Дисертації: "Spatial host population structure"

1

Kendrick, Gary. "The epiphyte Microcladia coulteri (Rhodophyta) : changes in population structure with spatial and temporal variation in availablity of host species." Thesis, University of British Columbia, 1986. http://hdl.handle.net/2429/25881.

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A comparison of the population structures of the epiphyte, Microcladia coulteri and the three hosts: Prionitis lanceolata, Iridaea cordata and Odonthalia floccosa, was made at Beaver Point, Saltspring Island, British Columbia. The three host species had distinct seasonal patterns in density and size class distribution. By the use of ANOVA, the partitioning of variation in epiphyte population structure with the seasons, between host species and, within host species variations in size of thalli, reproductive status and spatial distribution was performed. Small percentages of total determined variation were accounted for by seasonality in the abundance of size class and reproductive components of the epiphyte population and distribution of the epiphyte between host species. Larger percentages were due to variations in epiphyte population structure with within host species variations in size and reproductive status and the spatial variation in availability of host substrata. It was concluded that persistence of M. coulteri in relatively stable populations, both temporally and spatially, was due to differential use of available host substrata combined with continuous reproductive output and recruitment of the epiphyte.
Science, Faculty of
Botany, Department of
Graduate

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2

Appelgren, Anais. "Evolutionay consequences of the population structure of an ectoparasite at different spatial scales : an empirical approach of the hen flea-passerines system." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10296/document.

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L’évolution divergente est un processus clef générant de la biodiversité. Elle peut avoir lieu entre localités, via la réduction des flux de gènes, et au sein des localités via la spécialisation écologique. Dans le cas des systèmes parasitaires multi-hôtes, l’adaptation dépend des taux relatifs de flux de gènes des hôtes et des parasites entre différentes localités, ainsi que des échanges locaux de parasites entre différents types d’hôtes. En combinant génétique des populations et expérimentations sur le système composé de la puce Ceratophyllus gallinae et deux de ses hôtes, la mésange charbonnière Parus major et le gobe-mouche à collier Ficedula albicollis dans un habitat fragmenté, nous avons examiné comment l’adaptation et l’isolation génétique façonnent l’évolution des parasites. Nous avons aussi testé comment les choix d’habitat des hôtes pouvaient influencer la rencontre avec des populations de parasites spécialisées. Les analyses de microsatellites révèlent que les populations de puce sont différenciées à une échelle spatiale fine, et fréquemment entre espèces hôtes. De plus, des populations de parasites semblent adaptées à chaque type d’hôte. Cependant, aucune variation dans les choix d’habitats par rapport aux parasites n’a été observée chez les hôtes. Enfin, la réponse des hôtes aux parasites variait entre nos deux zones réplica ; l’histoire des populations d’hôtes pourrait donc influer sur la coevolution avec leurs parasites. Ce système semble donc localement façonné à la fois par une isolation génétique et une sélection par différents hôtes. L’étude de nouveaux sites permettraient d’évaluer si cette évolution divergente peut être génératrice de biodiversité
Divergent evolution is a key process generating biodiversity. This can occur between localities, through reduced gene flow followed by local adaptation or genetic drift, and within localities through ecological specialization. In the case of multi-host parasite systems, adaptation can be driven by the relative rate of host-parasite gene flow among spatially isolated populations, and the amount of parasite exchange among local host types. Combining population genetics and field experiments, we examined how adaptation and genetic isolation shape parasite evolution. Focusing on the hen flea Ceratophyllus gallinae, a presumed host generalist, and two of its hosts, the great tit Parus major and the collared flycatcher Ficedula albicollis, we investigated parasite population structure and adaptation within a fragmented landscape. Additionally, we tested how hosts can influence encounter rates with specialized flea populations through their habitat choice. Neutral markers analyses show that flea populations are genetically differentiated at fine spatial scales, and frequently between the two host species. Evidence for parasite adaptation to each host type were also observed. Host specialization may therefore be ongoing in hen fleas. However, birds did not show specific habitat choice strategies regarding flea-infested nests. Host responses differed between two replicate sites, indicating that local population history may impact parasite evolution. Both isolation and host-based selection are therefore acting on hen flea populations at a local scale. Investigations in new localities will help to assess to what extend this divergent evolution may generate biodiversity

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3

Henri, Dominic Charles. "From individuals to ecosystems : a study of the temporal and spatial variation in ecological network structure." Thesis, University of Exeter, 2014. http://hdl.handle.net/10871/15726.

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Ecological network theory has developed from studies of static, binary trophic relationships to the analysis of quantitative, dynamic communities consisting of multiple link-types. Particularly, work has focused on the dynamic nature of ecological networks, which maintains stability in complex communities. However, there are few in situ network-level studies of the determinants of temporal and spatial variation in community structure. This thesis utilises data from a 10-year study of a host-parasitoid network and a collaborative study in an applied ecological setting to identify individual level factors important to network structure. The work aims towards an empirical, predictive framework linking adaptive foraging behaviour to ecological network structure. The results show that condition-dependent foraging behaviours structure host-parasitoid networks. The realised niches of the studied parasitoid species were generally biased towards larger host species and condition-dependent sex ratio allocation increased the likelihood that females would eclose from relatively larger hosts and males from relatively smaller hosts, which resulted in sex ratios deviating from Hamiltonian (50:50) predictions. Further, both of these aspects of behaviour are plastic, where parasitoid behaviour responded to environmental heterogeneity. Particularly, host preference behaviour conformed to an egg-/time-limitation framework, where the size dependency of the behaviour is greater when individuals have a greater likelihood of being egg-limited. Both the size-dependency and the plasticity of these behaviours differed significantly between secondary parasitoid species. This species identity effect interacted with landscape heterogeneity, which may explain some inter- and intra-specific variation in network structure. With respect to applied ecology, the results show that the benefits of natural vegetation for pest control are dependent upon the dispersal capabilities and the diet breadth of the pest and its natural enemies. The findings are evaluated towards a predictive framework for understanding the effects of future climate change on community structure and stability. We consider this framework in terms of applied ecology, particularly pest control ecosystem services provided by natural vegetation in an agricultural environment. The synergistic nature of the multiple determinants of network structure found in this thesis suggest that future studies should focus on the whole network, which is not necessarily the sum of its parts.

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4

Brouard, Vianney. "Cell dynamics of multitype populations in oncology and Invasion probability of cooperative parasites in structured host populations." Electronic Thesis or Diss., Lyon, École normale supérieure, 2024. http://www.theses.fr/2024ENSL0037.

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Cette thèse porte sur l'étude de deux modèles stochastiques liés à des problèmes médicaux. Le premier vise à comprendre le processus épidémique généré par des bactériophages coopératifs dans une population de bactéries résistantes aux antibiotiques. Pour cela, nous introduisons un modèle épidémiologique où les infections sont générées par la coopération de parasites dans une population d'hôtes structurée selon un modèle de configuration. Une transition de phase est observée pour la probabilité d'invasion dépendant du degré de connectivité des sommets et du nombre de parasites générés lors d'une infection d'un hôte. Au seuil critique, la probabilité d'invasion est identifiée comme la probabilité de survie d'un processus de Galton-Watson.Dans le but d'obtenir un modèle biologiquement plus pertinent, nous avons analysé un modèle similaire où une structure spatiale est ajoutée à la population d'hôtes en utilisant un "random geometric graph". Nous avons montré qu'une telle structure spatiale facilite la coopération des parasites. Une transition de phase similaire se produit où au seuil critique, des bornes supérieure et inférieure sont obtenues pour la probabilité d'invasion en tant que probabilités de survie de deux processus de branchement avec coopération.La deuxième question médicale concerne la compréhension de l'évolution de la composition génétique d'une tumeur en formation, en utilisant des processus de naissance et de mort multitypes branchants sur un espace de traits fini. Considérant une évolution neutre et délétère, nous fournissons des résultats au premier ordre asymptotique pour toutes les tailles des sous-populations mutantes. En particulier, nous capturons la stochasticité associée aux tailles des sous-populations mutantes lorsqu'une tumeur est observée cliniquement, et surtout nous caractérisons les chemins évolutifs effectifs, fournissant des informations sur le passé, le présent et le futur de l'évolution tumorale.Au-delà de ce cadre restrictif d'évolution neutre et délétère, nous proposons une nouvelle méthode pour comprendre le premier ordre asymptotique du premier trait mutant sélectif
This thesis focuses on the study of two stochastic models related to medical problems. The first one lies on understanding infection spread of cooperating bacteriophages on a structured multi-drug resistant bacterial host population. Motivated by this example, we introduce an epidemiological model where infections are generated by cooperation of parasites in a host population structured on a configuration model. We analysed the invasion probability for which we obtain a phase transition depending on the connectivity degree of the vertices and the offspring number of parasites during an infection of a host. At the critical scaling, the invasion probability is identified as the survival probability of a Galton-Watson process. With the aim to get a biological more relevant model, we analysed a similar model where a spatial structure is added for the host population using a random geometric graph. We have shown that such spatial structure facilitates cooperation of parasites. A similar phase transition occurs where at the same critical scaling the invasion probability is upper and lower bounded by the survival probabilities of two discrete branching processes with cooperation. The second medical question deals with understanding the evolution of the genetic composition of a tumor under carcinogenesis, using multitype birth and death branching process models on a general finite trait space. In the case of neutral and deleterious cancer evolution, we provide first-order asymptotics results on all mutant subpopulation sizes. In particular such results capture the randomness of all cell trait sizes when a tumor is clinically observed, and mostly it allows to characterize the effective evolutionary pathways, providing information on the past, present, and future of tumor evolution.Moving beyond this restrictive neutral and deleterious cancer evolution framework, we provide a new method to understand the first selective mutant trait size

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5

Vogwill, Tom. "The ecology and evolution of host-parasite interactions in spatially structured populations." Thesis, University of Liverpool, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.533910.

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6

Purves, Drew William. "Local spatial structure and plant population dynamics." Thesis, University of York, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251813.

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7

Hamid, Mohd Norowi. "The analysis of host-parasitoid relationships at various spatial scales." Thesis, University of Greenwich, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267350.

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8

Cheshire, J. A. "Population structure and the spatial analysis of surnames." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1324522/.

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Geographers have largely overlooked surnames (family names), and their geographic concentrations, as a valuable source of data to indicate the spatial structure of populations. This thesis seeks to provide a substantive contribution to the geographical literature by demonstrating how quantitative spatial analysis of surname data can be used as an aid to understanding population structure at a range of scales from the regional to the continental. The primary purpose of this research is not to develop detailed case studies or to investigate specific examples of population characteristics considered interesting for their novelty: rather, the core concern is to focus on the identification or confirmation of generalised trends. Much of the current research that uses surnames (for example in population genetics) contains a geographical element, yet stops short of exploiting and accommodating the effect of scale, shape and size of spatial units. The application of computationally intensive spatial analysis techniques to a comprehensive and innovative dataset (see worldnames.publicprofiler.org) makes it possible to address these issues for the first time. The thesis develops and applies a robust analytical and methodological framework for the analysis of surnames as a primary data source. Applications of the research are used to demonstrate the utility of surnames in studies of population genetics, in migration research, as well as in the spatial analysis of large datasets more generally.

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9

Penington, Sarah. "Branching processes with spatial structure in population models." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:361e5c58-e6dd-47a0-9a52-303e897547e8.

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We consider three different settings for branching processes with spatial structure which appear in population models. Firstly, we consider the effect of adding a competitive interaction between nearby individuals in a branching Brownian motion. Each individual has a mass which decays when other individuals are nearby. We study the front location: the location at which the local mass density drops to o(1). We show that there are arbitrarily large times t at which the front location is order of t^(1/3) behind the maximum displacement of a particle from the origin. Secondly, we study the strength of selection in favour of a particular allele in a spatially structured population required to cause a detectable trace in the patterns of genetic variation observed in the contemporary population. We suppose that the effective local population density is small. We show that whereas in dimensions at least three, selection is barely impeded by the spatial structure, in the most relevant dimension, d=2, selection must be stronger (by a factor of log(1/m) where m is the neutral mutation rate) if we are to have a chance of detecting it. Finally, we model the behaviour of what are known in population genetics as hybrid zones. These occur when two genetically distinct groups are able to reproduce, but the hybrid offspring have a lower fitness. We prove that on an appropriate time and space scale, the hybrid zone in our model evolves approximately according to mean curvature flow. We also give a probabilistic proof of a (well-known) analogous result for a special case of the Allen-Cahn equation. In the last two cases, we use the spatial Lambda-Fleming-Viot process to model the population (with different selection mechanisms), and our proofs rely on a duality with a system of branching and coalescing particles.

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10

Surendran, Anudeep. "Stochastic and continuum descriptions of population dynamics with spatial structure." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/207574/1/Anudeep_Surendran_Thesis.pdf.

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Spatial structures are ubiquitous in populations of plants, animals and cells, typically occurring as clustering or segregation. These spatial structures influence how individuals interact and the overall population dynamics. Yet, these details are rarely accounted for in classical population dynamics models. Through Individual-based and continuum models, I show that spatial structures can dramatically alter population dynamics. The thesis specifically explores the role of spatial structure in biologically and ecologically relevant scenarios, such as the movement of cells in the presence of biological obstacles, directional movement of animals in response to interaction with others (chase-escape dynamics), predator-prey dynamics, and Allee kinetics.

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11

Yin, Mingbo. "Population structure and host-parasite interactions in the Daphnia longispina hybrid complex." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-137838.

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12

King, Rachel, and n/a. "Spatial Structure and Population Genetic Variation in a Eucalypt Species Complex." Griffith University. Australian School of Environmental Studies, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20050113.091713.

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In this study, the relative influences of selection, gene flow, and other evolutionary forces on the spatial structure of genetic variation within a eucalypt species complex (the spotted gums: genus Corymbia, section Politaria) were assessed. The study investigated the spatial genetic structure among four putative species of spotted gum (broad-scale), as well as within a single population (fine-scale)of one species, using both molecular and quantitative markers. The spotted gum complex occurs naturally across a range of 2500 km in eastern Australia. Spatial genetic variation within and between the four putative spotted gum species was examined using both chloroplast and nuclear markers. No significant differentiation was found between the three northern species of the complex, C. citriodora, C. variegata and C. henryi. The southern species, C. maculata, shared no haplotypes with any of the three northern species. These results disagree in part with those reported in a previous allozyme based study in which C. henryi was found to be significantly divergent from C. variegata (with which it is sympatric) and more closely aligned with C. maculata. Re-analysis of the allozyme data provided evidence of selection acting at the PGM2 locus within populations of C. variegata and C. henryi. The exclusion of this locus from the data set led to concordance between the cpDNA and nDNA analyses. Restricted gene flow and evidence of isolation by distance were identified as the dominant processes influencing the contemporary distribution of the cpDNA haplotypes. No geographic structure of haplotypes was found and complex genealogical relationships between haplotypes indicated the combined effects of past fragmentation, range expansion and possible long distance dispersal events. The variation and spatial structure in both neutral molecular markers and quantitative genetic traits were compared to explore the relative influences of dispersal and selection within a single eucalypt population. Both mature trees (n=130) from a natural population of C. variegata and their progeny (n=127) were sampled. A very high outcrossing rate (98%) was estimated for the population based on data from seven microsatellite loci. This suggested regular pollenmediated gene flow into the population, further supported by the observed high levels of genetic diversity and polymorphism. Significant positive spatial structure was found between parent trees occurring up to 150 m apart in the natural forest, although genetic distance between these individuals suggested limited relatedness (i.e. less than half-sib relatedness). The effect of pollen-mediated gene flow appears, therefore, to swamp any effect of nearest neighbour inbreeding which has been reported in other studies of eucalypt populations and has been attributed to limited seed dispersal. Resistance to the fungal disease Sporothrix pitereka (Ramularia Shoot Blight) was measured on progeny from each of the population study trees. Substantial resistance variability was found, along with a high estimate in heritability of resistance (0.44 ± 0.06), indicating significant additive genetic variation within the population. Spatial analysis showed no significant spatial structure with resistant and susceptible genotypes apparently distributed randomly throughout the population. The lack of concordance between the molecular and quantitative markers suggests that there may be a cost to resistance. Temporal variation in the severity of disease outbreaks may have then led to differential selection of seedlings across many generations, maintaining variability in disease resistance and facilitating the apparent random distribution of disease resistant and susceptible genotypes throughout the population. C. variegata is an important commercial forestry species. The identification of strong genetic control in the disease resistance trait, as well as significant adverse genetic and phenotypic correlations between susceptibility and growth traits, will aid future breeding programs. Controlled crosses between resistant genotypes from this population should result in strong genetic gains in both resistance and growth, with little costs associated with inbreeding depression due to the highly outcrossed nature of the population.

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13

King, Rachel. "Spatial Structure and Population Genetic Variation in a Eucalypt Species Complex." Thesis, Griffith University, 2004. http://hdl.handle.net/10072/365496.

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In this study, the relative influences of selection, gene flow, and other evolutionary forces on the spatial structure of genetic variation within a eucalypt species complex (the spotted gums: genus Corymbia, section Politaria) were assessed. The study investigated the spatial genetic structure among four putative species of spotted gum (broad-scale), as well as within a single population (fine-scale)of one species, using both molecular and quantitative markers. The spotted gum complex occurs naturally across a range of 2500 km in eastern Australia. Spatial genetic variation within and between the four putative spotted gum species was examined using both chloroplast and nuclear markers. No significant differentiation was found between the three northern species of the complex, C. citriodora, C. variegata and C. henryi. The southern species, C. maculata, shared no haplotypes with any of the three northern species. These results disagree in part with those reported in a previous allozyme based study in which C. henryi was found to be significantly divergent from C. variegata (with which it is sympatric) and more closely aligned with C. maculata. Re-analysis of the allozyme data provided evidence of selection acting at the PGM2 locus within populations of C. variegata and C. henryi. The exclusion of this locus from the data set led to concordance between the cpDNA and nDNA analyses. Restricted gene flow and evidence of isolation by distance were identified as the dominant processes influencing the contemporary distribution of the cpDNA haplotypes. No geographic structure of haplotypes was found and complex genealogical relationships between haplotypes indicated the combined effects of past fragmentation, range expansion and possible long distance dispersal events. The variation and spatial structure in both neutral molecular markers and quantitative genetic traits were compared to explore the relative influences of dispersal and selection within a single eucalypt population. Both mature trees (n=130) from a natural population of C. variegata and their progeny (n=127) were sampled. A very high outcrossing rate (98%) was estimated for the population based on data from seven microsatellite loci. This suggested regular pollen–mediated gene flow into the population, further supported by the observed high levels of genetic diversity and polymorphism. Significant positive spatial structure was found between parent trees occurring up to 150 m apart in the natural forest, although genetic distance between these individuals suggested limited relatedness (i.e. less than half-sib relatedness). The effect of pollen-mediated gene flow appears, therefore, to swamp any effect of nearest neighbour inbreeding which has been reported in other studies of eucalypt populations and has been attributed to limited seed dispersal. Resistance to the fungal disease Sporothrix pitereka (Ramularia Shoot Blight) was measured on progeny from each of the population study trees. Substantial resistance variability was found, along with a high estimate in heritability of resistance (0.44 ± 0.06), indicating significant additive genetic variation within the population. Spatial analysis showed no significant spatial structure with resistant and susceptible genotypes apparently distributed randomly throughout the population. The lack of concordance between the molecular and quantitative markers suggests that there may be a cost to resistance. Temporal variation in the severity of disease outbreaks may have then led to differential selection of seedlings across many generations, maintaining variability in disease resistance and facilitating the apparent random distribution of disease resistant and susceptible genotypes throughout the population. C. variegata is an important commercial forestry species. The identification of strong genetic control in the disease resistance trait, as well as significant adverse genetic and phenotypic correlations between susceptibility and growth traits, will aid future breeding programs. Controlled crosses between resistant genotypes from this population should result in strong genetic gains in both resistance and growth, with little costs associated with inbreeding depression due to the highly outcrossed nature of the population.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
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14

Hopkins, Skylar R. "Multi-scale Transmission Ecology: How Individual Host Characteristics, Host Population Density, and Community Structure Influence Transmission in a Multi-host Snail Symbiont System." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/85567.

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We live in an era of global change, where emerging infectious diseases such as Ebola, Zika, bird flu, and white nose syndrome are affecting humans, wildlife, and domesticated species at an increasing rate. To understand and predict the dynamic spread of these infectious agents and other symbionts through host populations and communities, we need dynamic mathematical models that accurately portray host-symbiont transmission. But transmission is an inherently difficult process to measure or study, because it is actually a series of interacting processes influenced by abiotic and biotic factors at multiple scales, and thus empirical tests of the transmission function within epidemiological models are rare. Therefore, in this dissertation, I explore factors at the individual, population, and community-levels that influence host contact rates or symbiont transmission success in a common snail-symbiont system, providing a detailed description of the multi-faceted nature of symbiont transmission. From a review of the ecological literature, I found that most models assume that transmission is a linear function of host population density, whereas most empirical studies describe transmission as a nonlinear function of density. I then quantified the net nonlinear transmission-density relationship in a system where ectosymbiotic oligochaetes are directly transmitted among snail hosts, and I explored the ecological mechanisms underlying the nonlinear transmission-density relationship observed in the field via intraspecific transmission success and contact rate experiments in the laboratory. I found that the field results could be explained by heterogeneity in transmission success among snails with different characteristics and nonlinear contact-density relationships caused by non-instantaneous handling times. After I 'unpacked'population-level transmission dynamics into those individual-level mechanistic processes, I used this same approach to examine higher-level ecological organization by describing the mechanistic underpinnings of interspecific or community-level transmission in the same snail-symbiont system. I found that low interspecific transmission rates in the field were the product of opposing interactions between high population densities, high prevalences of infection, and very low interspecific transmission success caused by strong symbiont preferences for their current host species. Unpacking transmission in this way resulted in one of the most detailed empirical studies of transmission dynamics in a wildlife system, and yielded many surprising new insights in symbiont ecology that would not have been discovered with a purely phenomenological or holistic view of transmission. Though simple, linear, and holistic epidemiological models will always be important tools in disease ecology, 'unpacking'transmission rates and adding heterogeneity and nonlinearity to models, as I have done here, will become increasingly important as we work to maximize model prediction accuracy in this era of increased disease emergence.
Ph. D.

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15

Gordon, David M. "Population dynamics of a host-parasitoid system with particular reference to age-structure effects." Thesis, McGill University, 1987. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=75358.

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An experimental study of laboratory populations of the stored-products moth, Cadra cautella (Lepidoptera: Phycitidae) and its larval parasitoid, Venturia canescens (Hymenoptera: Ichneumonidae) identified and quantified density- and age-dependent demographic characteristics of the host-parasitoid system. Host imago longevity and fecundity depended on larval weight at pupation. Observed effects of C. cautella larval competition for food on larval mortality, stage duration, and weight at pupation were successfully captured in a mathematical model. Host larval age significantly influenced inter-stage cannibalism and susceptibility to mortality resulting from parasitoid oviposition wounds. Both larval parasitoid developmental rates and adult parasitoid attack rates depended on host larval age. Long-term population experiments of host and host-parasitoid populations revealed that host populations fluctuated with a period slightly in excess of host generation time and that parasitoid populations were in synchrony with host populations.

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16

Semeao, Altair Arlindo. "Spatial distribution, dispersal behavior and population structure of Tribolium castaneum herbst (Coleoptera: tenebrionidae)." Diss., Kansas State University, 2011. http://hdl.handle.net/2097/7135.

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Doctor of Philosophy
Department of Entomology
James F. Campbell
Phillip E. Sloderbeck
Robert "Jeff" J. Whitworth
Knowledge of factors influencing the establishment, persistence and distribution of stored-product pests aids the development of effective Integrated Pest Management (IPM) programs in food storage and processing facilities. This research focused primarily on Tribolium castaneum, which is one of the most important pests of mills. Populations of T. castaneum from different food facilities can potentially be interconnected by either their own dispersal behavior or by human transportation. Population genetic structure analyses based on microsatellites and other insertion-deletion polymorphisms (“indels”) showed that populations from different mills around the US are genetically distinct from each other, but the level of differentiation was not correlated with the geographic distance. A potential source of insect infestation within a food facility is spillage that accumulates outside or movement from bulk storage facilities on site. Results from three facilities showed that most stored-product species were captured both inside and outside buildings, but T. castaneum was rarely captured outside of the facilities. Spatial distribution of all species outside was associated with the proximity of buildings, not necessarily with areas with accumulated spillage. T. castaneum populations inside facilities are potentially exposed to frequent genetic bottlenecks resulting from structural fumigations. Changes in allele frequencies through time, based on the analysis of microsatellites and other indels in individuals collected in a mill, confirmed bottleneck effects. To understand how spatial distribution of T. castaneum within a mill could be influenced by environmental and physical factors, a range of variables were measured at each trap location. There was significant variation among trap locations regarding beetle captures and the variables measured, but increase in beetle captures correlated only with increase in temperature and spillage production. Tribolium castaneum response to visual cues could influence attraction to pheromone and kairomone olfactory cues used in traps. Results of laboratory experiments showed that adults respond to tall narrow black shapes and placing traps in front of these shapes can increase captures. This research provides new insights into factors influencing the spatial distribution of T. castaneum and could help in improving monitoring programs for this important pest of the food industry.

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17

Moore, Catrin Elisabeth. "Case-control study of invasive Staphylococcus aureus disease-host genetic susceptibility and bacterial population structure." Thesis, University of Oxford, 2002. https://ora.ox.ac.uk/objects/uuid:85a3a6b4-b0cc-48ed-b584-5037ea884250.

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Staphylococcus aureus is a major pathogen associated with serious community-acquired and nosocomial disease. It is carried nasally at some time by 70% of the population, yet severe disease is relatively uncommon. Two case-control studies were conducted in Oxford, UK and Thailand to examine bacterial and host genetic determinants of severe S. aureus disease. Over 800 cases and 1,600 healthy control individuals were recruited into the two studies. The genetic population structures of S. aureus disease and carriage isolate populations from the Oxford study were studied and compared using phage typing, pulsed-field gel electrophoresis, and multilocus sequence typing. Natural populations of S. aureus have a well-defined clonal population structure, but there was no evidence for the existence of hypervirulent clones. The presence or absence of 33 putative bacterial virulence determinants was examined. After adjusting for the effect of clonality, seven determinants (fhbA, cna, sdrE, sej, eta, hlg and ica) were significantly more common in invasive isolates; all contributed independently to virulence. In the host genetic studies a functional single nucleotide polymorphism at amino acid position 131 of the Fc gamma receptor IIA (FcyRIIA) gene was significantly associated with severe disease. In addition an additive x additive epistatic interaction was found between this FcyRIIA polymorphism and the functional FcyRIIIB NA1/NA2 polymorphism. These significant associations were present when community-acquired disease cases were considered alone, but absent in hospital-acquired disease cases. The putatively functional polymorphisms in genes coding for mannose binding lectin and Tolllike receptor 2 were not associated with disease. Both bacterial and host factors are important in determining the occurrence of severe S. aureus disease. In hospital-acquired infection it is likely that acquired host, bacterial and environmental factors predominate, lessening the importance of any host genetic component.

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18

Menard, Katrina Louise. "Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes." Texas A&M University, 2006. http://hdl.handle.net/1969.1/4210.

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Pine cone beetles (Conophthorus sp.) are serious pests of many forest ecosystems since they burrow into pine cone tissues for egg deposition, causing the death of the seeds. Management of these beetles in natural and commercial stands of pines has been problematic due to lack of understanding about species limits and distribution. This study was conducted to investigate the phylogeography and phylogenetics of the genus. Several species represented by disjunct populations appear to be monophyletic including Conophthorus edulis, C. mexicanus, C. coniperda, and C. conicollens, whereas C. ponderosae is polyphyletic with many distinct clades isolated by geography. This study explored whether host use or geography has played a greater role in the diversification of this genus, focusing on the polyphyletic C. ponderosae and the monophyletic C. edulis. In the first study, 751bp of the mtDNA CO1 gene were sequenced to reconstruct a phylogeny of the genus, and the distribution and host use were compared to investigate whether these factors were significantly associated. The second study addressed population structure and possible historical influences on the C. edulis and C. ponderosae populations using a nested clade analysis of the mtDNA haplotypes. Despite potential limitations due to sampling, several conclusions could be drawn. Three separate haplotype networks were found for the C. ponderosae haplotypes, indicating that there have been at least three lineages that have associated with P. ponderosa. Geography was significantly associated with the phylogeny at greater distances (>900km), but host use was not significant. At the species level, association with geography is variable. Population structure for C. ponderosae at the species level is minimal, and suggests that there has not been much time for lineage sorting of the haplotypes based on the nested clade analysis as compared to C. edulis.

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19

Teichert, Sonja. "Habitat use and population spatial structure of the forked fungus beetle, Bolitotherus cornutus Panzer." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ45379.pdf.

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20

Laurence, Sophie. "GENETIC VARIATION AND POPULATION GENETIC STRUCTURE OF MUSKRAT, ONDATRA ZIBETHICUS, AT DIFFERENT SPATIAL SCALES." Thesis, Laurentian University of Sudbury, 2014. https://zone.biblio.laurentian.ca/dspace/handle/10219/2171.

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Understanding the factors and processes that influence intraspecific genetic variation are essential to better understand evolutionary processes. In this research, I examined patterns of gene flow and their effects on the distribution of genetic variation and spatial genetic structuring at different spatial scales. I used a combination of population genetics, spatial analysis, morphometrics and phylogeography in order to understand the patterns of genetic variation and their resulting phenotypic variations in a semi-aquatic species, the muskrat (Ondatra zibethicus).

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21

Goldberg, Caren. "Habitat, spatial population structure, and methods for monitoring barking frogs (Eleutherodactylus augusti) in southern Arizona." Thesis, The University of Arizona, 2002. http://hdl.handle.net/10150/278788.

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Debate over global declines of amphibian populations has focused researchers' attention on the lack of basic life-history information about and appropriate monitoring methods for amphibian species. We studied barking frogs ( Eleutherodactylus augusti) in a canyon in the Huachuca Mountains of southern Arizona. Annual (capture) surveys and radio-tracking revealed that most barking frogs in this canyon are strongly associated with limestone. Adults rarely moved between limestone outcrops and numbers of frogs on each outcrop were small. Subpopulations consisting of frogs on sets of neighboring outcrops probably function as a metapopulation. We evaluated four methods for monitoring population size of this species: mark-recapture, distance sampling, visual encounter surveys, and call counts. We found none of these to be able to detect changes in population size powerfully enough to alert managers to declines as they occur. We suggest resource managers focus monitoring efforts on distribution rather than population size.

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22

Cilli, Elisabetta <1978&gt. "Spatial and temporal population structure and species traceability in fishery resources of the Mediterranean Sea." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1747/1/Elisabetta_Cilli_THESIS_PhD.pdf.

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23

Cilli, Elisabetta <1978&gt. "Spatial and temporal population structure and species traceability in fishery resources of the Mediterranean Sea." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1747/.

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24

Yin, Mingbo [Verfasser], and Wilfried [Akademischer Betreuer] Gabriel. "Population structure and host-parasite interactions in the Daphnia longispina hybrid complex / Mingbo Yin. Betreuer: Wilfried Gabriel." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2011. http://d-nb.info/1018615741/34.

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25

Oosthuysen, Wilhelm Frederick. "Population structure, host cell interactions and pathogenesis of Staphylococcus aureus strains isolated at Tygerberg hospital, South Africa." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/85580.

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Thesis (PhD)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: Numerous studies conducted internationally have identified and described several endemic methicillin-susceptible Staphylococcus aureus (MSSA) clones. However, only some of these clones are associated with methicillin resistance (CC5, CC8, CC22, CC30 and CC45). To date, studies reporting on the population structure of S. aureus isolated in South Africa represent limited demographic areas, focus on methicillin-resistant S. aureus (MRSA) only and have displayed little emphasis on virulence. This study was undertaken to elucidate the population structure of S. aureus isolated from specific clinical sources at Tygerberg hospital, and to investigate specific host-pathogen interactions of representative isolates. Consecutive non-repetitive clinical S. aureus isolates were collected over one year (September 2009/2010) with patient demographics and limited clinical information. Strains were typed by PFGE and molecular markers (spa, multi-locus sequence typing (MLST), agr, Staphylococcal Chromosome Cassette mec and Panton-Valentine leukocidin (PVL)). Representative isolates were selected and investigated for the presence of virulence genes, adherence (to immobilised fibronectin [Fn], fibrinogen [Fg], collagens IV [CnIV] and VI [CnVI]), cellular invasion and cell death induction. Statistical association were determined between all in vitro results and methicillin-resistance, clonality, patient HIV status and bacterial PVL status. Fifteen percent of the isolates (n = 367) were MRSA. Forty four present of isolates were PVL+. agr I-IV and SCCmec I-V were identified. The MSSA population was diverse: ST22 (dominant), ST1865 and ST121 were PVL+. ST45, ST1863 and ST15 were PVL-. PVL- MRSA were diverse: ST612-MRSA-IV (dominant), ST5-MRSA-I, ST239-MRSA-III, ST36-MRSA-II and ST22-MRSA-IV. The genes fnbA/B (fibronectin-binding protein A/B), clfA/B (clumping factor A/B), eap (extracellular adherence protein), nuc (nuclease), coa (coagulase) and hld (delta toxin) were detected in all representative isolates. The CC8 and CC6 isolates adhered strongly to all ligands (100-700% of control, ligand dependent), while isolates of CC45, CC22 and CC88 adhered strongly only to Fg and Fn. The CC30, CC15, and CC12 isolates adhered extremely strongly to CnIV (>300%) and CC8, CC15, and C6 to CnVI (>200%). Isolates from CC30, CC8, CC15, CC6, CC12, CC97, CC88 and CC45 were highly invasive (>100%). ST121 was non-invasive (>50%). Isolates of CC5, CC30 and CC121 were non-cytotoxic (<50%), while isolates of CC22, CC8, CC15, CC45 and CC88 were very cytotoxic (>70%). No significant difference was observed in adherence or cell death induction of MRSA vs. MSSA clones or between isolates from HIV+ vs. HIV- persons. PVL- isolates displayed higher cellular invasiveness than PVL+ isolates. The presence of ST612-MRSA-IV, ST22-MRSA-V and ST8-MRSA-V points to local SCCmec acquisition, as we found MSSA isolates with the same spa types. Numerous MSSA clones were prevalent, but do not appear to have a major common genetic background with MRSA. PVL was highly prevalent among MSSA, indicating acquisition of PVL genes independently of SCCmec. The abilities to adhere to specific immobilised ligands in vitro were diverse and grouped with the genetic background, while the vast majority of isolates were invasive and induced significant cell death. We can conclude that the population of S. aureus at Tygerberg hospital is composed of a vast number of MSSA and MRSA clones, which display varying patters of adherence to selected ligands and of which, the majority clones are invasive and cytotoxic.
AFRIKAANSE OPSOMMING: Talle internasionale studies het verskeie endemiese metisillien vatbare Staphylococcus aureus (MSSA) klone geïdentifiseer en beskryf. Slegs 'n paar van hierdie klone word geassosieer met metisillien weerstandigheid (Klonale kompleks (KK) 5, KK8, KK22, KK30 en KK45). Studies oor die bevolking struktuur van S. aureus geïsoleer in Suid-Afrika is tot dusver beperk tot demografiese gebiede, fokus slegs op metisillien-weerstande S. aureus (MRSA) en het min klem op virulensie geplaas. Hierdie studie is onderneem om die bevolking struktuur van S. aureus, geïsoleer vanaf spesifieke kliniese bronne, in die pasiëntpopulasie van Tygerberg-hospitaal te ondersoek en om ondersoek in te stel na spesifieke gasheer-patogeen interaksies van verteenwoordigende isolate. Opeenvolgende, nie-herhalende en suiwer kliniese S. aureus isolate is versamel oor ´n periode van een jaar (September 2009/2010), tesame met pasiënt demografiese- en beperkte kliniese inligting. Stamme is deur PFGE en molekulêre merkers (spa, MLST, agr, SCCmec en PVL) beskryf. Verteenwoordigende isolate is gekies en ondersoek vir die teenwoordigheid van virulensie gene, aanhegting ( aan geïmmobiliseerde fibronektien [Fn], fibrinogeen [Fg], kollageen IV [CnIV] en kollageen VI [CnVI]), sellulêre indringing en die induksie van seldood. Statistiese assosiasies is bepaal tussen alle in vitro resultate en methicillin-weerstandigheid, klonaliteit, pasiënt MIV status en bakteriese PVL status. Fyftien persent van die isolate (n = 367) was MRSA. Vier-en-veertig van die isolate was PVL+. agrI-IV en SCCmec I-V is geïdentifiseer. Die MSSA bevolking was divers: ST22 (dominant), ST1865 en ST121 PVL +. ST45, ST1863 en ST15 was PVL+. PVL- MRSA was divers: ST612-MRSA-IV (dominant), ST5-MRSA-I, ST239-MRSA-III, ST36-MRSA-II en ST22-MRSA-IV. Die gene fnbA/B (fibronektien A/B), clfA/B (klontings faktor A/B), eap (ekstrasellulêre aanhegtings protein), nuc (nukease), coa (koagulase) en hld (delta toksien) was aangetref in alle verteenwoordigende isolate. Isolate van KK8 en KK6 het sterk aan alle ligande (100-700% van kontrole, ligand-afhanklike) aangeheg, terwyl isolate van KK45, KK22 en KK88 slegs sterk aand fibronektien en fibrinogeen aangeheg het. Isolate van KK30, KK15, en KK12 het baie sterk aan CnIV (> 300%) aangeheg en KK8, KK15, en KK6 and CnVI (> 200%). Isolate van KK30, KK8, KK15, KK6, KK12, KK97, KK88 en KK45 was hoogs indringend (> 100%). ST121 was nie-indringende (> 50%). Isolate van KK5, KK30 en KK121 was nie-sitotoksiese (<50%), terwyl isolate van KK22, KK8, KK15, KK45 en KK88 baie sitotoksies was (> 70%). Geen betekenisvolle verskil is waargeneem in die aanhegting of seldood induksie van MRSA teenoor MSSA klone of tussen isolate van MIV+ teenoor MIV- persone nie. PVL- isolate het hoër sellulêre indringing as PVL+ isolate vertoon. Die teenwoordigheid van ST612-MRSA-IV, ST22-MRSA-V en ST8-MRSA-V verwys na die plaaslike verwerwing van SCCmec, aangesien ons MSSA isolate beskryf het met dieselfde spa-tipes. Talle MSSA klone was algemeen, maar het nie 'n beduidende genetiese agtergrond met MRSA vertoon nie. PVL was baie algemeen onder MSSA isolate en die PVL gene is dalk onafhanklik van SCCmec verkry. Die vermoë om aan spesifieke geïmmobiliseer ligande in vitro aan te heg was divers en groepeer met die genetiese agtergrond, terwyl die meerderheid van die isolate indringend was en kon betekenisvolle sel dood veroorsaak. Ons kan aflei dat die bevolking van S. aureus by die Tygerberg hospitaal saamgestel is uit 'n groot aantal van MSSA en MRSA klone, wat verskillende patrone van aanhegting aan geselekteerde ligande vertoon en waarvan die meeste klone indringende en sitotoksies is.
DFG/NRF International Research and Training Group (IRTG) 1522 “HIV and associated infectious diseases in Southern Africa”
National Research Foundation
Medical Research Council, Medi-Clinic
Harry Crossley Fund (Stellenbosch University)
Stellenbosch University

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26

De, Wit Erika. "Analysis of host determining factors in susceptibility to tuberculosis in the South African coloured population." Thesis, Stellenbosch : University of Stellenbosch, 2009. http://hdl.handle.net/10019.1/4584.

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Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2009.
Dissertation presented for the degree of Doctor of Philosophy in Medical Biochemistry at Stellenbosch University.
ENGLISH ABSTRACT: The infectious disease tuberculosis (TB) still represents a global threat due to its devastating effect on health and the subsequent high mortality rate. Previous studies have indicated that host genetic factors are implicated in host susceptibility to TB. Since TB is a complex disease, it can be assumed that susceptibility to M. tuberculosis has multiple genetic causative factors (as well as environmental causes). The current study focussed on a number of South African Coloured (SAC) individuals, some of whom were TB cases and others controls. Population substructure was tested in the admixed SAC population as it can be a strong confounding factor for association studies. Our results using the programme STRUCTURE indicated no population substructure in the SAC population. We further investigated the population structure of the SAC group using Affymetrix 500k SNP chip data which showed that the SAC population group has 4 major ancestral components: the Khoesan, European, African and Asian (Indian). A number of candidate polymorphisms in eight genes, previously indicated to play an important role in TB susceptibility, were tested in case-control associations studies. We found statistically significant associations between IFNGR1, IL-8, IL-1Ra and NRAMP1 polymorphisms and TB susceptibility in the SAC population. It has become increasingly evident that gene-gene interactions play a far more important part in an individual’s susceptibility to a complex disease than single polymorphisms would on their own. The importance of epistasis was clearly identifiable in this study with only four associations found between the individual variants and TB susceptibility, but eight instances of statistically significant gene-gene interactions. A combined data set consisting of 106 variants constructed from our database and also used for gene-gene interaction analysis yielded numerous statistically significant interactions. The interaction between the genotype of the human host and the bacterial strain genotype was also investigated and yielded interesting results. Owing to various polymorphisms in several cytokine genes, the protein levels of the main modulators of the immune system, cytokines and chemokines, are changed in several diseases such as infectious diseases and may affect susceptibility or resistance to TB. The functional polymorphisms or haplotype patterns in some of these cytokine genes might be vital for protective immune responses and may serve as biomarkers of protection or susceptibility to TB. The present study investigated 18 cytokines including pro-inflammatory, anti-inflammatory and chemokine factors in healthy (mantoux positive or negative) children using the Linco-plex immunoassay, and investigated potential interactions. The basic research will one day contribute to personalised genetics which may benefit infectious diseases such as TB. If individuals can be identified as potentially more vulnerable, they may require different vaccination strategies, a higher index of suspicion if exposed to TB, and prophylactic treatment.
AFRIKAANSE OPSOMMING: Die infektiewe siekte tuberkulose (TB) is steeds ‘n gevaar wat die hele wêreld bedreig weens die groot impak op gesondheid en die gevolglike hoë mortaliteit. Vorige studies het bevind dat die gasheer se genetiese faktore wel betrokke mag wees by die gasheer se vatbaarheid vir TB. Aangesien TB ‘n komplekse siekte is, kan dit aanvaar word dat vatbaarheid tot M. tuberculosis veelvuldige genetiese oorsaaklike faktore (sowel as omgewingsoorsake) het. Hierdie studie het gefokus op ‘n aantal Suid-Afrikaanse Kleurling (SAC) individue, waarvan sommige TB pasiënte en ander kontroles was. Die gemengde SAC populasie is getoets vir populasie-stratifikasie, aangesien stratifikasie ‘n sterk verwarrende invloed op pasiënt-kontrole studies kan hê. Ons resultate is verkry met behulp van die program STRUCTURE en het aangedui dat daar geen populasie sub-struktuur tussen die pasiënte en kontroles was nie. Ons het ook die populasiesamestelling van die SAC groep ondersoek met data verkrygbaar van die Affymetrix 500k enkel nukleotied polimorfisme mikroskyfie. Hierdie data het getoon dat die SAC populasie uit 4 hoof voorouerlike komponente bestaan naamlik die Khoesan, Europeërs, Afrikane en Asiate (Indiërs). ‘n Aantal kandidaat polimorfismes in agt gene, wat volgens vorige studies ‘n belangrike rol in TB vatbaarheid te speel, was in hierdie pasiënt-kontrole assosiasie studie bestudeer. Ons het statistiese beduidende verwantskappe tussen IFNGR1, IL-8, IL-1Ra en NRAMP1 polimorfismes en TB vatbaarheid in die SAC populasie gevind. Dit het al hoe meer duidelik geword dat geen-geen interaksies ‘n baie belangriker rol in ‘n individu se vatbaarheid vir ‘n komplekse siekte speel as enkel polimorfismes op hul eie. Die belang van epistase kon duidelik in hierdie studie geïdentifiseer word met slegs vier assosiasies wat tussen die individuele variante en TB vatbaarheid gevind is, in vergelyking met agt statisties beduidende geen-geen interaksies. ‘n Gekombineerde datastel wat uit ons databasis saamgestel is en wat 106 variante bevat is ook in ‘n aparte geen-geen interaksie analise gebruik, wat verskeie statisties beduidende interaksies getoon het. Die interaksie tussen die menslike gasheer genotipe en die bakteriese stam genotipe is ook in hierdie studie ondersoek en het interessante resultate opgelewer. Veranderde proteïen uitdrukking van die hoofmoduleerders van die immuunsisteem, sitokine en chemokine, kom voor in verskeie siektes soos infektiewe siektes weens verskillende polimorfismes in verskeie sitokien-gene. Sulke polimorfismes kan ook vatbaarheid vir of weerstandigheid teen TB beïnvloed. Die funksionele polimorfismes of haplotipe patrone in sommige van hierdie sitokien-gene mag noodsaaklik wees vir beskermende immuunresponse en mag ook as biomerkers vir beskerming teen of vatbaarheid vir TB dien. Hierdie studie het 18 sitokiene (insluitend pro-inflammatoriese-, anti-inflammatoriese- en chemokiene faktore), sowel as potensiële interaksies in gesonde (mantoux positiewe of negatiewe) kinders, ondersoek met behulp van die Linco-plex immuno-analise. Hierdie basiese navorsing sal eendag in die toekoms bydrae tot persoonlike genetiese analises wat tot voordeel kan wees vir infektiewe siektes soos TB. Indien individue as potensieël meer vatbaar vir TB geïdentifiseer kan word, kan sulke persone ander vaksineringstrategieë sowel as voorkomende behandeling vereis.

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27

Piri, Rebecca D. "Spatial Genetic Structure and Local Adaptation within and among Foxtail Pine (Pinus balfouriana subsp. balfouriana) Populations Located in the Klamath Mountains, California." VCU Scholars Compass, 2019. https://scholarscompass.vcu.edu/etd/6018.

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Foxtail pine (Pinus balfouriana) is a subalpine conifer endemic to California, notably separated into two disjunct subspecies. Previous studies have described the northern subspecies,Pinus balfouriana subsp. balfouriana,as having an uncommonly high level of genetic differentiation and no discernible spatial patterns in phenotypic variation. This study seeks to characterize the spatial genetic structure and patterns of selection of the northern subspecies (Pinus balfouriana subsp. balfouriana) using genome-wide data and to identify the influence of ecology and environment on the unique genetic patterns. I show that genetic differentiation among populations is much less than previously estimated (FST= 0.000644) and there is weak isolation-by-distance structure, but ongoing gene flow is unlikely. Within populations, stand density and competitor effects contribute to inbreeding. I also show that previously measured traits are predominantly determined by genetics. Analyzing by sliding window in the genome, I show that connectivity patterns vary widely throughout the genome and identify several areas that are important to the genetic architecture of the phenotypic traits and plasticity (GxE). Overall, there is high connectivity, genetic similarity, and genetically based trait variation among and within populations of the northern subspecies of foxtail pine due to historical processes, despite biotic interactions driving inbreeding. Persistent genetic isolation, however, may make adaptation to future climate a challenge for the subspecies.

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28

Hailu, Solomon Ghebremeskel. "THE EFFECT OF HABITAT FRAGMENTATION ON THE SPATIAL POPULATION GENETIC STRUCTURE OF SOUTHERN PINE BEETLE (DENDROCTONUS FRONTALIS)." OpenSIUC, 2011. https://opensiuc.lib.siu.edu/theses/624.

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Southern pine beetle (SPB), Dendroctonus frontalis (Zimmerman), is one of the most destructive insect pests of pine trees in southern United States, Mexico and Central America. There is relatively little information on the effect of habitat fragmentation on the connectivity and the spatial population genetics of SPB. This study therefore, adds to previously generated information by assessing how habitat fragmentation affects the spatial population genetic structure of SPB. It also introduces a new approach to the study of bark beetle population dynamics by assessing how landscape variables shape their effective dispersal. To address this issue, a suite of eight highly polymorphic DNA microsatellite markers were used to measure SPB movement over a representative range of SPB habitat and non-habitat (matrix). At the broadest scale, highly significant genetic differentiation suggests that the sampled populations are not panmictic. Loci with higher variability yielded higher resolution for both the infinite allele model based measure of differentiation (FST) and the stepwise mutation based measure (RST) estimates. It is apparent that allelic frequency differences, allelic size ranges and repeat motif played a role in the observed patterns of pair-wise differentiations between the sampled localities. It is supposed that gene flow, wide-range dispersal and recent divergent time could have contributed to the lower level of genetic structure observed in the pair wise estimates. The sampled populations did not show any differentiation attributable to the host species from which they were collected. Mantel test of genetic distance and Euclidean geographic distance revealed no correlation. Mantel tests of the correlation between genetic distance and cost weighted Euclidean distances also suggest that dispersal of SPB across geographic barriers is not significantly reduced. Thus, landscape features and host preference do not appear to have had an impact on population genetic structure of SPB. Since movements of these beetles were not significantly hindered by environmental factors like major rivers, roads, elevation and host type, it is advisable for regional pest management offices to put an effort and coordinate their prevention and management plans in a broader scale to alleviate the problem associated with this native insect pest. Disequilibrium in the observed homogenized pattern of the beetle in this study suggests human contribution in the dispersal of SPB. Therefore, stringent control is deemed necessary in transportation of logs. This could improve our pest management system hence its positive implication in timber industry is obvious.

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29

Forien, Raphael. "The spatial structure of genetic diversity under natural selection and in heterogeneous environments." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX082/document.

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Cette thèse porte sur la structure spatiale de la diversité génétique. Dans un premier temps, nous étudions un processus à valeurs mesure décrivant l'évolution de la composition génétique d'une population soumise à la sélection naturelle. Nous montrons que ce processus satisfait un théorème de la limite centrale, et que ses fluctuations sont données par la solution d'une équation aux dérivées partielles stochastique. Nous utilisons ce résultat pour donner une estimation du fardeau de dérive au sein d'une population structurée en espace.Dans un deuxième temps, nous nous intéressons à la composition génétique d'une population lorsque les individus se déplacent plus facilement dans une région de l'espace que dans l'autre (on parle alors de dispersion hétérogène). Nous démontrons dans ce cas la convergence des fréquences alléliques via la convergence des lignées ancestrales vers un système de mouvements browniens de Walsh.Nous détaillons également l'impact d'une barrière géographique traversant l'habitat d'une population sur sa diversité génétique. Nous montrons que les lignées ancestrales décrivent dans ce cas des mouvements browniens partiellement réfléchis, dont nous donnons plusieurs constructions.Dans le but d'appliquer ces travaux, nous adaptons une méthode d'inférence démographique au cas de la dispersion hétérogène. Cette méthode utilise les blocs continus de génome hérités d'un même ancêtre entre les paires d'individus dans l'échantillon et permet d'estimer les caractéristiques démographiques d'une population lorsque celles-ci varient dans l'espace. Pour terminer nous démontrons l'efficacité de notre méthode sur des données simulées
This thesis deals with the spatial structure of genetic diversity. We first study a measure-valued process describing the evolution of the genetic composition of a population subject to natural selection. We show that this process satisfies a central limit theorem and that its fluctuations are given by the solution to a stochastic partial differential equation. We then use this result to obtain an estimate of the drift load in spatially structured populations.Next we investigate the genetic composition of a populations whose individuals move more freely in one part of space than in the other (a situation called dispersal heterogeneity). We show in this case the convergence of allele frequencies via the convergence of ancestral lineages to a system of skew Brownian motions.We then detail the effect of a barrier to gene flow dividing the habitat of a population. We show that ancestral lineages follow partially reflected Brownian motions, of whom we give several constructions.To apply these results, we adapt a method for demographic inference to the setting of dispersal heterogeneity. This method makes use of long blocks of genome along which pairs of individuals share a common ancestry, and allows to estimate several demographic parameters when they vary accross space. To conclude, we demonstrate the accuracy of our method on simulated datasets

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30

Boothe, Rena Almena. "Influence of host plant and host population structure on physiological and behavioural characteristics of Chilocorus nigritus and the efficacy of control of the scale insect, Aspidiotus nerii (Bouche)." Thesis, University of Kent, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.523517.

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31

Zehetbauer, Josef [Verfasser], and Christoph [Akademischer Betreuer] Walker. "Stability of equilibria for a nonlinear population model with age- and spatial-structure / Josef Zehetbauer ; Betreuer: Christoph Walker." Hannover : Gottfried Wilhelm Leibniz Universität Hannover, 2019. http://d-nb.info/1204459304/34.

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32

Lee, David Jung-Hwi. "Optimal Regional Allocation of Population and Employment: Application of a Spatial Interaction Commuting Model." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1276787325.

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33

McConway, Alex. "The effects of trace metals on juvenile cockles (Austrovenus stutchburyi)." Thesis, University of Canterbury. Biological Sciences, 2008. http://hdl.handle.net/10092/1696.

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This thesis investigated the population structure and spatial distribution of the cockle Austrovenus stutchburyi in estuaries and bays around the Canterbury coastline. Surveys investigated population attributes (average density and density of small cockles (< 10mm)) of Austrovenus stutchburyi in relation to physical environmental characteristics such as trace metals (copper, cadmium and zinc), sediment particle size, nitrogen and phosphorus levels, pore water and percentage organic matter of the sediment. Surface cover of flora and number of fauna present was also correlated with the density of cockles and small cockles < 10mm. MDS and PCA ordination showed that the biota was similar at 14 sites but differed significantly at the Pleasant Point Yacht Club (PPY) site. There was a positive correlation between fine sand (125 μm) and the average density of cockles and small cockles < 10 mm. High population densities of Austrovenus stutchburyi were also positively correlated with phosphorus levels, and percentage cover of Sea Grass (Ulva sp). However, Austrovenus stutchburyi density was negatively correlated with cadmium and zinc concentration, and percentage of mud present. The density of small cockles < 10 mm was negatively correlated with copper and cadmium concentration in the sediment and positively correlated with Topshell (Diloma subrostrata) numbers, Sea grass (Zostera muelleri) percentage cover, Sea lettuce (Ulva sp), percentage cover, and sediment particles sizes of < 63 μm (mud), 63 μm (very fine sand), and 125 μm (fine sand). Survival and behavioural changes of juvenile Austrovenus stutchburyi were investigated in relation to increased levels of copper, cadmium, and zinc in aqueous solution and sediment in the laboratory, and artificially increased levels in the field. In laboratory experiments in contaminated seawater it was found that, over time, copper and zinc had a detrimental effect on the percentage of juvenile cockles with their siphons extended as did copper concentration. Cockles 10 - 12 mm shell length exposed to different concentrations of copper had the lowest survival rate (25%) whilst cockles that were 5 - 7 mm in length had the greatest survival rate (69%). Cadmium did not affect survival or siphon extension in aqueous experiments. In the contaminated sediment experiments in the laboratory, the concentration of zinc (0, 20, 40, 80, 160 mg Zn/kg (dry weight)) and cadmium (0, 1.8, 5.6, 18, 36 mg Cd/kg (dry weight)) both decreased survival and burial of juvenile cockles in higher concentrations. Copper concentration (0, 5, 10, 25, 50 mg Cu /kg (dry weight)) decreased burial rates of juvenile cockles but did not affect survival. Transfer of juvenile Austrovenus stutchburyi within three sites in the Avon Heathcote Estuary during May 2007, found that site and exposure to copper, cadmium and zinc decreased the survival of the juvenile cockles. However, transfer of cockles between estuaries (Takamatua, Saltwater Creek and Avon – Heathcote Estuary) in May 2007 found that exposure to copper, cadmium and zinc had the main effect on survival of juvenile cockles. In July 2007 transfers of cockles between estuaries, site and exposure to copper, cadmium and zinc had an effect of survival on juvenile cockles. Cockle populations in the present research have shown a strong correlation with environmental variables, which can be used for management and conservation. The research in this thesis is a start to understanding the effects and implications of contaminants on survival, behaviour and recruitment of juvenile cockles. This research will benefit management strategies for increasing population numbers of Austrovenus stutchburyi.

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34

Stasek, David Jon. "BUTTERFLY MOVEMENTS AMONG ISOLATED PRAIRIE PATCHES: HABITAT EDGE, ISOLATION, AND FOREST-MATRIX EFFECTS." Oxford, Ohio : Miami University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=miami1150217598.

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35

Woo, Myungje. "Impacts of urban containment policies on urban growth and structure." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1195263668.

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36

Brewer, Andrew M. "Interactions between demographic rates, population density and the environment : the spatial structure of the range of the holly leaf-miner." Thesis, University of Sheffield, 2001. http://etheses.whiterose.ac.uk/14830/.

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Generalisations about the abundance structure of species' geographic ranges may have implications within a number of areas of applied ecology. However, empirical data is largely restricted to a single taxonomic group within one geographic region. One approach to the study of range structure and its ecological consequences is to examine the relationship between demographic rates and environmental conditions. However, most studies of population processes are at small spatial scales and it is not known to what extent patterns found at these scales may be extrapolated. This thesis addresses these issues using surveying techniques to measure spatial structure in both the densities and demographic rates of the holly leaf-miner (Phytomyza ilicis Curt.) at a wide variety of spatial scales. Geostatistical tools are used to analyse the data collected. At a regional scale, spatial structure in leaf-miner densities is apparent despite considerable variation between hosts within individual habitat patches. This structure can in part be accounted for by variation in habitat and altitude. Over the entire range, broad scale trends in population density can be detected which can also, be correlated with environmental variation.' Many demographic rates components exhibit spatial structure. However, their relationships both with population density and environmental variation are more complex. Per capita mortality rates did not correlate well with population density at any spatial scale. The difficulties inherent in relating population density with demographic rates and regulation by natural enemies are discussed. The demographic approach has also been used to explain.the positive interspecific abundance-distribution relationship. Computer simulation techniques are employed to explore this model. The results indicate that the positive relationship should be extremely robust under a high degree of variation between the demographic rates. However, data from the holly leaf-miner surveys suggest that current. models of range structure make unrealistic assumptions about environmental variation. The key to understanding range structure and its consequences may lie in our ability to make. generalisations about environmental structure.

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Straulino, Daniel. "Selection in a spatially structured population." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:3a20f7a3-27cd-4cbb-9e88-7ebb21ce4e0d.

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This thesis focus on the effect that selection has on the ancestry of a spatially structured population. In the absence of selection, the ancestry of a sample from the population behaves as a system of random walks that coalesce upon meeting. Backwards in time, each ancestral lineage jumps, at the time of its birth, to the location of its parent, and whenever two ancestral lineages have the same parent they jump to the same location and coalesce. Introducing selective forces to the evolution of a population translates into branching when we follow ancestral lineages, a by-product of biased sampling forwards in time. We study populations that evolve according to the Spatial Lambda-Fleming-Viot process with selection. In order to assess whether the picture under selection differs from the neutral case we must consider the timescale dictated by the neutral mutation rate Theta. Thus we look at the rescaled dual process with n=1/Theta. Our goal is to find a non-trivial rescaling limit for the system of branching and coalescing random walks that describe the ancestral process of a population. We show that the strength of selection (relative to the mutation rate) required to do so depends on the dimension; in one and two dimensions selection needs to be stronger in order to leave a detectable trace in the population. The main results in this thesis can be summarised as follows. In dimensions three and higher we take the selection coefficient to be proportional to 1/n, in dimension two we take it to be proportional to log(n)/n and finally, in dimension one we take the selection coefficient to be proportional to 1/sqrt(n). We then proceed to prove that in two and higher dimensions the ancestral process of a sample of the population converges to branching Brownian motion. In one dimension, provided we do not allow ancestral lineages to jump over each other, the ancestral process converges to a subset of the Brownian net. We also provide numerical results that show that the non-crossing restriction in one dimension cannot be lifted without a qualitative change in the behaviour of the process. Finally, through simulations, we study the rate of convergence in the two-dimensional case.

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38

Tambarussi, Evandro Vagner. "Contemporary gene flow, mating system, and spatial genetic structure in a Jequitibá-rosa (Cariniana legalis Mart. Kuntze) fragmented population by microsatellite markers." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-24032014-101908/.

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Cariniana legalis Mart. O. Kuntze (Lecidiaceae) is the largest tree of the Atlantic Forest. To contribute to in situ and ex situ genetic conservation programs for the species, herein we investigate the genetic diversity, inbreeding, intrapopulation spatial genetic structure (SGS), mating system and contemporary pollen flow in three fragmented populations of this species. We found 65 adult trees in the Ibicatu population, 22 in MGI, and four in MGII. Seeds were hierarchically sampled among and within fruits directly from the canopy of 15 seed-trees in Ibicatu (n= 40), five seed-trees in MGI (n= 50), and two seed-trees in MGII (n= 100). Thirteen specific microsatellite loci were developed and validated for 51 C. legalis trees. Eleven loci were polymorphic, revealing a maximum of two to 15 alleles per locus. Using the progeny arrays and seed-tree genotypes, we investigated the Mendelian inheritance, genetic linkage and genotypic disequilibrium of seven microsatellite loci specifically isolated for C. legalis and two previously developed heterologous microsatellite loci. No notable deviations from the expected Mendelian segregation, linkage, or genotypic disequilibrium were detected. The average allelic richness in the adult cohort of Ibicatu was 11.65 and 14.29 for MGI-II and for seeds it was 14.18 in Ibicatu and 10.85 in MGI-II; the average observed heterozygosity for adults of Ibicatu was 0.811 and 0.838 for MGI-II and for seeds it was 0.793 in Ibicatu and 0.786 in MGI-II; the average expected heterozygosity for adults of Ibicatu was 0.860 and 0.900 for MGI-II and for seeds it was 0.856 in Ibicatu and 0.853 in MGI-II. The average fixation index was significantly greater than zero for adults and seeds from both populations. Multilocus outcrossing rate ( m t ) in the three populations was significantly lower than unity (1.0), especially in MGII ( m t = 0.830). The rate of mating among relatives was significant when compared to zero only for Ibicatu ( ????0.266) m s t t . Paternity correlation is substantially higher within than among fruits. The average coancestry coefficient ( ??) was higher and variance effective size ( e N ) was lower than expected for halfsib progenies in all three populations. The number of seed-trees necessary for seed collection to obtain progeny arrays with an effective size of 150 was estimated between 54 to 58 seedtrees. The pollen immigration rate was low, especially for the small stands (maximum of 0.4% for MGI), indicating significant genetic isolation of MGI and MGII. The effective pollination radius was also low in MGI (68 m) and MGII (191 m). For MGII, we also found higher levels of selfing (18%) than for Ibicatu (6%) and MGI (6.4%). The substantial genetic isolation of these stands suggest that we can expect an increase in SGS in the future and strategies to increase gene flow and effective population size, such as transplanting individuals among the populations, are desirable for long term in situ conservation. In conclusion, this study produced valuable information for the management of fragmented populations of C. legalis, contributing to breeding programs and providing guidelines for seed collection aimed at conservation and reforestation programs.
Cariniana legalis Mart. O. Kuntze (Lecidiaceae) é a maior árvore da Mata Atlântica. Para contribuir com a conservação in e ex situ nós investigamos a diversidade genética, endogamia, estrutura genética espacial intrapopulacional (EGE), sistema de reprodução e fluxo contemporâneo de pólen em três populações fragmentadas da espécie. Encontrámos 65 árvores adultas na população Ibicatu, 22 em MGI, e quatro em MGII. As sementes foram colhidas e amostradas hierarquicamente entre e dentro de frutos diretamente da copa de 15 árvores matrizes em Ibicatu (n = 40), cinco em MGI (n = 50), e duas em MGII (n = 100). Treze locos microssatélites foram desenvolvidos e validados em 51 indivíduos de C. legalis. Onze deles foram polimórficos, revelando um máximo de dois a 15 alelos por loco. Usando os genótipos das progênies e matrizes, foi investigada a herança mendeliana, ligação genética e desequilíbrio genotípico de sete locos isolados de C. legalis e dois heterólogos. Não foram detectados desvios notáveis da segregação mendeliana, de ligação, ou desequilíbrio genotípico. A riqueza alélica média de adultos de Ibicatu foi 11,65 e 14,29 para MGI-II e para as sementes foi de 14,18 em Ibicatu e 10,85 na MGI-II, a heterozigosidade média observada para adultos em Ibicatu foi 0,811 e 0,838 para MGI-II, para as sementes foi de 0,793 em Ibicatu e 0,786 em MGI-II, a heterozigosidade média esperada para adultos de Ibicatu foi 0,860 e 0,900 para MGI-II, para as sementes foi de 0,856 em Ibicatu e 0,853 em MGI-II. O índice médio de fixação foi significativamente maior do que zero para adultos e sementes de ambas as populações. A taxa de cruzamento Multilocus (? ) nas três populações foi significativamente menor do que a unidade (1,0), especialmente para MGII ( = 0,830). A taxa de acasalamento entre parentes foi significativa apenas para Ibicatu ( . A correleção de paternidade foi substancialmente maior dentro do que entre os frutos. O coeficiente médio de coancestria (?) foi maior e variação de tamanho efetivo (Ne ) foi menor do que o esperado para progênies de meio-irmãos em todas as populações. O número estimado de árvores matrizes necessárias para a coleta de sementes para se obter um tamanho efetivo de 150 foi de 54-58 árvores. A taxa de imigração de pólen foi baixa, especialmente para os fragmentos menores (máximo de 0,4% para MGI), indicando isolamento genético significativo. O raio efetivo de polinização foi baixo em MGI (68 m) e MGII (191 m). Para MGII também encontramos níveis mais elevados de autofecundação (18%) do que para Ibicatu (6%) e MGI (6,4%). O isolamento genético substancial desses estandes sugerem que podemos esperar um aumento na EGE e que estratégias para aumentar o fluxo gênico e tamanho efetivo da população, como o transplante de indivíduos nas populações, são desejáveis para o longo prazo. Em conclusão, este estudo gerou informações valiosas para a gestão de populações fragmentadas de C. legalis, contribuindo para programas de melhoramento e fornecendo orientações para a coleta de sementes destinadas a programas de conservação e reflorestamento.

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Adams, Thomas P. "Reconstructing Scotland's pine forests." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4730.

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The Caledonian pinewoods are a habitat of crucial environmental and cultural importance, and the sole home of many rare species. However, they have seen steady decline in recent centuries, through the establishment of hunting estates and forestry plantations. A recent trend in management is the attempted transformation of existing plantations (dense communities with a regular spatial structure and low variance in size and age) towards a state mimicking the perceived natural condition, which has a lower density, irregular spatial pattern, high variance in size and age. This presents a problem for traditional forestry practices, which were conceived primarily with “even-aged” plantation populations in mind. The shift towards management of an uneven-aged structure requires a more in-depth consideration of individual trees’ lifecycles and their effect upon long-term population dynamics. In recent years, great advances in computational and mathematical models for spatially interacting populations have been made. However, certain complications have prevented them from being utilised to their full potential for the purposes of forest management. Forest communities are not only spatially structured; the size of each tree plays a role in its ability to acquire resources for growth and survival. Existing models of population dynamics are discussed, and their extension to incorporate both size- and spatially- structured interactions is presented. The key aspects of populations’ structural development are studied. Data from both plantation and semi-natural Scots Pine stands in Scotland allow parameterisation of a stochastic individual-based model, which in turn provides insights into the behaviour of real populations, and the importance of spatial effects and heterogeneity in individuals. A partial differential equation (moment) approximation to the stochastic model is presented. While this is analytically intractable, numerical integration and heuristic analysis of the equations enable clearer identification of the drivers of population structure. Many results are concordant with existing models of both qualitative forest stand development and theoretical dynamics of spatially-structured populations, while others are specific to joint size-space structure. This deeper understanding of the population dynamics allows robust recommendations for diverse uneven-aged stand management objectives to be made. Approaches to accelerating the transformation of plantation stands towards a “natural” state (using two key operations: thinning – removal of trees, and planting) are investigated. Finally, approaches to so-called “continuous cover forestry” – the practice of maintaining a quasi-natural state while also obtaining economic value from a forest – are also considered. In both cases, the model’s simplicity enables clearer conclusions than would be possible using other approaches.

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40

Corrales, Duque Carolina. "Population Genetic Structure of Black Grouse (Tetrao tetrix) : From a Large to a Fine Scale Perspective." Doctoral thesis, Uppsala universitet, Institutionen för ekologi och genetik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-150117.

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Black grouse (Tetrao tetrix) is a bird species with a lek mating system found in the Palearctic boreal taiga. It is assumed that it has a continuous distribution along Scandinavia and Siberia, whereas in Central Europe it has declined during the last decades. The primary objective of this thesis was to obtain a deeper understanding of the history, systematic classification and the genetic structure of black grouse on different geographical scales using microsatellites and control region mtDNA sequences (CR). I determined how much the mating system, habitat fragmentation and historical population processes have influenced the partitioning of genetic diversity in this species. Phylogeographical results are consistent with a demographic population expansion, and the patterns of postglacial dispersal suggest that a glacial refugium was located somewhere in central Asia, and from there black grouse spread out to Europe following the retreat of glacial ice sheets. I suggest that the two European black grouse subspecies, T. t. Tetrix and T. t. britannicus correspond to only one subspecies: T. t. tetrix, and that this lineage has diverged from T.t. viridanus, a subspecies found in Kazakhstan. The British population is significantly divergent from the remaining Eurasian samples for microsatellites but it is not for mtDNA. Therefore, they should regard as a separate Management Unit and not as a subspecies. Furthermore, British black grouse occur in three independent genetic units, corresponding to Wales, northern England/southern Scotland and northern Scotland. There was also genetic structure within Sweden. Habitat fragmentation is the main cause of population genetic structure in southern Swedish black grouse. In contrast, low levels of genetic differentiation and high connectivity were found in northern Sweden due to female-biased dispersal. On a finer geographical scale, I found genetic differences between leks due to a mixture of related and unrelated individuals within leks. However, mean relatedness values hardly differed from zero. Some leks were similar to one another and I interpret this as a result of variation in local reproductive success and philopatry. These factors would cause genetic structuring but this by itself would not reveal that kin selection is operating within black grouse leks.

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41

Puncher, Gregory Neils <1980&gt. "Assessment of the population structure and temporal changes in spatial dynamics and genetic characteristics of the Atlantic bluefin tuna under a fishery independent framework." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/7227/4/Puncher_Gregory_Neils_tesi.pdf.

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As a large and long-lived species with high economic value, restricted spawning areas and short spawning periods, the Atlantic bluefin tuna (BFT; Thunnus thynnus) is particularly susceptible to over-exploitation. Although BFT have been targeted by fisheries in the Mediterranean Sea for thousands of years, it has only been in these last decades that the exploitation rate has reached far beyond sustainable levels. An understanding of the population structure, spatial dynamics, exploitation rates and the environmental variables that affect BFT is crucial for the conservation of the species. The aims of this PhD project were 1) to assess the accuracy of larval identification methods, 2) determine the genetic structure of modern BFT populations, 3) assess the self-recruitment rate in the Gulf of Mexico and Mediterranean spawning areas, 4) estimate the immigration rate of BFT to feeding aggregations from the various spawning areas, and 5) develop tools capable of investigating the temporal stability of population structuring in the Mediterranean Sea. Several weaknesses in modern morphology-based taxonomy including demographic decline of expert taxonomists, flawed identification keys, reluctance of the taxonomic community to embrace advances in digital communications and a general scarcity of modern user-friendly materials are reviewed. Barcoding of scombrid larvae revealed important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. Using a Genotyping-by-Sequencing a panel of 95 SNPs was developed and used to characterize the population structuring of BFT and composition of adult feeding aggregations. Using novel molecular techniques, DNA was extracted from bluefin tuna vertebrae excavated from late iron age, ancient roman settlements Byzantine-era Constantinople and a 20th century collection. A second panel of 96 SNPs was developed to genotype historical and modern samples in order to elucidate changes in population structuring and allele frequencies of loci associated with selective traits.

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42

Puncher, Gregory Neils <1980&gt. "Assessment of the population structure and temporal changes in spatial dynamics and genetic characteristics of the Atlantic bluefin tuna under a fishery independent framework." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/7227/.

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Анотація:

As a large and long-lived species with high economic value, restricted spawning areas and short spawning periods, the Atlantic bluefin tuna (BFT; Thunnus thynnus) is particularly susceptible to over-exploitation. Although BFT have been targeted by fisheries in the Mediterranean Sea for thousands of years, it has only been in these last decades that the exploitation rate has reached far beyond sustainable levels. An understanding of the population structure, spatial dynamics, exploitation rates and the environmental variables that affect BFT is crucial for the conservation of the species. The aims of this PhD project were 1) to assess the accuracy of larval identification methods, 2) determine the genetic structure of modern BFT populations, 3) assess the self-recruitment rate in the Gulf of Mexico and Mediterranean spawning areas, 4) estimate the immigration rate of BFT to feeding aggregations from the various spawning areas, and 5) develop tools capable of investigating the temporal stability of population structuring in the Mediterranean Sea. Several weaknesses in modern morphology-based taxonomy including demographic decline of expert taxonomists, flawed identification keys, reluctance of the taxonomic community to embrace advances in digital communications and a general scarcity of modern user-friendly materials are reviewed. Barcoding of scombrid larvae revealed important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. Using a Genotyping-by-Sequencing a panel of 95 SNPs was developed and used to characterize the population structuring of BFT and composition of adult feeding aggregations. Using novel molecular techniques, DNA was extracted from bluefin tuna vertebrae excavated from late iron age, ancient roman settlements Byzantine-era Constantinople and a 20th century collection. A second panel of 96 SNPs was developed to genotype historical and modern samples in order to elucidate changes in population structuring and allele frequencies of loci associated with selective traits.

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43

Hannunen, Salla. "Trivial movements and redistribution of polyphagous insect herbivores in heterogeneous vegetation /." Uppsala : Swedish Univ. of Agricultural Sciences, Dept. of Entomology, 2003. http://epsilon.slu.se/a376.pdf.

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44

Banda, Jo Ann. "Temporal and Spatial Genetic Consistency of Walleye (Sander vitreus) Spawning Groups." University of Toledo / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1321498533.

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45

Andersson, Bea Angelica. "Analysis of Selection and Genetic Drift in a Dioecious Plant : Spatial Genetic Structure and Selection in Phenotypic Traits in a Young Island Population of Silene dioica." Thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-96275.

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Selection and genetic drift are often competing forces in shaping genetic structure in populations. Genetic drift will often effectively cancel out the effect of selection when population sizes are small, such as in colonizing island populations. On a small island in the Skeppsvik Archipelago in northern Sweden, a newly founded population of Silene dioica has been monitored since it first established around 1993. Though inhabiting an area of merely 173 m2, the population has been shown to exhibit a genetically differentiated patch structure where closely related individuals are tightly grouped, distanced from other family groups. In this study, the effect of selection was evaluated as compared to that of genetic drift. Variation in phenotypic traits in flowers, leaves and stalks were compared to that of neutral markers, in the form of PST and FST measures, to assess a measure of what proportion of differentiation among patches in phenotypic traits could not be attributed to genetic drift. Males and females were analysed separately to obtain measures of sex specific selection. Signs of divergent and stabilizing selection were found in several traits in both males and females despite the small spatial scale and short time since colonization. Further analysis is needed to assess explanations for trait divergence among patches and direction of selection.

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46

Sjolund, M. Jennifer. "Interactions between natural and anthropogenic impacts on the genetic diversity and population genetic structure of European beech forests." Thesis, University of Stirling, 2014. http://hdl.handle.net/1893/21657.

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Анотація:

The accurate assessment of forest persistence under environmental change is dependent on the fundamental understanding of the genetic consequences of human intervention and its comparison to that of natural processes, as declines in genetic diversity and changes in its structuring can compromise the adaptive ability of a population. The European beech, Fagus sylvatica, has experienced prolonged human impact over its 14 million ha range with contemporary forests harbouring high ecological, economic, and cultural value. Historical traditional management practices, such as coppicing and pollarding, have impacted a large portion of Europe’s forests. This form of management encouraged vegetative regeneration, prolonging the longevity of individual trees. In several cases, the structure and function of managed trees and their associated ecosystems were significantly altered. Specifically, coppiced beech forests in Europe displayed significantly larger extents of spatial genetic structuring compared to their natural counterparts, revealing a change in the genetic composition of the population due to decades of management. Humans have also aided in the dispersal of beech within and outside of its natural range. In Great Britain, the putative native range retained signals of past colonisation dynamics. However, these signals were obscured by the wide-spread translocation of the species throughout the country. Evidence of post-glacial colonisation dynamics can be found in Sweden as well. In contrast to Britain, the structure of this natural leading range edge displays a gradual reduction in population size where isolation was found to have acted as an effective barrier to gene flow reducing the genetic diversity of populations.

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47

Clostio, Rachel Wallace. "Use of environmental variables to infer gene flow and population structure in the gopher tortoise (Gopherus polyphemus) and predict the seroprevalence of an emerging infectious disease." ScholarWorks@UNO, 2010. http://scholarworks.uno.edu/td/1230.

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Understanding worldwide declines in reptiles due to factors such as habitat loss and emerging infectious disease has become an increasingly important focus in conservation biology. Here, I use novel approaches from the field of landscape genetics to combine spatial genetic data with landscape data at both regional and local spatial scales to explore natural and anthropogenic landscape features that shape population structure and gene flow in a federally threatened reptile, Gopherus polyphemus. I also utilize approaches from the field of spatial epidemiology to examine the extent to which environmental variables can be used to predict the seroprevalence of an associated pathogen Mycoplasma agassizzi in gopher tortoise populations. Using mitochondrial data, I find evidence of a historical barrier to gene flow that appears to coincide with the Apalachicola River. I also discover low genetic diversity and evidence of population bottlenecks in the western portion of the range. My evaluation at the regional scale shows that dispersal is limited by geographic distance, areas of low elevation and major roads ways. A finescale study reveals no evidence of spatial genetic structure within a 14 x 35 km area. However, soil type is significantly correlated with pairwise genetic distances between individuals, suggesting that this variable influences fine-scale population structure in the gopher tortoise. In addition to soil, high density canopy cover is an important factor impeding gene flow at the local level for females, while land cover type explains some of the genetic variance between males. Finally, temperature and precipitation appear to be important predictors of the seroprevalence of the pathogen Mycoplasma agassizii in gopher tortoises. The probability of an individual testing seropositive for exposure to this disease increased with high temperature and low precipitation values. The methods presented in this dissertation evaluate novel approaches for assessing the influence of environmental variables on population structure, dispersal and disease occurrence and could be applied in future studies of other threatened and endangered taxa.

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48

Fisco, Dana. "Reef Fish Spatial Distribution and Benthic Habitat Associations on the Southeast Florida Reef Tract." NSUWorks, 2016. http://nsuworks.nova.edu/occ_stuetd/408.

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The Florida Reef Tract (FRT) extends from the tropical Caribbean up the southeast coast of Florida into a temperate environment where tropical reef assemblages diminish with increasing latitude. This study used data from a three-year comprehensive fishery-independent survey to quantify reef fish spatial distribution along the Southeast FRT and define where the assemblage shifts from tropical to temperate. A total of 1,676 reef fish visual census samples were conducted to assess the populations on a stratified-random selection of sites of marine hardbottom habitats between the Miami River and St. Lucie inlet. Multivariate analyses were used to investigate differences in assemblages among sites. Depth (m), general habitat (reef or hardbottom), and slope (high or low) strata were examined to explain the dissimilarities between assemblages. A general trend of cold-tolerant temperate fish dominated the northern assemblages and more tropical species dominated further south. Seven reef fish assemblage biogeographic regions were determined. In shallow habitats the data clustered in three spatial regions: One south of Hillsboro inlet, one in Northern Palm Beach south of Lake Worth inlet, and one north of Lake Worth inlet. The assemblage in deep habitats mainly split in close proximity to the Bahamas Fracture Zone south of Lake Worth Inlet. The presence of reef habitat aided in splitting the southern assemblage regions from the northern all-hardbottom assemblage regions in both the shallow and deep habitats. Substrate relief was significantly correlated with the differences in the northernmost deep assemblages but did not appear to affect the remainder of the shallow and deep assemblages. This bioregional study creates a baseline assessment of reef fish assemblages of the Southeast FRT for future analyses.

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Chumacero, de Schawe Claudia [Verfasser], Teja [Akademischer Betreuer] Tscharntke, Michael [Akademischer Betreuer] Kessler, Isabell [Akademischer Betreuer] Hensen, and Dirk [Akademischer Betreuer] Gansert. "Pollination ecology and spatial genetic population structure of wild and cultivated species of cacao (Theobroma) in Bolivia / Claudia Chumacero de Schawe. Gutachter: Michael Kessler ; Isabell Hensen ; Dirk Gansert. Betreuer: Teja Tscharntke." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2014. http://d-nb.info/1048734498/34.

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50

Leger, Elsa. "Structure de la communauté d'hôtes et évolution de la spécialisation chez la tique Ixodes ricinus." Thesis, Montpellier 1, 2013. http://www.theses.fr/2013MON13512.

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Le degré de spécialisation d'hôte des parasites peut considérablement modifier la nature des interactions interspécifiques. Lorsque les parasites sont également vecteurs, leur capacité d'adaptation et leur réponse aux changements dans la communauté d'hôtes aura des conséquences importantes sur la dynamique de leurs populations, mais aussi sur les microparasites qu'ils transmettent. Une première étape pour mieux appréhender l'importance de ce phénomène sur l'écologie et l'évolution des systèmes vectoriels est d'étudier la divergence génétique associée à l'hôte. Nous avons utilisé cette approche dans le système hôte-vecteur-pathogène impliquant la tique européenne Ixodes ricinus, ses différents hôtes vertébrés et les bactéries responsables de la maladie de Lyme (Borrelia burgdorferi sl). Ce travail a notamment consisté à tester si les communautés les plus anciennes montraient des divergences associées à l'hôte plus importantes que celles récemment colonisées. Nous avons combiné des échantillonnages de terrain sur un transect européen (comprenant la distribution historique d'I. ricinus et des zones nouvellement colonisées) et, des analyses moléculaires basés sur 14 marqueurs microsatellites (dont 9 nouvellement développés). Comme un obstacle majeur pour aborder la question de la spécificité d'hôte dans le système I. ricinus, ainsi que chez d'autres vecteurs, est de déterminer l'utilisation des hôtes, nous avons également testé expérimentalement les biais rencontrés lors de la détection moléculaire de l'hôte. Nos résultats révèlent un schéma complexe de l'adaptation des tiques à travers l'Europe ; la spécialisation d'hôte peut évoluer, mais l'âge de la communauté ne semble pas être un facteur décisif. Plus généralement, les résultats de cette thèse soulignent que l'écologie des vecteurs en eux-mêmes (et pas seulement les interactions hôtes-pathogènes) doit être considérée avec attention si on veut améliorer notre compréhension de ces systèmes
The degree of host specialization in parasites can greatly modify the nature of interspecific interactions. When parasites are also vectors, their ability to adapt to new hosts and their response to changes in the host community will have important consequences for both their population dynamics and evolution, but may also cascade down to the microparasites they transmit. A first step to better apprehend the importance of this phenomenon for the evolution and ecology of vector-borne disease systems is to study patterns of host-associated genetic divergence across diverse vector populations. We used this approach in the host-vector-pathogen system involving the European tick Ixodes ricinus, its various vertebrate hosts and the bacteria responsible for Lyme disease Borrelia burgdorferi sl. We predicted that longer established interactions would show stronger patterns of host-associated divergence than more recently established ones. We tested this prediction by combining field samples from a European-wide transect (including both historical and newly colonized zones) and molecular analyses based on 14 microsatellite markers (9 newly developed). As a major obstacle for tackling the question of host associations in the I. ricinus system is determining local host use, we also experimentally tested for biases in molecular host detection. Our results reveal a complex pattern of tick adaptation across the European landscape; host specialization does evolve, but not in a predictable way in relation to the evolutionary age of the interaction. More generally, the results of this thesis highlight that vector ecology (and not just host-pathogen interactions) require careful consideration, if we are to improve our understanding of these systems

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