The genealogy of a random sample of a population of organisms can be represented as a rooted binary tree. Population dynamics determine a distribution over sample genealogies. For large populations of constant size and in the absence of selection effects, the coalescent process of Kingman determines a suitable distribution. Neuhauser and Krone gave a stochastic model generalising the Kingman coalescent in a natural way to include the effects of selection. The model of Neuhauser and Krone determines a distribution over a class of graphs of randomly variable vertex number, known as ancestral selection graphs. Because vertices have associated scalar ages, realisations of the ancestral selection graph process have randomly variable dimensions. A Markov chain Monte Carlo method is used to simulate the posterior distribution for population parameters of interest. The state of the Markov chain Monte Carlo is a random graph, with random dimension and equilibrium distribution equal to the posterior distribution. The aim of the project is to determine if the data is informative of the selection parameter by fitting the model to synthetic data. / Foundation for Research Science and Technology Top Achiever Doctoral Scolarship

Orientadores: Vera Nisaka Solferini, John Wakeley / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-07T07:06:17Z (GMT). No. of bitstreams: 1 Jesus_FlaviaFuchsde_D.pdf: 1710104 bytes, checksum: 93b6ea526e59cb2c39bdd80b1e9207ba (MD5) Previous issue date: 2006 / Resumo: A estrutura populacional é um dos principais fatores moldando os padrões de variabilidade genética no tempo e no espaço. Devido às flutuações climáticas que ocorreram durante o período Quaternário, muitas espécies podem ter sofrido redução e fragmentação populacional, ficando restritas a "refúgios" durante períodos glaciais e se expandindo novamente durante os interglaciais. Isto tem sido utilizado para explicar alguns padrões encontrados nas espécies atualmente. O presente trabalho consistiu no desenvolvimento e estudo de modelos para auxiliar na compreensão das conseqüências genéticas de mudanças cíclicas na estruturação e tamanho populacionais, como as que teriam ocorrido ao longo das flutuações climáticas do Quaternário. A redução populacional é capaz de causar redução do tamanho efetivo populacional, do tempo médio de coalescência e da variabilidade genética, ao passo que um aumento na subdivisão populacional pode ter o efeito oposto. Para investigar estes efeitos opostos, foram estudados dois modelos, ambos com alternância de duas fases correspondendo aos períodos glaciais e interglaciais. Em ambos os modelos permitiram-se mudanças na estrutura populacional, além de mudanças no tamanho populacional, de uma maneira cíclica. No primeiro modelo, fases totalmente panmíticas alternaram-se com fases totalmente estruturadas. A partir deste modelo, obteve-se uma expressão para a esperança do tempo de coalescência de duas seqüências e, a partir desta, uma expressão para a esperança do número de sítios polimórficos. Tanto o aumento do número de demes quanto da duração das fases estrutura das causaram um aumento do tempo de coalescência e dos níveis de variabilidade genética. Os resultados obtidos foram comparados com os que seriam esperados para uma população panrnítica de tamanho constante. Verificou-se que a estruturação pode superar o efeito da redução populacional durante os períodos glaciais. Especificamente, o número médio de sítios polimórficos pode ser maior no modelo proposto, mesmo quando o támanho populacional é muito reduzido durante as fases estruturadas. No segundo modelo, permitiu-se subdivisão populacional de acordo com o modelo de finitas ilhas em ambas as fases, com migração. O tamanho populacional, a taxa de migração e o número de demes variaram entre as fases. Para este modelo, além de uma expressão para a o tempo médio de coalescência, obteve-se também uma expressão para a distribuição dos tempos de coalescência de duas seqüências. As distribuições observadas foram muito diferentes do que seria esperado para uma população panrnítica de tamanho constante. Um tamanho populacional reduzido durante os períodos glaciais causou descontinuidades e picos múltiplos na distribuição dos tempos de coalescência, bem como uma redução dos tempo médios. O aumento da estrutura populacional, através da redução da taxa de migração, aumentou os tempos médios e atenuou os picos da distribuição. O tempo médio de coalescência, em geral, também aumentou em decorrência de um maior número de demes durante os períodos glaciais. Os resultados encontrados ajudam na compreensão das conseqüências genéticas de ciclos glaciais e, em especial, da importância da estrutura populacional na manutenção da variabilidade genética. Além' disso, oferecem uma possível explicação para padrões genéticos observados em muitas espécies em que genealogias gênicas muito longas são econtradas, com o ancestral comum mais recente antecedendo em muito ao último período glacial / Abstract: Population structure is one of the major factors shaping the pattems of genetic variation across time and space. Due to the climatic fluctuations of the Qua terna ry, several species may have suffered population reduction and fragmentation, becoming restricted to refugia during glacial periods and expanding again during interglacials. This has been used to explain some patterns currently observed in several species. The present work consisted in the development and study of models to help understand the genetic consequences of cyclic changes in population structure and size, such as the ones that may have occurred throughout the climatic fluctuations of the Quatemary. Population reduction may cause reduction in population effective size, mean coalescence time and genetic variation; whereas an increase in population subdivision may have the opposite effect. In order to investigate these two opposite effects, two models were studied, both with two alternating phases, corresponding to the glacial and interglacial periods. Both models included changes in population structure, besides those in population size, in a cyclic manner. In the first model, completely panrnictic phases were alternated with completely structured ones. Based on this model, an expression was derived for the expectation of coalescence times of two sequences and, from this, an expression for the expectation of the number of segregating sites. Both an increase in the number of demes and in the duration of the structured phases caused an increase in coalescence times and levels of genetic variation. The results obtained were compared to what would be expected for a panrnictic population of constant size. It was verified that population structure may outhweigh the effect of population reduction during glacial periods. Specifically, the mean number of segregating sites can be greater in the proposed model, even when population size is quite reduced during the structured phases. In the second mode!, population subdivision was allowed in both phases' - according the finite island model with migration. Population size, migration rate and number of demes varied between phases. For this model, besides an expression for the mean coalescence time, an expression for the distribution of coalescence times was also obtained. The distributions observed were quite different from what would be expected for a panrnictic population of constant size. Population reduction during glacial periods caused discontinuities and multiple peaks in the distribution of coalescence times, as well as a reduction in the expected times. An increase in population structure, through reducing migration rates, increased the mean times and attenuated the peaks of the distribution. Mean coalescence times, in general, also increased with a greater number of demes during glacial periods. The results obtained help understand the genetic consequences of glacial cycles, and, especially, point to the importance of population structure for the maintenance of genetic varlation. Besides, they offer a potential explanation for the genetic pattems observed in several species, for which long gene genealogies are observed, with the most recent ancestor predating by far the last glacial period / Doutorado / Genetica Animal e Evolução / Doutor em Genetica e Biologia Molecular

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Phylogeography and molecular phylogenetics have proven remarkably useful for understanding the patterns and processes influencing historical diversification of biotic lineages at and below the species level, as well as delimiting morphologically cryptic species. In this dissertation, I used an integrative approach coupling comparative phylogeography and coalescent-based species delimitation to improve our understanding of the biogeography and species limits of Central American freshwater fishes. In Chapter 1, I conducted a literature review of the contributions of phylogeography to understanding the origins and maintenance of lower Central American biodiversity, in light of the geological and ecological setting. I highlighted emerging phylogeographic patterns, along with the need for improving regional historical biogeographical inference and conservation efforts through statistical and comparative phylogeographic studies. In Chapter 2, I compared mitochondrial phylogeographic patterns among three species of livebearing fishes (Poeciliidae) codistributed in the lower Nicaraguan depression and proximate uplands. I found evidence for mixed spatial and temporal divergences, indicating phylogeographic “pseudocongruence” suggesting that multiple evolutionary responses to historical processes have shaped population structuring of regional freshwater biota, possibly linked to recent community assembly and/or the effects of ecological differences among species on their responses to late Cenozoic environmental events. In Chapter 3, I used coalescent-based species tree and species delimitation analyses of a multilocus dataset to delimit species and infer their evolutionary relationships in the Poecilia sphenops species complex (Poeciliidae), a widespread but morphologically conserved group of fishes. Results indicated that diversity is underestimated and overestimated in different clades by c. ±15% (including candidate species); that lineages diversified since the Miocene; and that some evidence exists for a more probable role of hybridization, rather than incomplete lineage sorting, in shaping observed gene tree discordances. Last, in Chapter 4, I used a comparative phylogeographical analysis of eight codistributed species/genera of freshwater fishes to test for shared evolutionary responses predicted by four drainage-based hypotheses of Neotropical fish diversification. Integrating phylogeographic analyses with paleodistribution modeling revealed incongruent genetic structuring among lineages despite overlapping ancestral Pleistocene distributions, suggesting multiple routes to community assembly. Hypotheses tests using the latest approximate Bayesian computation model averaging methods also supported one pulse of diversification in two lineages diverged in the San Carlos River, but multiple divergences of three lineages across the Sixaola River basin, Costa Rica, correlated to Neogene sea level events and continental shelf width. Results supported complex biogeographical patterns illustrating how species responses to historical drainage-controlling processes have influenced Neotropical fish diversification.

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Understanding the transmission dynamics of infectious diseases is important to well-informed public health policy, responsive infection control and individual patient management. The on-going revolution in whole-genome sequencing provides unprecedented resolution for detecting evidence of recent transmission and characterising population-level transmission dynamics. In this thesis, I develop and apply evolutionary approaches to investigating transmission, focusing on three globally important pathogens. Hepatitis C virus (HCV) is a major cause of liver disease affecting 150 million people and killing 350,000 annually. I conducted a meta-analysis of twentieth-century HCV epidemics, finding that the age of the epidemic can be predicted by genetic diversity. Using the coalescent, I fitted classic susceptible-infected (SI), susceptible-infected-susceptible (SIS) and susceptible-infected-recovered (SIR) epidemiological models. Most epidemics showed signatures of SI dynamics, but three, from Argentina, Hong Kong and Thailand, revealed complex SIR dynamics. Norovirus is the leading viral cause of diarrhoea, estimated to cost the NHS around £115 million annually. I analysed whole norovirus genomes via a stochastic transmission model, finding that up to 86% of hospital infection was attributable to transmission from another patient in the hospital. In contrast, the rate of new introductions to hospital by infected patients was extremely low (<0.0001%), underlining the importance of ward management during outbreaks. Campylobacter is the most commonly identified cause of bacterial gastroenteritis worldwide. I developed a zoonotic transmission model based on phylogeography approaches to test whether three strains previously associated with multiple host species were in fact aggregates of strongly host-restricted sub-strains, or genuine generalists. Members of the same strain isolated from different host species were often more closely related than those isolated from the same host species. I estimated 419, 389 and 31 zoonotic transmissions in ST-21, ST-45 and ST-828 respectively, strongly supporting the hypothesis that these strains are adapted to a generalist lifestyle.

The subject of this thesis is the study of certain stochastic models arising in Population Genetics. The study of biological evolution naturally motivates the construction and use of sometimes sophisticated mathematical models. We contribute to the study of the so-called Lambda models. Our work is divided into two parts. In Part I, we study non-spatial models, introduced in 1999. Although there is a very rich literature concerning the description of genetic diversity thanks to the genealogies arising in these models, we obtain new results by considering the dynamics of the full population. We also contribute by presenting the first Bayesian method that allows us to reconstruct the genealogies generated by these models from data. In Part II, we study a recent extension of these models to the spatial setting. In particular, we prove a non trivial result concerning the geographical dispersal of a new mutant under this model.

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Section Restricti is one of the last sections of the genus Aspergillus that hasn't been revised in the modern taxonomic era. All species are osmophilic, have simple morphology and they are mainly important because of the food, feed and seed spoilage, some of them also have negative influence to the indoor air. The section consists of seven species according to the last taxonomic revision from 2008 based only on molecular data. It currently consists of six asexual and one homothalic species. 126 isolates from the section coming from four continents were studied in this thesis, including ex-type strains. Revision of the section was carried out combining molecular phylogenetic analysis and conventional taxonomic methods. Modern methods of species delimitation based on multispecies coalescent model were used for the phylogenetic reconstruction. From the conventional methods analysis of morphology (macro- and micromorphology including scanning electron microscopy) and physiology (ability of growing in osmotic gradient and several different temperatures) was performed. Apart from the seven known species, eight new undescribed species were discovered. Majority of the new species belongs to the Aspergillus penicillioides species complex. Key words: Aspergillus restrictus, osmophilic fungi, species...

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