We present an investigation into the design of an evolutionary mechanism for multiagent protocol constraint optimisation. Starting with a review of common population based mechanisms we discuss the properties of the mechanisms used by these search methods. We derive a novel algorithm for optimisation of vectors of real numbers and empirically validate the efficacy of the design by comparing against well known results from the literature. We discuss the application of an optimiser to a novel problem and remark upon the relevance of the no free lunch theorem. We show the relative performance of the optimiser is strong and publish details of a new best result for the Keane optimisation problem. We apply the final algorithm to the multi-agent protocol optimisation problem and show the design process was successful.

The major histocompatibility complex (MHC) is one of the most variable regions in the vertebrate genome. Many genes within the MHC play important roles in the development of an immune response, including the response to pathogens, by presenting pathogen fragments to T cells. Pathogen-mediated balancing selection is thought to be important in maintaining the high levels of allelic variation at these loci, though the precise mechanism remains unclear. The number of studies of MHC diversity in non-model organisms has increased dramatically in recent years as genotype data have become cheaper and easier to generate; however, key limitations in many such studies remain a lack of high quality MHC genotypes and associated phenotype data. Many studies focus on a single MHC locus, assuming that one locus will represent the full range of variation within each MHC haplotype. Alternatively, the products of different loci may co-amplify, preventing locus-specific genotypes and hence heterozygosity being accurately determined. Non-model systems are also often limited by small sample sizes and limited recording of associated host and pathogen measures, which, combined with high levels of allelic variation at MHC loci, can limit statistical power. Finally, few MHC studies control for the general effect of relatedness in explaining host traits before testing for MHC effects. With so many methodological impediments, it is challenging to identify robust associations between MHC variation and host phenotypes, such as parasite burden or fitness, and to draw conclusions about the mechanisms underpinning the maintenance of diversity at MHC loci. In this thesis, I address these problems by developing a SNP-based haplotyping system for a population of unmanaged Soay sheep (Ovis aries) on Hirta, St. Kilda, for which data is available on pedigree, phenotypic traits and fitness and its components over a 30- year study period. The ovine MHC consists of four classes of loci, within which loci are tightly clustered and show reduced recombination rates compared to the genome average. Although the mammalian MHC is usually highly variable, one would expect that the number of haplotypes within an MHC class in an island population of sheep with no immigration to be limited. The class IIa region of the ovine MHC includes the classical class II loci which are typically thought to be involved in the presentation of peptides derived from extracellular pathogens, including gastrointestinal helminths, in sheep and other mammals. In chapters 2 to 4, I describe the characterisation of class IIa haplotypic diversity in the Soay sheep using direct Sanger sequencing of PCR amplified fragments, which, in combination with cloning, revealed eight distinct haplotypes. With this knowledge of haplotypic diversity, and genotypes for a sample of Soay sheep typed on the Ovine Infinium HD chip (approximately 600K SNPs), I developed a panel of 13 SNPs which could be used to impute the class IIa haplotypes. This panel was genotyped by KASP (Kompetitive Allele Specific PCR) in 6034 samples and used to impute the class IIa haplotypes. After quality control measures, class IIa haplotypes were successfully imputed for 5349 individuals. Evidence of balancing selection was identified using the Ewens-Watterson test at different life history stages and within the standing population each year between 1985 and 2012, showing that allele frequencies were more even than would be expected under neutrality. However, there was no evidence of deviation from Hardy-Weinberg equilibrium identified at different life stages or in the standing population in any year. In chapter 5, I investigate associations between the MHC class IIa haplotypes and individual-level data on host phenotypes - body weight, plasma immunoglobulin levels (measured as anti-Teladorsagia circumcincta third larval stage IgA, IgE and IgG) and strongyle faecal egg counts (FEC). Associations were tested within mixed effects models which were used to account for repeated measures and control for fixed effects known to affect the response variables, as well as within an animal model framework to account for relatedness between individuals. Haplotype heterozygosity was unrelated to any of the traits investigated, suggesting a general heterozygote advantage is unlikely to be operating within the Soay sheep. Six of the eight class IIa haplotypes were associated with multiple traits in different age-sex classes, although many of these associations were removed after inclusion within animal models. The evidence of balancing selection and associations between class IIa haplotypes and phenotypes related to health offers a promising glimpse into the evolutionary mechanisms which may be operating to maintain diversity within this region.

Polyploidy, or whole genome duplication (WGD), is a fundamental evolutionary mechanism for diverse organisms including many plants and some animals. Duplicate genes from WGD are a major source of expression and functional diversity. However, the biological and evolutionary mechanisms for gene expression changes within and between species following WGD are poorly understood. Using genome-wide gene expression microarrays and high-throughput sequencing technology, I studied the genetic and evolutionary mechanisms for gene expression changes in synthetic and natural allopolyploids that are derived from hybridization between closely related species. To investigate evolutionary fate of duplicate genes, I tested how duplicate genes respond to developmental and environmental changes within species and how ancient duplicate genes contribute to gene expression diversity in resynthesized allopolyploids. We found that expression divergence between gene duplicates was significantly higher in response to environmental stress than to developmental process. Furthermore, duplicate genes related to external stresses showed higher expression divergence between two closely related species and in resynthesized and natural allotetraploids than single-copy genes. A slow rate of expression divergence of duplicate genes during development may offer dosage-dependent selective advantage, whereas a high rate of expression divergence between gene duplicates in response to external changes may enhance adaptation. To investigate molecular mechanisms of expression diversity among allopolyploids, I analyzed high-throughput sequencing data of small RNAs in allopolyploids and their progenitors. Small interfering RNAs (siRNAs) induce epigenetic modification and gene silencing of repeats, while microRNAs (miRNAs) and trans-acting siRNAs (ta-siRNAs) induce expression modulation of protein coding genes. Our data showed that siRNA populations in progenitors were highly maintained in allopolyploids, and alteration of miRNA abundance in allopolyploids was significantly correlated with expression changes of miRNA target genes. These results suggest that stable inheritance of parental siRNAs in allopolyploids helps maintain genome stability in response to genome duplication, whereas expression diversity of miRNAs leads to interspecies variation in gene expression, growth, and development. Results from these research objectives show that genome-wide analysis of high throughput gene expression and small RNAs provides new insights into molecular and evolutionary mechanisms for gene expression diversity and phenotypic variation between closely related species and in the new allopolyploids. / text

Orientador: Vera Nisaka Solferini / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-06T20:52:47Z (GMT). No. of bitstreams: 1 Alcantara_Suzana_M.pdf: 3488910 bytes, checksum: ea2df0c2f9926f7db5e7ad46a5df0d26 (MD5) Previous issue date: 2006 / Resumo: Populações espacialmente estruturadas tendem a apresentar alta diferenciação genética e forte evidência de processos micro-evolutivos. Indivíduos de Brugmansia suaveolens (Solanaceae) são restritos a manchas populacionais. Neste trabalho, a diversidade genética de nove populações de B. suaveolens foi estimada através de isoenzimas (capítulo 1). Nossos resultados demonstram alta variabilidade e estruturação genética entre as populações. O comportamento do polinizador e a dispersão hidrocórica parecem determinar a estruturação intrapopulacional. Existem evidências de que efeitos estocásticos (i.e.: fundação e migração) afetam o padrão de diferenciação interpopulacional. A maioria dos resultados pode ser esperada sob dinâmica de estabelecimento de metapopulações. Tais populações são bastante susceptíveis à diferenciação de caracteres quantitativos, seja devido à evolução fenotípica neutra (causada por deriva) ou ação de seleção (adaptação local). Para avaliar o papel da deriva e da seleção nessa diferenciação, a variação genética de caracteres pode ser comparada à variação neutra estimada por marcadores moleculares. Quatro caracteres foram avaliados em quatro das populações de B. suaveolens estudadas (capítulo 2), três deles relacionados à defesa química contra herbívoros (concentração de alcalóides). Nossos resultados mostram uma diferenciação genética ca. de três a quatro vezes maior que a estimada por marcadores neutros para três dos caracteres, embora essa diferença não seja significativa. A exceção ocorre para a razão de indução de alcalóides, que mostra sinais de seleção estabilizadora (ausência de diferenciação interpopulacional), contrariando o padrão esperado pela teoria / Abstract: Populations patchily distributed tend to show high genetic structure and strong micro-evolutionary process evidences. Brugmansia suaveolens (Solanaceae) individuals are restrict to population patches. In this work, the genetic diversity of nine B. suaveolens populations was estimate by means of allozyme electrophoresis (chapter 1). Our results indicate high variability and genetic structure among populations. The pollinator behaviour and the hydrochoric dispersal seem determine the intrapopulation structure. There are signals that stochastic effects (i.e.: migration and foundation) affect the differentiation among populations. The most of genetic patterns found can be created by a metapopulational establishment. These populations are very susceptible to the quantitative traits differentiation, due to neutral phenotypic evolution (generated by drift) or selection action (local adaptation). To evaluate the relative action of drift and selection on population differentiation, the genetic variation in quantitative traits can be compared to neutral variation estimated by molecular markers. Four traits were evaluated in four of the B. suaveolens populations studied (chapter 2), and three of them were related to chemical defense against herbivores (tropane alkaloids concentrations). Our results show a genetic differentiation ca. three to four times higher than the differentiation estimated by molecular markers for three of characters analyzed, although no significant. The exception is ¿alkaloids induction¿ trait, which show stabilizing selection signals (absence of interpopulation differentiation), instead of differentiation pattern expected by theory / Mestrado / Mestre em Ecologia

Les protozoaires parasites du genre Leishmania infectent de très nombreuses espèces de mammifères à travers le Monde. Transmis par des insectes vecteurs, ces pathogènes sont endémiques dans une centaine de pays et chez l'Homme l'incidence de la maladie est estimée à environ 2 millions de nouveaux cas chaque année. Les questions qui se posent aujourd'hui sur les modalités de reproduction et d'échanges génétiques chez ces protozoaires sont multiples. Elles ont des prolongements sur l'évolution, l'adaptation à de nouveaux cycles, la virulence, l'identification spécifique, la taxonomie ou la prise en charge thérapeutique.Au cours de ce travail, nous avons d'abord eu pour objectif d'aborder ces questions par une analyse génétique globale de toutes les espèces de Leishmania d'Eurasie et d'Afrique par une approche de type MLSA (MultiLocus Sequence Analysis) à partir d'un jeu de plus de 220 souches provenant de 43 pays. Nous avons ensuite essayé de comprendre en participant à l'analyse de données isoenzymatiques de plus de 2200 souches de Leishmania viscérotropes quelle pouvait être la structuration de ce groupe controversé. Enfin, à partir de données sur un foyer très restreint de l'espèce anthoponotique Leishmania tropica, nous avons contribué à l'analyse des données de caractérisation isoenzymatique de cette population et à l'étude des possibles cycles de transmission.Nos résultats mettent en évidence un certain nombre de points importants. Ils montrent d'abord que les différentes espèces de Leishmania présentes en Afrique et en Eurasie se répartissent en sept groupes distincts, recouvrant partiellement les dix espèces définies jusqu'ici sur des critères essentiellement biochimiques. Le système multilocus que nous avons développé s'avère plus résolutif que celui basé sur les isoenzymes. La mise en place d'un schéma MLST pour l'identification des souches pourrait être une contribution significative à la prise en charge thérapeutique des Leishmanioses de l'Ancien Monde. D'un point de vue taxonomique et épidémiologique, les trois espèces viscérotropes séparées jusqu'ici (L. infantum, L. donovani et L. archibaldi) apparaissent former un continuum génétique (complexe d'espèces). Nos analyses des données isoenzymatiques élargie à 2200 souches vont dans le même sens.Nos résultats montrent également que les sept loci génomiques étudiés par MLSA présentent une congruence phylogénétique remarquable. Ceci est en défaveur d'éventuels échanges génétiques et de recombinaisons entre les différentes espèces, contrairement à ce qui était supposé jusqu'ici. Potentiellement fréquente, l'hybridation inter-spécifique ne contribuerait pourtant pas à l'évolution des génotypes et serait un évènement transitoire, instable, incapable de se fixer dans les génomes. Il sera cependant sans doute indispensable d'explorer de façon exhaustive différents modèles avant d'en tirer des conclusions définitives.Enfin l'étude des corrélations entre structuration génétique et distance géographique révèle à la fois la focalisation de très nombreux génotypes mais également une dispersion très forte de certains autres, sans qu'on puisse proposer pour l'instant d'hypothèse robuste pour rendre compte de ces différences. Dans le même sens, notre analyse de données isoenzymatiques de souches de L. tropica provenant du même micro-foyer palestinien semble montrer une hétérogénéité intra-spécifique qui pourrait reposer malgré la proximité géographique sur des cycles parasitaires différenciés. / Parasitic protozoa of the Leishmania genus infect many mammal species throughout the world. Transmitted by insect vectors, these pathogens are endemic in a hundred countries. In humans, the incidence of the disease is estimated at about 2 million new cases each year. Today, multiple issues arise on the modes of reproduction and genetic exchanges among these protozoa. They have implications on evolution, adaptation to new cycles, virulence, specific identification, taxonomy or therapeutic management.In this work, we first aimed at addressing these issues through a comprehensive genetic analysis of all Leishmania species from Eurasia and Africa, using a MLSA (MultiLocus Sequence Analysis)-based approach, from a dataset of more than 220 strains from 43 countries. We then tried to understand the structuration of this controversial group by participating in the isozyme data analysis of more than 2200 strains of viscerotropic Leishmania. Finally, using data from a very small focus of the anthoponotic species Leishmania tropica, we contributed to the analysis of isozyme characterization of this population and to the study of possible transmission cycles.Our results highlight a number of important points. They first show that the different Leishmania species found in Africa and Eurasia are divided into seven distinct groups, partially overlapping the ten species identified so far mainly on biochemical criteria. The multilocus system we developed is more resolutive than that based on isozymes. Implementing a MLST scheme for strain identification could contribute significantly to the therapeutic management of leishmaniases in the Old World. From taxonomic and epidemiological points of view, three viscerotropic species which were separated so far (L. infantum, L. archibaldi, L. donovani) appear to form a genetic continuum (species complex). Our analyzes of isozyme data extended to 2200 strains are in line with this conclusion. Our results also show a remarkable phylogenetic congruence of the seven genomic loci studied by MLSA. This does not support potential genetic exchanges and recombinations between different species, contrary to what was assumed so far. Potentially frequent, inter-specific hybridization would not contribute to the evolution of genotypes and would be a transient and unstable event, unable to settle in genomes. However, it will probably be necessary to explore different models exhaustively before drawing definitive conclusions.Finally, the study of correlations between geographic distance and genetic structuration revealed the focus of many genotypes but also a very high dispersion of some others, even if no convincing hypothesis can be made to explain such differences. In the same way, our analysis of isozyme data of L. tropica strains from the same Palestinian micro-focus seems to show an intra-specific heterogeneity which could be due to differentiated parasitic cycles, despite the geographical proximity.