Doctor of Philosophy / Department of Electrical and Computer Engineering / Caterina Scoglio / Vector-borne diseases not only cause devastating economic losses, they also significantly impact human health in terms of morbidity and mortality. From an economical and humane point of view, mitigation and control of vector-borne diseases are essential. Studying dynamics of vector-borne disease transmission is a challenging task because vector-borne diseases show complex dynamics impacted by a wide range of ecological factors. Understanding these factors is important for the development of mitigation and control strategies. Mathematical models have been commonly used to translate assumptions concerning biological (medical, demographical, behavioral, immunological) aspects into mathematics, linking biological processes of transmission and dynamics of infection at population level. Mathematical analysis translates results back into biology. Classical deterministic epidemic models do not consider spatial variation, assuming space is homogeneous. Spatial spread of vector-borne diseases observed many times highlights the necessity of incorporating spatial dynamics into mathematical models. Heterogeneous demography, geography, and ecology in various regions may result in different epidemiological characteristics. Network approach is commonly used to study spatial evolution of communicable diseases transmitted among connected populations. In this dissertation, the spread of vector-borne diseases in time and space, is studied to understand factors that contribute to disease evolution. Network-based models have been developed to capture different features of disease transmission in various environments. Network nodes represent geographical locations, and the weights represent the level of contact between regional pairings. Two competent vector populations, Aedes mosquitoes and Culex mosquitoes, and two host populations, cattle and humans were considered. The deterministic model was applied to the 2010 Rift Valley fever outbreak in three provinces of South Africa. Trends and timing of the outbreak in animals and humans were reproduced. The deterministic model with stochastic parameters was applied to hypothetical Rift Valley fever outbreak on a large network in Texas, the United States. The role of starting location and size of initial infection in Rift Valley fever virus spread were studied under various scenarios on a large-scale network. The reproduction number, defined as the number of secondary infections produced by one infected individual in a completely susceptible population, is typically considered an epidemic threshold of determining whether a disease can persist in a population. Extinction thresholds for corresponding Continuous-time Markov chain model is used to predict whether a disease can perish in a stochastic setting. The network level reproduction number for diseases vertically and horizontally transmitted among multiple species on heterogeneous networks was derived to predict whether a disease can invade the whole system in a deterministic setting. The complexity of computing the reproduction number is reduced because the expression of the reproduction number is the spectral radius of a matrix whose size is smaller than the original next generation matrix. The expression of the reproduction number may have a wide range of applications to many vector-borne diseases. Reproduction numbers can vary from below one to above one or from above one to below one by changing movement rates in different scenarios. The observations provide guidelines on executing movement bans in case of an epidemic. To compute the extinction threshold, corresponding Markov chain process is approximated near disease free equilibrium. The extinction threshold for Continuous-time Markov chain model was analytically connected to the reproduction number under some assumptions. Numerical simulation results agree with analytical results without assumptions, proposing a mathematical problem of proving the existence of the relationships in general. The distance of the extinction threshold were shown to be closer to one than the reproduction number. Consistent trends of probability of extinction varying with disease parameters observed through numerical simulations provide novel insights into disease mitigation, control, and elimination.

O presente trabalho teve como objetivo conhecer os fatores que propiciam as grandes densidades ecológicas de capivaras, através da comparação das dinâmicas populacionais de dois agrupamentos, em diferentes localidades do município de Pirassununga, SP (Campus Administrativo da Universidade de São Paulo – USP/Pirassununga e o Centro de Pesquisa e Gestão de Recursos Pesqueiros e Continentais – CEPTA/Ibama), para que futuramente seja possível propor uma metodologia de manejo que promova o controle populacional dessa espécie no Estado de São Paulo. Para tanto, foi realizado o monitoramento populacional de ambos agrupamentos durante 15 meses, através da contagem direta dos animais, constituindo na principal fonte de informação para determinar as dinâmicas populacionais. Adicionalmente realizaram-se as capturas dos indivíduos de ambas populações pelo uso de bretes fixos, para que fossem feitas as pesagens, sexagens e marcações eletrônicas pelo uso de microchips e assim, conhecer a distribuição etária, bem como a proporção entre sexos. O uso de ceva no interior dos bretes, para a atração dos animais, possibilitou a realização das contagens diretas e das capturas e recapturas. Para a análise das dinâmicas populacionais foram realizadas as comparações descritivas e estatísticas das densidades ecológicas das populações e das respectivas classes etárias, além do cálculo da taxa de crescimento das mesmas. A alimentação em ceva apresentou-se influenciada pela hierarquia de dominância social, o que fez com que apenas as parcelas dominantes fossem capturadas. Percebeu-se, através das capturas, que o número de fêmeas apreendidas foi superior ao de machos nas parcelas dominantes das duas populações. Por meio das observações foram detectados indivíduos satélites e subagrupamentos, cuja ocorrência pode caracterizar um sistema biológico de metapopulação. A comparação descritiva e estatística das densidades ecológicas das populações, bem como a comparação das taxas de crescimento revelaram superioridade populacional do agrupamento do CEPTA/Ibama em relação ao Campus da USP/Pirassununga, provavelmente pelo maior número de picos de acasalamentos observados, os quais possivelmente são influenciados pelo tipo de habitat antropizado e abundante em recursos hídricos presente no CEPTA/Ibama. / The present research aimed the knowledge of the factors that allow the high ecological densities of capybaras through the population dynamics comparison of two capybara groups in the district of Pirassununga, SP (Campus Administrativo da Universidade de São Paulo – USP/Pirassununga and Centro de Pesquisa e Gestão de Recursos Pesqueiros e Continentais – CEPTA/Ibama), intending to propose forward a management methodology for capybara population control in the State of São Paulo. The populations monitoring was carried out through direct count of animals during 15 months, which played the main role to determine the population dynamics. Fixed traps were used to allow the weightings, sex definitions and identification through microchips, and also to know the age distribution and sex ratios. It was used bait inside the traps to attract animals and thus make direct counting and capture possible. To analyze population dynamics it was used the population ecological densities comparisons (statistically and descriptively) and also their rates of increase. It was detected social dominance hierarchy inside the traps, thus only the dominant part of population could be caught. Females represented the majority among captured animals. Satellites individuals and new groups were seen during observations and their existence might characterize a biological system of metapopulation. The descriptive and statistic comparisons of population ecological densities, as well as their rates of increase showed population superiority of CEPTA/Ibama’s group probably for its bigger reproduction effort detected, which possibly receives influence of anthropogenic and water abundant habitats of CEPTA/Ibama.

Habitat loss and fragmentation are among the greatest threats to biodiversity, and these threats can be exacerbated or alleviated by the presence of interacting species. The effect of habitat loss and fragmentation on predator-prey systems has received extensive theoretical attention, but empirical studies of these systems yield few clear patterns. I examined the influence of prey abundance and spatial distribution on the foraging ecology and spatial ecology of Masticophis flagellum (Coachwhip) using capture-mark-recapture and radio telemetry techniques. I also examined the influence of saurophagous snake abundance on the survival rate of Sceloporus woodi (Florida Scrub Lizard) populations. Masticophis flagellum positively selected lizard and mammal prey, but within these categories it consumed prey species in proportion to their availability. Masticophis flagellum was vagile and constrained its movements within large home ranges. At all spatial scales examined, M. flagellum strongly selected Florida scrub habitat and avoided wetland habitats. The negative effect of saurophagous snake abundance best explained differences in S. woodi survival rates among patches of Florida scrub. Further loss and fragmentation of Florida scrub habitat will likely have a strong negative impact upon M. flagellum. Because it is precinctive to Florida scrub, Sceloporus woodi will also be negatively affected by the loss of this unique habitat. The potential positive effects of reduced predation pressure from M. flagellum that may accompany loss and fragmentation of Florida scrub is likely to be offset by increased predation rates by habitat and dietary generalist predators that incidentally prey upon S. woodi. Despite the sensitivity of these species to loss and fragmentation of Florida scrub, the prognosis is good for both M. flagellum and S. woodi on relatively large protected sites containing xeric habitats managed with prescribed fire.

Watersheds are often managed without direct knowledge of how salmonid species use spatially-distinct spawning habitats within their watersheds, and rarely take into account the relationship between fish movement and potential population structure when making management decisions. The population of native Bonneville cutthroat trout (Oncorhynchus clarki utah) within the Logan River is the largest documented population remaining for this imperiled species, and still maintains extremely high densities of native fish in the upper river. Currently, fishing is not allowed in the upper 20 kilometers of the Logan River watershed during spawning, based on the assumption that cutthroat trout migrate to and spawn primarily in this section. I redetected cutthroat trout tagged (2,271) during years 2008-2012 in seven mainstem and tributary reaches of the Logan River during spawning months (April-June) of 2013 using a combination of stationary detection systems and mobile scanning techniques. Cutthroat trout in both mainstem and tributary reaches exhibit a leptokurtic movement distribution, indicating most fish spawn near to their original tagging site; however, small percentages of trout moved long distances to seek out spawning sites throughout the watershed. Growth, length, and condition estimates between mobile and non-mobile tagged fish demonstrate that while mobile fish tend to growth faster, be slightly larger, and in some cases be in relatively poorer condition, these differences are often biologically insignificant and dependent on site location within the watershed. A genetic microsatellite DNA analysis conducted on trout sampled from each study site confirms the assumption of panmixia, and I observed very little evidence of sub-population structure. Using River Styles® to assess geomorphically distinct reaches, I created a large-scale population estimate of spawning individuals, which found approximately 61% of spawning cutthroat trout are not subject to angling during the spawning season, while 39% could be susceptible to harvest in the lower basin and its tributaries. Most trout within the Logan River likely spawned very close to initial tagging locations and microsatellite analyses confirmed the population is genetically well-mixed, indicating conservation efforts should promote risk-averse management throughout the watershed, rather than focus heavily on any one section of the river.

Effective conservation strategies for imperiled species require an understanding of processes that influence fitness throughout the organism's life cycle and across the range of habitats needed to complete that cycle. I evaluated factors that affect population viability of bull trout Salvelinus confluentus, a threatened freshwater char species, throughout individual life stages and over the entire life cycle. I assessed the relationship between bull trout egg incubation success and environmental variables. Egg survival was negatively related to the percent of fine sediment in redds and positively related to hydraulic conductivity and the strength of downwelling. Next, I quantified juvenile bull trout survival rates and described movement patterns for this life stage. Juvenile bull trout emigrated from natal headwaters into larger rivers throughout the entire year and across a range of sizes. Estimates of juvenile survival rates improved dramatically when emigration was incorporated into the analysis. I integrated my observations of bull trout survival, growth, and movement to create a life-cycle model, which I used to better understand how populations respond to changes in specific demographic rates. Bull trout populations were particularly sensitive to changes in juvenile growth and survival. The relative effect of changes to fertility rates and adult survival varied depending upon whether a population was composed primarily of large, migratory, or smaller, resident individuals. Dispersal helped to lower the probability of extinction for small or declining populations when neighboring populations were stable. My research demonstrates that bull trout require access to habitats throughout entire watersheds to maintain population viability. My results suggest that limiting anthropogenic sources of fine sediment and maintaining areas of channel complexity that promote downwelling can be important for bull trout embryo survival. Management decisions should also consider the diverse behavior of juvenile bull trout and the wide range of habitat they use. Additionally, connectivity between populations is likely to be important for declining populations to persist. The diversity of life-history strategies expressed by bull trout helps maintain demographic stability within and among populations. As such, preservation of habitat integrity and full life-history diversity is imperative for conservation and recovery of bull trout populations range-wide.

Ces dernières années plusieurs maladies infectieuses sont apparues ou ré-apparues. Ce phénomène n'est pas nouveaux et de nombreux facteurs, tels que les changements climatiques, l'intensification des échanges et des voyages, favorisent l'extension, le maintien ou l'émergence de nombreuses maladies infectieuses. L'étude de ces maladies dites (ré-)émergentes est relativement récente (années 1990, concept introduit par S. Morse). Dans cette thèse nous nous intéressons au cas d'une maladie tropical : le Chikungunya. Cette maladie due à un arbovirus (\textit{arthropod-borne virus}) est une maladie vectorielle transmise par les moustiques du genre \textit{Aedes}. Depuis une cinquantaine d'années, plusieurs épidémies ont été recensées, notamment en Afrique et en Asie et plus récemment sur l'île de la Réunion (2005-2006) et en Italie (2007). À l'heure actuelle, il n'est malheureusement pas possible de prédire l'émergence de nouveaux évènements, ceux-ci pouvant être plus ou moins localisés géographiquement, sporadiques ou épidémiques. La modélisation mathématique de ces maladies se révèle donc un atout considérable dans la tentative de compréhension de leur évolution. Ces modèles aident ainsi la prise de décisions et orientent les différentes actions. Dans ce travail nous présentons dans un premiers temps, les caractéristiques biologiques du vecteur et le mode transmission de la maladie à la population humaine. Nous formulons et étudions plusieurs modèles (EDO, Contrôle, EDR) décrivant la dynamique de croissance des différents stades d'évolution du vecteur (œuf/larve/nymphe/adulte) en utilisant des modèles structurés par classes. Cette dynamique est alors couplée à un modèle de transmission de la maladie, décrit par des modèles de type SI-SIR. Différentes stratégies de contrôle, intégrant les techniques de luttes contre la maladie et la prolifération de la population de moustique sont également étudiées. La formulation d'un modèle de type métapopulationnel, décrivant les déplacements humains et vecteurs ainsi qu'une modélisation de l'environnement de l'Île de la Réunion, nous permettent de valider nos modèles grâce à une comparaison aux données de seroprévalence enregistrées et estimées par l'INVS (Institut de Veille Sanitaire).

<p>Landscape effects on species performance currently receives much attention. Habitat loss and fragmentation are considered major threats to species diversity. Deciduous forests in southern Sweden are previous wooded pastures that have become species-rich communities appearing as islands in agricultural landscapes, varying in species composition. <i>Actaea spicata</i> is a long-lived plant occurring in these forests. In 150 populations in a 10-km² area, I studied pre-dispersal seed predation, seed dispersal and pollination. I investigated spatio-temporal dynamics of a tritrophic system including<i> Actaea</i>, a specialist seed predator, <i>Eupithecia immundata</i>, and its parasitoids. In addition, effects of biotic context on rodent fruit dispersal and effects of flowering time and flower number on seed set, seed predation and parasitization were studied. Insect incidences of both trophic levels were related to resource population size and small <i>Eupithecia</i> populations were maintained by the rescue effect. There was a unimodal relationship between seed predation and plant population size. Seed predator populations frequently went extinct in small plant populations, resulting in low average seed predation. Parasitoids were present in large plant populations but did not affect seed predator density. Seed predators aggregated at edges, relaxing seed predation in patch interiors. Flowering phenology was unrelated to seed set and insect incidence. A higher flower number did not influence seed predation but was associated with higher seed set and a tendency for a higher parasitization rate. In the study on fruit dispersal more fruits were removed inside than outside populations. Within plant populations more fruits were removed from large aggregations. Overall, this thesis underlines the importance of plant-animal interactions during different phases of the life cycle. The spatial configuration of host plants plays an important role for the outcome of plant-animal interactions and trophic cascades.</p>

Le fonctionnement du cycle parasitaire de l'échinocoque alvéolaire (Echinococcus multilocularis) est étudié en Franche-Comté (France) à travers (i) la distribution des prévalences chez le renard (Vulpes vulpes) au niveau régional, (ii) distribution des cas humains, au niveau régional et (iii) la distribution des rongeurs, du renard, du chat forestier (Felis silvestris et domestique (Felis catus) au niveau du biotope. Cette dernière étude, menée au niveau d'organisation du peuplement et comparée à celles menées aux autres niveaux de perception aboutit à formuler une théorie selon laquelle le cycle de l'échinococcose alvéolaire se maintiendrait en Franche-Comté grâce à un fonctionnement en mosaïque: la parasitose serait temporaire en un secteur donné (= tesselle), la permanence de l'enzootie dans la région étant due à l'alimentation de zones "indemnes' par les zones temporairement favorables et infestées (vecteur principal = renard). Le caractère temporaire de l'infestation d'une tesselle serait dû au fait que convergent un nombre de conditions: abiotiques (mésoclimatologie) et biotiques (cinétique des populations de rongeurs et utilisation par le renard dans une relation prédateur/proie conditionnée par le paysage). L'appréciation du caractère "fonctionnel" de la mosaïque tiendrait donc à l'analyse simultanée de relations et de dynamiques qui s'expriment à des niveaux de perception différents (station : conservation des œufs de Ténia selon les conditions édaphiques et la climatologie saisonnière ; biotope: distribution des peuplements de rongeurs; secteur: cinétique des peuplements de rongeurs dépendant de l'organisation de l'espace agricole; région: mésoclimatologie et arrangement spatial des secteurs).

<p>Traditional forest reserves are protected natural forests established by ancestors to perform many socio-cultural functions and are protected in accordance to customary laws, not based on government legislation. These reserves generally have a long history with well preserved forests that could demonstrate what the surrounding environment could have looked liked, if humans had not altered it. Therefore, the traditional forest reserves might have significant ecological value and a potential high biodiversity. During February and March of 2009 a field study with semi-structured interviews and field observations was carried out in Babati District in Manyara Region in Tanzania, to study the possible contribution TFRs might have to conservation. The information collected were then analysed using Metapopulation Theory, Island Biogeography Theory and local knowledge concepts. The analysis indicates that there is a higher biodiversity in TFRs compared to surrounding areas and unprotected forests as a result of a rigid traditional protection that local people respect. Further on the MPT and IBT show how TFRs could benefit conservation as islands of refuge for threatened species or as migration corridors between nearby forest reserves and national parks. The future for TFRs and possible conversion into CBFM must include respect and support for the local beliefs as a basis for protection and thereby conservation.</p>

Understanding complex population dynamics is critical for both basic and applied ecology. Analysis of genetic data has been promoted as a way to reconstruct recent non-equilibrium processes that influence the apportioning of genetic diversity among populations of organisms. In a structured-deme context, where individual populations exist as geographically distinct units, island biogeography theory and metapopulation genetics predict that the demographic processes of extinction, colonization, and migration will affect the magnitude and rate of genetic divergence between demes. New methods have been developed to attempt to detect the influence of non-equilibrium dynamics in structured populations. I challenged two of these methods: decomposed pairwise regression and allele frequency analyses, using simulations of genetic data from structured demes. I found that these methods suffer from a high type II error rate, or failure to reject the null hypothesis of mutation-migration-drift equilibrium for demes experiencing historical demographic events. In addition, island biogeography and metapopulation ecology predict that at equilibrium, some species in a patch will be recent colonists, as equilibrium indicates a balance between colonization of the patch and extinction from the patch. Recent colonists are unlikely to have reached population mutation-migration-drift equilibrium; hence a paradox exists between population and community level equilibrium. I used nuclear and mitochondrial genetic data from populations of two species of reptiles from the Turks and Caicos Islands, British West Indies to test for patterns of equilibrium vs. non-equilibrium. I found unexpected shallow genetic divergence in the Turks Island boa (Epicrates chrysogaster), indicating that this species likely existed as a panmictic population prior to the inundation of the Turks and Caicos Banks during the last glaciation. As the initial methods I tested using simulations proved unreliable, I used methods from phylogeography, landscape genetics, and island biogeography to detect significant non-equilibrium dynamics in the Turks and Caicos curly-tailed lizard (Leiocephalus psammodromus), finding evidence for high levels of biased gene flow. I propose that studies of genetic diversity on island archipelagos use tools from all three of these methods to evaluate empirical data in the context of equilibrium and the null hypotheses offered by island biogeography and population genetics theory. I frame the results both in the context of conservation and an understanding of equilibrium and non-equilibrium dynamics.