns outbreak. Depletion of scleractinian corals resulted in significant reductions in the abundance of seven butterflyfish species (Chaetodon auriga, C. citrinellus, C. kleinii, C. plebius, C. rainfordi, C. trifascialis, and C. unimaculatus), whereas there was no change in the abundance of C. aureofasciatus, C. baronessa, C. ephippium, C. lunulatus, C. melannotus or C. vagabundus. Chaetodon species affected by coral depletion mostly had a high dependence on live coral for food. However, at least on non-coral feeding butterflyfish, C. auriga, was also affected. Among corallivorous butterflyfish, impacts of coral depletion varied in accordance with their degree of feeding specialisation. For example, declines in the abundance of the coral-feeding specialist, C. trifascialis were much more pronounced than declines in the abundance of the generalist coral feeding species C. baronessa. Chaetodon baronessa responded to the depletion of prey resource by expanding both the range of prey it consumed and also its depth distribution, thereby mediating impacts of resource depletion on its population size. This study demonstrates that major disturbances to coral reef habitats can have significant follow-on affects for coral feeding butterflyfishes. However, the specific responses of individual species vary in accordance with their diet, distribution and ecological versatility (specialist versus generalist). In addition to feeding on scleractinian coral, many reef fish species also rely on scleractinian corals for shelter. Therefore, declines in coral cover may lead to a reduction in habitat availability, and corresponding declines in the local abundance of coral reef fishes. This study explores changes in the abundance and habitat associations of six coral-dwelling damselfish species, during extensive and wide-spread reductions in the availability of suitable host corals, caused by outbreak populations of A. planci. Coral-dwelling damselfishes occupied a very limited suite of available habitat categories, showing strong preference for only a limited range of habitat types (mostly specific coral species). Patterns of habitat use by coral-dwelling damselfish were also very consistent among locations and between years, despite significant variation in both the total abundance of corals and the relative abundance of different coral species. Live coral cover declined by 16-59% at locations affected by A. planci, causing declines in the abundance of Chromis viridis, Dascyllus aruanus, D. reticulatus and Pomacentrus moluccensis, but not C. atripectoralis or P. amboinensis. Species not affected (C. atripectoralis and P. amboinensis) often inhabited skeletons of dead corals, whereas all other species were strongly dependent on live coral as shelter. Variation in the abundance of obligate coral-dwelling species (C. viridis, D. aruanus, D. reticulatus and P.moluccensis) was strongly associated with variation in the abundance of corals that they most frequently occupied. This study demonstrates that infestations of A. planci can significantly [a]ffect the distributions and abundances of reef fishes with strong dependence on live corals.

范家偉.
論文(博士)--香港中文大學歷史學部, 1997.
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中英文摘要.
Available also through the Internet via Dissertations & theses @ Chinese University of Hong Kong.
Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web.
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Lun wen (Bo shi)--Xianggang Zhong wen da xue li shi xue bu, 1997.
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