Digitized by Kansas Correctional Industries

Digitized by Kansas Correctional Industries

In this thesis I have investigated variation in the effective population size (Ne) between species, and the impact that this population genetics parameter has on molecular evolution. In Chapter 1 I review literature in order to outline our present understanding of variation in Ne, both between species and within a genome. In Chapter 2 I determine whether island species have lower effective population sizes than their mainland counterparts. I found that island species did not differ substantially from mainland species in terms of molecular evolution, despite their considerably smaller ranges. Chapter 3 examines the role of life history and demographic traits in shaping molecular evolution in mammals. Using mitochondrial DNA, I found significant correlations with species range for both genetic diversity (pS) and the efficiency of selection (pN/pS). Both latitude and body mass are also predictive of pS. However, these relationships are surprisingly weak. Additionally, no trait was predictive of nuclear molecular evolution. In Chapter 4 I determine whether there is adaptive evolution in animal mitochondrial DNA using McDonald-Kreitman style tests. While mitochondrial evolution is dominated by deleterious mutations, mitochondria also experience adaptive evolution, such that 26% of all nonsynonymous mutations are fixed by adaptive evolution. I also found evidence to suggest that the rate of adaptive evolution is correlated to Ne. In Chapter 5 I explore the relationship between pN/pS and pS, two variables that are expected to depend on Ne. I quantified the relationship between pS and pN/pS, after controlling for the statistical nonindependence between the two, to show that as πS doubles, πN/πS is reduced by 34%. I also investigated whether the slope of the regression between these variables is predicted by the shape parameter of the distribution of fitness effects. In Chapter 6 I give a general overview of my research, and bring together the key findings of this thesis.

Orientador: Roberto André Kraenkel / Banca: André M. de Roos / Banca: Marcus A.M. de Aguiar / Resumo: Predação intraguilda é um tipo de interação muito comum entre as espécies e pode influenciar fortemente na composição das comunidades ecológicas. Ela ocorre quando dois consumidores que compartilham de um mesmo recurso, e portanto competem, também apresentam comportamento predatório entre si. O consumidor que preda o seu competidor é frequentemente chamado de predador intraguilda, enquanto aquele que é predado é conhecido como presa intraguilda. Nesse trabalho nós investigamos alguns aspectos teóricos sobre esse tipo de interação. Primeiramente analisamos um experimento com ácaros predadores que foi realizado para testas as predições da teoria sobre padrões de exclusão em um gradiente de produtividade. Embora esse experimento foi cuidadosamente projetado para testar afirmações da teoria, seus resultados não concordam com ela. Utilizando um modelo bem simples para predação intraguilda que serve como uma representação daquele sistema, nós mostramos que: se levarmos em conta a dinâmica durante os transientes, e não apenas os resultados no equilíbrio, em que a teoria usual se baseia, e considerarmos que quando uma população atinge níveis muito baixos corresponde a uma extinção na realidade, os resultados experimentais concordam com a teoria. Em seguida nós estudamos questões que dizem respeito a influência dos diferentes estágios de vida dos indivíduos para a dinâmica da predação intraguilda. Nós introduzimos um modelo com estrutura de estágio em ambos os consumidores e consideramos a predação ocorrendo apenas dos adultos do predador intraguilda sobre os juvenis da presa intraguilda. Tem-se acreditado que essa interação dependente de estágio pode ter grandes efeitos sobre a dinâmica, uma vez que a pressão predatória sobre a presa intraguilda é reduzida... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Intraguild predation is a widespread interaction between species and can strongly influence communities composition. It occurs when two consumers which share a common resource, and hence compete, also engage into predation. The consumer which can prey on its competitor is often referred to as the intraguild predator while the other is called intraguild prey. In this work we investigate some theoretical aspects about these interactions. First we analyse an experiment with predatory mites which was carried to test patterns of exclusion along a productivity gradient, predicted by theory. Although this experiment was carefully designed to test the theoretical assertions, their results do not agree with theory. Through a very simple model for intraguild predation which serves as a representation of that system, we show that: if the short-term dynamics is taken into account rather than only equilibrium states, in which the usual theory is based, and we consider that populations that attain levels very close to zero are extinct, experimental results meet theory. Then we study questions concerning the influence of different life stages of individuals on the dynamics of intraguild predation. We introduce a model with stage structure in both consumers and consider predation occurring only from adults of the intraguild predator on juveniles of the intraguild prey. This stage dependent interaction was believed t ohave great effects on the dynamics, once predation pressure on the intraguild prey is reduced, and has been proposed as one feature that could promote coexistence. We check the outcomes of the system along a productivity gradient and show that stage structure do not induce great qualitative changes on the dynamics and the more likely resulting dynamics continues being the extinction of one of the consumers... (Complete abstract click electronic access below) / Mestre

The way malaria parasites are transmitted in space will have an influence on their genetic relationships. It can be expected that parasites collected within close geographic distances of each other would be more closely related than those across large geographic distances. Further to this, because malaria transmission is focal and heterogeneous in space, then the genetic relatedness between malaria parasites in these foci of malaria transmission would be greater within tightly clustered regions. Thus, using the level of genetic relatedness of these parasites would reveal how they are transmitted not only within these foci but at different geographic settings. This knowledge would offer insight on how malaria control methods can be effectively disseminated. In field settings malaria infections are polyclonal and each of the clones represented within these infections occur at different proportions. With the aid of genetic markers such as single nucleotide polymorphisms (SNPs) or microsatellites, parasite clonal genotypes can be identified. In this study, the genetic markers of choice are SNPs. Using a method that can quantify these SNPs representing the different clones occurring at different proportions in an isolate, then each of the clonal genotypes can be determined. Microsatellites were also used as additional markers in the study. In this thesis, 1.Genetic markers (SNPs) across the P. falciparum genome were identified (Chapter 3); 2. PyrosequencingTM was validated as a technique that would enable the identification of each genetically distinct clone represented in an infection by assigning proportions to the SNPs representing each genetically distinct clone and enabling the identification of parasite clonal genotypes in every isolate analysed. This was validated using laboratory prepared clone mixtures of P. falciparum. In addition; the progeny from a cross derived from genetically characterised 3D7 and HB3 isolates was analysed in preparation for the analysis of the field isolates (Chapter 4). , 4. In Chapter 5, field isolates were tested and clonal genotypes identified using both SNPs and microsatellites. A detailed population genetic analysis was also performed and finally in Chapter 6, evidence for correlation between the genetic relationships of these parasites and geographic distance was investigated. The results from field isolates summarised in this thesis were from analysis of 54 isolates; 7 samples collected from Cameroon, 13 from Kenya and 34 from Mali. The data consists of 13 SNPs analysed by PyrosequencingTM and 8 microsatellites. 84 clonal genotypes were identified by both genetic markers from the analysed isolates. Analysis of both SNPs and microsatellites revealed that microsatellites were more informative than the SNPs based on the observed allelic richness and heterozygosity (genetic diversity) across all loci analysed. The overall FST value was 0.061 using SNPs and 0.043 by microsatellites analysis. These values were low but consistent with what is typically observed in African P falciparum populations. Finally, analyses of the combined data set revealed that no statistically significant levels of spatial autocorrelation existed within the studied parasite populations. However, there was evidence of within host mixed parasite infections exhibiting a high level of genetic relatedness compared to between host infecting clones.

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La radiothérapie utilise les radiations dans le but d’éradiquer les cellules cancéreuses, principalement par la génération de cassures double-brin de l’ADN. Un des effets secondaires de la radiothérapie est l’émergence de seconds cancers, préférentiellement en bordure du volume traité, où des cellules normales reçoivent un niveau de dose non létal. Ces seconds sarcomes se développent principalement après une période de latence de 3 à 20 ans. Nous avons déterminé la distribution des dommages à l’ADN (CSB et CDB) dans le champ d’irradiation et en bordure de celui-ci, après différentes conditions d’irradiations. Nous avons évalué les dommages à l’ADN et l’induction de sénescence après un traitement fractionné. La détection des foyers XRCC1 et 53BP1 par immunofluorescence a été utilisé comme marqueurs des CSB et CDB respectivement. Enfin, la sénescence a été évaluée par la mesure de l’activité de l’enzyme SA-beta-galactosidase. Nous avons également développé un modèle théorique d’évolution cellulaire, avec pour objectif le suivi des cellules après l’action d’un traitement géno-toxique, tel que la radiothérapie ou la chimiothérapie. Les caractéristiques principales de cycle cellulaire, d’endommagement et de réparation de l’ADN, et de la diffusion chimique ont été incluses. Le modèle d’évolution cellulaire est basé sur la théorie des chaines de Markov. Deux applications du modèle sont présentées (survie cellulaire et effet bystander). / Radiotherapy uses ionizing radiations in order to eradicate cancer cells mainly through the generation of DNA double-strand breaks. A side effect of radiotherapy is the emergence of second cancer, preferentially at the border of the treated volume, where normal cells receive some non-lethal leaking radiations. These second cancers are mainly sarcomas and develop with a latency of 3 to 20 years. We have determine the distribution of DNA damage (SSBs and DSBs) both in-and at the border of the irradiation field following various conditions of irradiation. We also investigated DNA damages and induction of senescence after multi-session of treatment. Fluorescent detection of 53BP1 and XRCC1 foci was used as a marker of DSBs and SSBs respectively. Finally senescence state has been tested by measurement of SA-beta-galactosidase activity. We also developped a theoretical agent-based model of cell evolution under the action of cytotoxic treatments, such as radiotherapy or chemotherapy. The major features of cell cycle and proliferation, cell damage and repair, and chemical diffusion are included. Cell evolution is based on a discrete Markov chain. Two showcase applications of the model are then presented (survival curves and bystander effect).

Studying how new insect species originate can help us better understand the evolutionary processes that lead to the rich insect biodiversity found in the tropics. New insect species arise via the evolution of reproductive isolation, a result of the accumulation of reproductive isolating barriers. Reproductive isolating barriers can arise in the context of geographical isolation and/or can be influenced by differences in ecology. Complex evolutionary mechanisms may underlie the origins of the more than 40 species of neotropical fruit flies in the genus Blepharoneura (Diptera: Tephritidae). The immature stages of these flies are specialist feeders on plants in the Cucurbitaceae (cucurbit) family in Central and South America. Previous research focusing on six geographically widespread Blepharoneura species used 18 microsatellite loci to identify patterns of geographical and ecological divergence. While conclusions from microsatellite data are valid, these markers provide only a limited signal of genetic structure. Fine-scale, genome-wide data can reveal patterns of genetic differentiation that may help us discover and date historical and recent lineage divergence. Here I use double-digest restriction-associated DNA (ddRAD) sequencing to explore the hypothesis that geographic and ecologic barriers are restricting gene flow in one species of Blepharoneura, B. sp10. First, I use two methods to detect population structure within B. sp10 individuals. I find evidence for three distinct genetic groups characterized by geography and one genetic group defined by a difference in host plant use. Then I investigate these relationships using Mantel tests and pairwise spatial-genetic plots, which reveal distinct biogeographical genetic patterns. Finally, I infer the evolutionary history of B. sp10 using approximate Bayesian computation and find that the timing of divergence between flies collected from the Amazon Basin and those collected from the Guiana Shield coincides with the late Pleistocene, between 24,412 and 83,000 years ago. Connecting these results to historical climate data from the Late Pleistocene may help explain evolutionary processes that contributed to the patterns of genetic diversity that we see in Blepharoneura. This research provides a framework for investigating the biogeographic and evolutionary history of the more than 50 species in the Blephaorneura genus, a step towards understanding the complexity of insect diversity in the tropics.

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