Dissertations / Theses: 'Genetic diversity and divergence'

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Dhami, Kirandeep K. "AMONG-LOCUS HETEROGENEITY IN GENETIC DIVERSITY AND DIVERGENCE IN TWO PAIRS OF DUCK SPECIES (GENUS: ANAS)." Wright State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=wright1357230023.

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Ferrer, i. Admetlla Anna. "Human genetic diversity in genes related to host-pathogen interactions." Doctoral thesis, Universitat Pompeu Fabra, 2009. http://hdl.handle.net/10803/7163.

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La tesi que teniu a les mans recull quatre treballs amb un objectiu comú; determinar si els patògens (virus, bacteris, paràsits.) han exercit pressions selectives sobre els genomes dels seus hostes (com per exemple els humans).
Sabent que la detecció de l'empremta de la selecció permet identificar aquelles regions del genoma que han estat rellevants al llarg de l'evolució d'una espècie, ja que a nivell local és la variació funcional qui acaba essent objecte de la selecció, ens hem disposat a estudiar els possibles senyals de selecció en gens relacionats amb la interacció hoste-patògen. En concret, hem analitzat gens que codifiquen per: a) components del sistema immunitari innat i, b) enzims de glicosilació, la majoria dels quals s'inclouen en quatre de les principals rutes biosintètiques de glicans, en diferents poblacions humanes.
Com a conclusió principal; ambdós conjunts de gens mostren clars senyals de selecció. A més hem vist que segons el context biològic on és troben certs gens és veuen més afectats per l'acció de la selecció natural.
The present thesis includes four studies with a common objective: determining whether pathogens (virus, bacteria, parasites.) have exerted selective pressures on the genome of their hosts (for example, humans).
Detecting signatures of positive selection is a useful tool to identify functionally relevant genomic regions since selection locally shapes the functional variation. Based on this premise, we have studied the possible signatures of selection in genes related to host-pathogen interactions. Specifically, we have analyzed those genes encoding: a) components of the innate immunity response; and ii) glycosylation enzymes most of them involved in four major glycan biosynthesis pathways, in different human populations.
The main conclusion obtained from these studies is that both studied gene categories show clear signatures of selection. Moreover, we have determined that according to their biological context certain genes are more prone to the action of selection.

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Redondo, Mariana Letícia Costa. "Caracterização molecular por AFLP (Amplified Fragment Length Polymorphism) de acessos de pinhão manso (Jatropha curcas L.)." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-03102011-094124/.

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O pinhão-manso (Jatropha curcas L.) é uma planta versátil e com diversos usos potenciais em especial para produção de biodiesel. O óleo obtido de suas sementes é seu produto mais rentável e atualmente desperta grande interesse econômico em diversos setores. A caracterização molecular e a avaliação do potencial reprodutivo dos acessos de pinhão-manso são aspectos ainda pouco abordados no Brasil, sendo necessária a caracterização de acessos brasileiros e suas potencialidades. Os objetivos do presente trabalho foram analisar a diversidade genética e a divergência genética em acessos comerciais de pinhão-manso, coletados no estado de São Paulo (Alvinlândia, Lins, Itatinga e Jales), Minas Gerais (Janaúba) e Mato Grosso do Sul (Dourados). Primeiramente, foram comparadas as técnicas de RAPD (Random Amplified Polymorphic DNA), RAPD-RFLP (Restrinction Fragment Length Polymorphism a partir do RAPD) e AFLP (Amplified Fragment Length Polymorphism), quanto à potencialidade de detectar polimorfismos dentro dos acessos e entre os acessos. Posteriormente, os acessos foram caracterizados através de AFLP. Além disso, este trabalho visou detectar se há diferença nas estruturas e no desenvolvimento floral e na taxa de viabilidade polínica dos acessos de São Paulo (Alvinlândia), Minas Gerais e Mato Grosso do Sul. Nessa parte do estudo, foram analisadas e identificadas as estruturas dos órgãos florais e do grão de pólen através das técnicas de microscopia de luz, eletrônica de varredura e transmissão. Na comparação entre as técnicas moleculares, apenas AFLP permitiu a detecção de polimorfismos, com base em um acesso escolhido para os testes (Alvinlândia, SP). As análises de todos acessos através de AFLP mostraram considerável polimorfismo, que foi refletido nas estimativas de diversidade genética de Nei e Índice de Shannon. Na análise de agrupamento, as amostras de cada acesso foram agrupadas coerentemente. Os acessos de Dourados e de Itatinga formaram um grupo separado, apresentando cerca de 76% de similaridade com o segundo grupo (Alvinlândia, Jales, Lins, Janaúba). Dentro deste último, os acessos de São Paulo ficaram agrupados (com cerca de 84% de similaridade), enquanto que Janaúba mostrou-se separado, com 82% de similaridade genética. Estes resultados indicam que os acessos de São Paulo provavelmente tenham origem a partir de Janaúba. No entanto, Itatinga provavelmente tenha origem a partir de Dourados. Quanto à morfologia floral, não foi observada nenhuma diferença a nível microscópico na formação e nas estruturas dos órgãos florais. Quando comparada a viabilidade polínica entre os dois acessos coletados em campo (Minas Gerais e Mato Grosso do Sul), notou-se que há diferença significativa na taxa de viabilidade, mesmo os valores sendo muito próximos (Mato Grosso do Sul - 81,91% e Minas Gerais - 77,20%), mostra que tanto os acessos de Minas Gerais como os de Mato Grosso do Sul podem ser utilizados como parentais masculinos em programas de melhoramento genético. A divergência genética moderada e a baixa variabilidade morfológica sugerem que coletas de materiais em poucos locais poderiam representar a diversidade genética da espécie. Estudos mais aprofundados, empregando técnicas como de microssatélites e mais acessos, são 11 necessários para o conhecimento da diversidade e estrutura genética do pinhão-manso no Brasil
Physic nut (Jatropha curcas L) is a very versatile plant with several potential uses especially for the production of biodiesel. The oil obtained from its seeds is the most profitable product of this specie and it is currently attracting great interest in various economic sectors. Molecular characterization and evaluation of reproductive potential of the accessions of pysic nut have still little attention in Brazil, it still need the characterization of Brazilian accessions and its potenciality. The ains of this study were: to analyze the genetic diversity and genetic divergence in commercial accessions of physic nut, from the States of São Paulo (Alvinlândia, Lins, Jales and Itatinga), Minas Gerais (Janaúba)and Mato Grosso do Sul (Dourados). Firstly we compared the RAPD (Random Amplified Polymorphic DNA) RAPD-RFLP (Fragment Length Polymorphism Restriction from RAPD) and AFLP (Amplified Fragment Length Polymprphism) regarding the potencial to detect polymorphism within the accessions and among accessions. Subsequently, the accessions were characterized by AFLP. Moreover this work aimed to detect whether there are differenced on flower structures and development and the rate of pollen viability on the accessions of São Paulo (Alvinlândia), Minas Gerias and Mato Grosso do Sul. On this part of the study were analysed and identified the structures of the floral organs and pollen grain through the techniques of, light microscopy, scanning electron and transmission microscopy. Comparing the molecular techniques, only AFLP allowed the detection of polymorphisms based on the accession chosen for testing (Alvinlândia, SP). Analyses of all accesses by AFLP showed considerable polymorphism, wich was reflected in estimates of genetic diversity index of Nei and Shannon. In cluster analysis, samples of each accessions were grouped consistently. The accessions of Dourados and Itatinga formed a separated group, with approximately 76% similarity with the second group (Alvinlândia, Jales, Lins, Janaúba). Within the last, accessions of São Paulo werte grouped (about 84% similarity), while Janaúba showed p separately, with 82% of genetic similarity. These results indicates that the accessions of São Paulo probably originates from Janaúba. However Itatinga probably originates from Dourados. As floral morphology, we observed no difference at microscope level on the formation and on the structures of floral organs. When compared the pollen grain viability between the two accessions collected in the field (Minas Gerais and Mato Grosso do Sul), it was noted that the viability rated were significantly different, even though the values being very close (Mato Grosso do Sul Minas Gerais 81,91% - 77,20%), shows that both the accessions of Minas Gerais as the Mato Grosso do Sul can be used as male parental in breeding programs. The moderate and low genetic divergence suggests that morphological variability collections of materials in a few locations could represent the genetis diversity of the species. Further studies employing techniques such as microsatellite and more accessions are required for an understanding of diversity and genetic structure of physic nut in Brazil

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Souza, Ueric José Borges de. "Variabilidade genética em espécies de plantas do cerrado: uma avaliação cienciométrica e meta-analítica." Universidade Federal de Goiás, 2014. http://repositorio.bc.ufg.br/tede/handle/tede/6507.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
The Cerrado biome of Brazil originally occupied approximately 2 million km2 of the country. It is formed by a heterogeneous mosaic of distinct habitats and has the richest flora of the savanas of the world, with high diversity at level of genera and families. It is also currently classified as a priority for conservation because of its rich biodiversity and simultaneous high level on threat due to the destruction of natural habitats resulting from anthropogenic activities. The advent of molecular biology techniques has allowed direct access to the genetic variability of species and populations and made it possible to infer the genetic variability within and among populations, increasing the interest in studying genetic diversity and structure in plant species population of the Cerrado biome. It was conducted here an exhaustive survey of scientific platforms such as the Web of Science, Scopus, Scielo and Google Scholar, to carry out an analysis of published papers evaluating the genetic variability within and among populations in plant species from the Cerrado biome, and to quantify and describe aspects of scientific production in the field of population genetics to plant species from the Cerrado using a scientometric approach, and using a meta-analytic approach to evaluate genetic variability, it was collected some of the genetic parameters estimated in the studies (observed (HO) and expected (HE) heterozygosities and the F statistics of Wright (FIS; FST or analogs)) to test the effect of this genetic parameters in some life history and ecological traits of the species and in methodological characteristics of the article. It was obtained 176 publications from 45 journals through the period of 1999-2012 and the number of studies published has increased significantly through this period. The journal “Genetics and Molecular Research” published the highest number of papers. Ninety-six species from 32 plant families were studied, with highest numbers from the family Fabaceae. Although the species comprised a wide sample of plants with different characteristics, trees, shrubs and herbs were the main life forms and “Mata de galeria”, “cerrado” and “cerradão” were the main fitofisionomies studied. The molecular markers used included microsatellites, cpDNA, isoenzymes, RAPDs, AFLPs and ISSRs and the Microsatellites were the most popular marker used and also show the highest mean value from the genetic variability within populations when compared across studies. It was observed that population genetics parameters molecular derived from molecular markers are closely associated with some life history traits and ecological traits of the species and with methodological characteristics of the article. The analyses allows a better understanding of the current knowledge on plant population genetics in Cerrado biome and the association with the population genetics parameters and some ecological, life history and methodological traits has considerable importance and may be useful to guide future research programs in this system with potential to produce information with important implications in evolutionary biology and ecology as well as in conservation biology
O bioma Cerrado ocupa aproximadamente 2 milhões km2 do Brasil. É formado por um mosaico heterogêneo de tipos de vegetação e tem a mais rica flora entre as savanas do mundo, com alta diversidade em nível de gêneros e famílias. Atualmente tem sido classificado como prioridade em programas de conservação devido à sua rica biodiversidade e perda de habitats naturais resultantes das atividades antropogênicas. Com o advento de técnicas moleculares, tornou-se possível o acesso direto da variabilidade genética das espécies e do modo como essa variabilidade genética se encontra distribuida dentro e entre populações, aumentando assim o interesse em estudar a diversidade genética e estrutura populacional de espécies de plantas do bioma Cerrado. Foi conduzida uma busca usando as bases de dados “Web of Science”, “Scopus”, “Scielo” e “Google Scholar” com o objetivo de realizar uma análise dos artigos publicados que avaliaram a variabilidade genética dentro e entre populações de espécies de plantas do bioma Cerrado, de modo a quantificar e descrever aspectos da produção científica na área de genética de populacões para espécies de plantas do Cerrado utilizando uma abordagem cienciométrica, e utilizando uma abordagem meta-analítica foi coletado alguns dos parâmetros genéticos estimados nos estudos (heterozigosidade esperada (HE) e observada (HO) e as estatísticas F de Wright (FIS (coeficiente de endogamia); FST ou análogos)) para testar o efeito destes parâmetros genéticos em caracteristicas ecológicas e de história de vida das espécies, bem como para características metodológicas extraídas dos artigos. A busca na base de dados resultou em um total de 176 publicações de 45 periódicos durante o período de 1999-2012 e o número de estudos publicados tem aumentado significativamente durante este período. A revista Genetics and Molecular Research apresentou o maior número de artigos publicados. Noventa e seis espécies, envolvendo 32 famílias botânicas foram estudadas, sendo Fabaceae representada pelo maior número de espécies. Diferentes características entre as espécies estudadas foi observado, sendo árvores, arbusto e ervas as principais forma de vida e mata de galeria, cerrado e cerradão os principais tipos fitofisionômicos das espécies. Diferentes tipos de marcadores moleculares, incluindo microssatélites, cpDNA, isoenzimas, RAPDs, AFLPs e ISSRs foram utilizados, sendo os microssatélites o marcador mais frequentemente usado, e também o com o maior valor médio para os parâmetros de variabilidade genética dentro de populações quando comparados entre os estudos. Foi observado que os parâmetros estimados nos estudos de genética de populações obtidos via marcadores moleculares estão relacionados com características ecológicas e de história de vida das espécies e com características metodologicas das publicações. A análise permitiu uma melhor compreensão atual sobre a genética de populações de plantas do bioma Cerrado e a associação encontrada entre parâmetros genético-populacionais e diferentes características das espécies tem importância no sentido de orientar pesquisas futuras, com potencial para produzir informações com implicações importantes para ecologia, biologia evolutiva e biologia da conservação.

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Carvalho, Tiago Loureiro de 1987. "Tandem repeat variation in human and great ape populations and its impact on gene expression divergence." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/383060.

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Genetic variation in humans and the great apes has been amply explored using a wide variety of markers, among them tandem repeats (TRs). Because of the nature of TRs, highly variable in length due to its high mutation rate, they are an important source of genetic variation, and thus especially informative in fields such as population and conservation genetics. Particularly, they are still often used to illuminate natural populations complex evolutionary histories and structure. TR variation is also associated with several pathological conditions, and hypothesized to have an important role in the evolution of gene regulation. In this work a recently developed TR genotyping algorithm was applied on human and nonhuman great apes whole-genome sequencing data. The analysis of the TR variation indicate that this information is useful to describe fine scale population variation, and hints at a substantial contribution of TRs to gene expression divergence during great apes evolution.
La variación genética en los seres humanos y grandes simios ha sido ampliamente explorada usando una gran variedad de marcadores, entre ellos repeticiones en tándem (RT). Debido a la naturaleza de las RT, muy variables en longitud debido a su alta tasa de mutación, estas constituyen una importante fuente de variación genética, y por lo tanto altamente informativas en áreas como la genética de poblaciones y de la conservación. En particular, a menudo aún se utilizan para elucidar las complejas historias evolutivas de las poblaciones naturales y su estructura genética. La variación de RT está también asociada con varias enfermedads, y se cree que desempeña un papel importante en la evolución de la regulación génica. En este trabajo un algoritmo desarrollado recientemente que genotipa RT a nivel de todo el genoma, se aplicó sobre datos de secuenciación de genomas humanos y de grandes simios. El análisis de la variació de RT sugiere que esta información es útil para describir la variación en poblaciones, y alude a una aportación sustancial de las RT a la divergencia de expresión génica durante la evolución de los grandes simios.

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Montaigne, William. "Diversité génétique et adaptation au milieu chez les arbres forestiers tropicaux : étude chez le genre Virola (Myristicaceae)." Thesis, Antilles-Guyane, 2011. http://www.theses.fr/2011AGUY0480/document.

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Le maintien de ressources génétiques suffisamment larges est nécessaire pour assurer la viabilité et le potentiel évolutif des populations naturelles. Cette thèse a le principal objectif de caractériser la diversité et la variabilité génétique chez le genre Virola (Myristicaceae) pour décrire les processus évolutifs qui en sont à l'origine. Premièrement,une étude de la régénération d'un échantillonnage exhaustif de V. michelii a été menée dans une parcelle du dispositif expérimental de Paracou ayant subi une exploitation forestière de faible intensité et comparée à une parcelle témoin. La diversité génétique mesurée à partir de marqueurs AFLP (Amplified Fragment-Length Polymorphism, N=229) en zones perturbées s'est révélée être plis grande qu'en zone non-perturbées. Puis, l'adaptation locale a été étudiée à travers ces mêmes individus et certains loci (AFLP) montrent une sélection divergente pour des environnements contrastés, indiquant un signe d'adaptation. Enfin, l'étude des niveaux de divergence génétique chez trois espèces de Virola du bouclier guyanais (V. michelii, V. surinamensis et V. kwatae) montrent que deux d'entre elles (V. surinamensis et V. kwatae) montrent de fortes similarités génétiques malgré leur distribution sur des environnements contrastés. des Flux de gènes intersécifiques ont été mis en évidence chez ces deux espèces-soeurs et l'hypothèse d'une spéciation écologique est avancée. Ce travail a permis d'aborder différents processus évolutifs à l'origine de la diversité génétique actuelle chez ces espèces forestières tropicales et peut fournir une contribution pour appréhender le devenir des populations
Genetic diversity is an essential component of biodiversity. The maintenance of sufficient genetic resources is needed to ensure the adaptive potential and the viability of natural populations. In the current context of global changes, the study of adaptation in living organisms is a key task, particularly for tropical forest trees that are dominant components (in terms of biomass and as ecological drivers) of some of the most diverse ecosystems on Earth. The main objective of this thesis is to characterize genetic diversity and genetic variability to understand the evolutionary processes that act on them. This ecological-genetic study was carried out at the interspecific and intraspecific level in the Virola genus.If overall high levels of genetic diversity are a guarantee of prosperity for the future of the species, it seems essential to perform studies on the impact of environmental disturbance on genetic diversity. In the first section, the genetic consequences of regeneration dynamics were studied in an exhaustive sample of V. michelii in a low-intensity logging plot and in a control plot at the Paracou experimental site. A greater genetic diversity, measured from AFLP markers (Amplified Fragment Length Polymorphism, N = 229), was found in perturbed areas. Because studying genetic diversity within species may be useful for understanding species adaptation to environmental changes, in the second section. I studied local adaptation in a population of V. michelii on the Paracou experimental site. A genome scan approach with AFLPs (N = 229) was conducted on 77 adult individuals and 401 juveniles to identify genetic differences between populations associated to contrasting conditions for an array of environmental variables. Some loci (N = 2) were found to be subject to divergent selection, indicating adaptation to contrasting habitats.In the third section, the study of levels of genetic divergence in three Virola species of the Guiana Shield (V. michelii, V. surinamensis and V. kwatae) was investigated for nuclear and chloroplast molecular markers. V. surinamensis and V. kwatae showed strong genetic similarities despite their contrasting habitats preferences. Coalescent analyses have revealed, on one hand, a recent divergence between these two species suggesting an ecological speciation, and one the other hand that interspecific gene flow occurs between these sister-species.This work focuses on understanding evolutionary processes shaping genetic diversity and provides a useful contribution for biodiversity conservation programs

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Barry, Pierre. "Rôles des contraintes génomiques et des traits d'histoire de vie dans la spéciation : une approche de génomique comparative." Thesis, Université de Montpellier (2022-….), 2022. http://www.theses.fr/2022UMONG007.

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La spéciation est le processus évolutif au cours duquel une espèce se scinde en deux lignées qui divergent en accumulant des barrières reproductives, jusqu'à l’acquisition d’un isolement reproductif total. Durant ce processus, les lignées divergentes peuvent toujours s’échanger des gènes par hybridation, mais le flux génique est progressivement limité par l’accumulation des barrières. Il en résulte une semi-perméabilité des génomes, où certains locus s’échangent librement entre lignées et restent indifférenciés tandis que d’autres n’introgressent pas, contribuant ainsi à l’établissement de régions génomiques divergentes, appelées îlots génomiques de spéciation. L'étude de l’établissement, l’accumulation, l’érosion et la maintenance de ces barrières et de leurs effets sur la semiperméabilité des génomes de lignées en cours de spéciation permet de comprendre comment de nouvelles espèces se forment. L'avènement des techniques de séquençage à haut débit a permis de caractériser le paysage génomique de divergence chez de multiples lignées en cours de spéciation à travers l’arbre du vivant. Ces études ont permis de mesurer l’influence de l’histoire démographique et de l’architecture génomique comme déterminants majeurs du paysage génomique de divergence. Toutefois, d'autres facteurs pourraient intervenir et expliquer la diversité des trajectoires évolutives pouvant conduire ou non à la spéciation. Le principal objectif de cette thèse est d'évaluer l'impact des traits d'histoire de vie des espèces sur la spéciation. Nous avons choisi d’étudier 20 espèces de poissons marins subdivisées en deux lignées (Atlantique et Méditerranéenne), et présentant une large diversité de niveaux de divergence et de traits d’histoire de vie. Dans le premier chapitre, nous avons étudié les déterminants de la diversité génétique, substrat sur lequel s’établit la divergence lors de la séparation initiale des lignées. Nous avons observé que la longévité adulte des po issons marins est corrélée négativement à la diversité génétique, et nous avons démontré que cette relation pouvait s’expliquer par une plus grande variance du succès reproducteur chez les espèces longévives à cause de stratégies reproductives particulières aux poissons marins (forte mortalité juvénile, faible mortalité adulte et augmentation de la fécondité avec l’âge). Puis, dans un second chapitre, nous avons détecté une grande diversité d’histoires évolutives entre espèces, caractérisée par un fort gradient de divergence génétique entre lignées atlantiques et méditerranéennes. Ce gradient reflète en partie le niveau de semi-perméabilité des génomes. Les espèces à faible différentiation présentent un isolement reproductif faible, alors que les espèces les plus fortement différenciées montrent un isolement reproductif quasi-complet. Les traits d’histoire de vie des espèces expliquent en partie cette diversité de niveaux d’isolement via différents mécanismes. La durée de vie larvai re influence négativement la différenciation génétique en modulant les capacités de dispersion, l’effet de la taille du corps indique un effet négatif de l’abondance long-terme sur la divergence, et la longévité semble impacter le nombre de générations écoulées depuis la séparation ancestrale. En conclusion, les 20 espèces étudiées présentent une variabilité surprenante d’histoires évolutives au regard des similitudes de leur histoire biogéographique et leur architecture génomique. Les relations entre traits d’histoire de vie et histoire évolutive des espèces sont complexes, mais nous avons pu éclairer certaines d’entre elles en décomposant l’implication des traits dans les différentes étapes de la spéciation. L’application de l’approche de génomique comparative développée au cours de cette thèse dans d’autres zones de suture permettra d’étendre nos connaissances des déterminants du tempo et du mode de la spéciation
Speciation is the evolutionary process through which a species splits into two lineages that diverge and accumulate reproductive barriers, until complete reproductive isolation is achieved. During this process, the diverging lineages can still exchange genes by hybridisation, but gene flow is progressively restricted by the accumulation of barriers. This results in semi-permeable genomes, whereby some loci exchange freely between lineages and remain undifferentiated while others do not introgress, thus contributing to the establishment of divergent genomic regions, called genomic islands of speciation. The study of the establishment, accumulation, erosion and maintenance of these barriers and their effects on the semipermeability of the genomes of lineages undergoing speciation helps to understand how new species are formed. The advent of high-throughput sequencing techniques has made it possible to characterise the genomic landscape of divergence in multiple lineages undergoing speciation across the tree of life. These studies have shown the influence of the demographic history and genomic architecture as major determinants of the genomic landscape of divergence. However, other factors could intervene and explain the diversity of evolutionary trajectories that may or may not lead to speciation. The main objective of this thesis is to assess the impact of species' life history traits on speciation. We have chosen to study 20 marine fish species subdivided into two lineages (Atlantic and Mediterranean), and presenting a wide diversity of degrees of divergence and life history traits. These traits are thought to impact on the intensity of genetic drift, dispersal abilities and generation time of the species. In the first chapter, we studied the determinants of genetic diversity, the substrate on which divergence is built during the initial separation of lineages. We observed that adult longevity of marine fishes is negatively correlated w ith genetic diversity, and we demonstrated that this relationship could be explained by a greater variance in reproductive success in long-lived species due to reproductive strategies specific to marine fishes (high juvenile mortality, low adult mortality and increased fecundity with age). Then, in a second chapter, we discovered a great diversity of evolutionary histories between species, characterised by a strong gradient of genetic divergence between Atlantic and Mediterranean lineages. This gradient partly reflects the level of semi-permeability of the genomes. Species with low differentiation show low reproductive isolation, whereas the most highly differentiated species show almost complete reproductive isolation. Species' life history traits partly explain this diversity in isolation levels via different mechanisms. Larval duration negatively influences genetic differentiation by modulating dispersal capacities, the effect of body size indicates a negative effect of long-term abundance on divergence, while longevity seems to impact the number of generations elapsed since ancestral separation. In conclusion, the 20 species studied show a surprising variability of evolutionary histories considering the similarities of their biogeographic history and genomic architecture. The relationships between life-history traits and the evolutionary history of the species proved to be complex, but we were nevertheless able to shed light on some of them by decomposing the involvement of traits in the different stages of speciation. The application of the comparative genomics approach developed in this thesis to other suture zones will further extend our knowledge of the determinants of the tempo and mode of speciation

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Ghaleb, Wagdi. "Analyse de la diversité génétique de la réponse germinative à la température de populations de Lolium perenne L., Festuca arundinacea Schreb et Dactylis glomerata L." Thesis, Poitiers, 2019. http://www.theses.fr/2019POIT2273.

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La germination des graines est une étape importante dans le cycle biologique de la plante, car elle affecte le développement, la survie et la dynamique des populations de semis. La germination commence par l'absorption de l'eau par la graine et se termine par l'allongement de l'axe embryonnaire en dehors du tégument.Elle est influencée par des facteurs environnementaux et le patrimoine génétique de la graine. La température est l'une des factures les plus importants, car elle régule la germination de trois façons: en déterminant la capacité germinative et la vitesse de germination, en enlevant la dormance primaire et/ou secondaire, et en induisant la dormance secondaire.L'objectif de ce travail est d'analyse de la diversité génétique de la réponse germinative à la température de populations de Lolium perenne L., Festuca arundincea Schreb et Dactylis glomerata L.Dans cette étude, nous avons distingué différents types de réponses à la température, ce qui indique que de la diversité génétique existe entre les lots de chaque espèce. Ces différences dans les réponses, aux températures constantes entre 5 et 32 °C, ont été observées au niveau du pourcentage de germination maximale, de la vitesse de germination (α), lu temps de début de germination (tc) et du temps nécessaire pour attendre 95 % de germination finale (t95%). Des sélections divergentes ont été réalisées sur la capacité à germer à des températures non optimales chez des populations de Lolium perenne L. Sur une population issue de la région de Reims, il ressort un effet important de la sélection pour la capacité à germer à 10 °C qui pourrait être expliqué par la présence d'un gène majeur dominant de dormance des graines à faible température, en ségrégation au sein de la population.La comparaison des fréquences alléliques pour de nombreux marqueurs répartis sur le génome entre les individus germant et ceux ne germant pas à différentes températures a permis d'identifier de nombreux gènes potentiellement impliqués dans la capacité des individus à germer à ces températures. L'effet de ces gènes reste à être validé, par exemple par des études d'expression ou par l'étude de populations crées par sélection pour porter des allèles contrastés
Seed germination is an important step in the plant's life cycle, affecting the development, survival and dynamics of seedling populations. Germination begins with the absorption of water by the seed and ends with the elongation of the embryonic axis outside the integument.It is influenced by environmental factors and the genetic heritage of the seed. Temperature is one of the most important factors, which regulates germination in three ways: by determining germination capacity and germination rate, by removing primary and/or secondary dormancy, and by inducing secondary dormancy.The objective of this work is to analyze the genetic diversity of the germinative response to temperature of populations of Lolium perenne L, Festuca arundinacea Schreb, and Dactylis glomerata L.In this study, we distinguished different types of temperature responses, indicating that genetic diversity exists between lots of each species. In this study, we distinguished different types of responses to temperature, indicating that genetic diversity exists between lots of each species. These differences in responses, at constant temperatures between 5 and 32°C, were observed in terms of maximum germination percentage, germination rate (α), germination start time (tc) and time required to reach 95 % of final germination (t95%).Divergent selections were made on the capacity to germinate at sub-optimal temperatures in populations of Lolium perenne L. In a population from the Reims region, there is an important effect of selection for the capacity to germinate at 10 °C, which could be explained by the presence of a major dominant gene for seed dormancy at low-temperature, in segregated within the population. The comparison of allelic frequencies for many markers distributed over the genome between individuals germinating and those not germinating at different temperatures has identified many genes potentially involved in the ability of individuals to germinate at these temperatures. The effect of these genes has yet to be validated, for example by expression studies or by the study of populations created by selection to carry contrasting alleles

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Mason, Deborah J. "Genetic divergence in the C.biguttulus group (Orthoptera : Acridiae)." Thesis, Cardiff University, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.306507.

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Shields, Christopher C. "Nudibranchs of the Ross Sea, Antarctica phylogeny, diversity, and divergence /." Connect to this title online, 2009. http://etd.lib.clemson.edu/documents/1252937231/.

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Divis, P. "Population genetic structure and genomic divergence in Plasmodium knowlesi." Thesis, London School of Hygiene and Tropical Medicine (University of London), 2017. http://researchonline.lshtm.ac.uk/4398418/.

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Plasmodium knowlesi infections in humans have been increasingly seen in many countries across Southeast Asia, with cases mainly concentrated in Malaysia, since a major focus of infections was first described in Malaysian Borneo over 10 years ago. Clinical presentations show a wide spectrum of illness from mild to fatal, with the possible occurrence of asymptomatic infections. Two monkey species have been identified as the chief reservoir hosts; long-tailed macaque (Macaca fascicularis) and pig-tailed macaque (M. nemestrina). In order to explore the transmission of P. knowlesi infections, it is important to study the population genetic structure of this parasite. To address this, a microsatellite genotyping toolkit consisting of 10 loci specific for P. knowlesi was developed and validated. Using these highly polymorphic markers, analysis of more than 500 P. knowlesi infections from human and wild macaque hosts across Malaysian Borneo and humans of peninsular Malaysia showed remarkable population genetic structure. Human clinical isolates were shown to comprise highly divergent subpopulations, respectively associated with forest-dwelling long-tailed macaque (Cluster 1) and pig-tailed macaque (Cluster 2) reservoir hosts. After analysis of initial whole genome sequence data, re-assessment of population genetic structure was undertaken by microsatellite analysis of more samples from wild macaques and humans from peninsular Malaysia, showing profound geographical divergence between Borneo (sympatric Cluster 1 and Cluster 2) and mainland peninsular Malaysia (Cluster 3). The overall three major subpopulations demonstrated by microsatellite 4 analyses matched the analysis inferred by the genome-wide sequence analysis of clinical isolates. To allow further investigation of variation in genome-wide divergence between the sympatric subpopulations in Borneo, a simple laboratory kit consisting of allele-specific PCR assays was developed to distinguish the two subpopulations. This eased in identifying to which subpopulations P. knowlesi infections belonged, and subsequently generating more genome-wide sequences for comparative study. Further analyses revealed remarkable heterogeneity in the level of divergence between the sympatric subpopulation across the genome. Genomic architectures showed 20 high-divergence regions scattered in different chromosomes. These findings suggest independent adaption of parasites in different macaque hosts that persist sympatrically.

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Onions, Patrick E. W. "A fragmented field : An investigation into knowledge management diversity and divergence." Thesis, Leeds Beckett University, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.528347.

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Many domains and disciplines have claimed territory in the field, yet knowledge management remains an extraordinarily difficult field to describe. It has an enormous breadth of relevance and has been regarded as an irreconcilable collection of concepts and techniques, a vague subject that is difficult to clarify and delineate. Diversity has been seen to afflict practitioners; displaying disorganised activities, being difficult to explain, risky, diluted by rebadged technology, and theory diverging from practice. An inductive research strategy was used to study diversity and divergence. A literature review established that diversity and divergence have been observed by literature, but their causes have not been formally studied. A review of literature discussing practice found far more concern for implementation issues, and that private sector KM appeared more likely to be generic than public sector. A review of the backgrounds, trends and PEST factors found that the South African context was unique and its knowledge management should reflect that. The study of research employed a content analysis method applied to a large volume of literature. This discovered that literature has a predominantly practical focus, verified the presence of diversity in literature, and that knowledge management diversity is far broader than recognised in literature. No single model or framework comprehensively embraces all the diversity found without being impractically abstract. The study of practice compared the theoretically derived models to the solutions constructed by practice. This found the projects did not tailor their solutions to the unique environment, practitioners chose to use a small subset of theory, and there was a strong bias towards technology. A Grounded Theory Method was then applied to four large South African knowledge management initiatives. This identified twenty phenomena that influenced project direction, many of which inhibiting diversity and few having previously been considered as factors by research. It is concluded that knowledge management should be regarded as an umbrella label and that a body of knowledge approach is the most suitable path forward for both research and practice in light of the diversity and divergence.

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Quinton, Margaret. "Genetic diversity in selected populations." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0016/NQ47407.pdf.

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14

Barker, Gary L. A. "Genetic diversity in Emiliania huxleyi." Thesis, University of Bristol, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294614.

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15

Fitzcharles, Elaine M. "Genetic diversity of Antarctic fish." Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/6860.

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Correct species identification is fundamental to all areas of biology, but particularly the policy related areas of conservation and fisheries management. To enable guidelines to be developed for environmental management and conservation, such identifications need links to studies of the evolutionary history, biological factors and environmental influences driving species divergence and population dynamics for the target species. This study concerns two genera of gadiform fish, Muraenolepis and Macrourus, found in southern temperate and Antarctic waters, with a single species, Macrourus berglax, present in the North Atlantic. With similar distribution patterns to toothfish species, Dissostichus eleginoides and D. mawsoni, they are a major food source and by-catch of the toothfish fishery. Both are slow growing and long lived, with different evolutionary histories, life expectancies and strategies for reproduction. For both genera, the accuracy of morphological keys, number of described species and their distribution is under debate. This study has identified specimens to species level using both morphological and genetic techniques, redefining the range for morphological features and taxonomic keys. For Muraenolepis, this has clarified confusion over Mu. marmoratus and Mu. microps being a single species, confirmed some mis-identification from sexual dimorphism and provided genetic evidence for the recently described species Mu. evseenkoi. For Macrourus, this work has identified a new species, now named Ma. caml, and found that Ma. holotrachys and Ma. berglax are genetically identical, raising the question of bipolar distribution or recent divergence. The low level of genetic variation within both species suggests a recent evolution and expansion into Antarctic waters. Similar geographic species limits imply common processes influencing divergence, with the oceanographic fronts as potential barriers. Further investigation of niche overlap and fine scale population structure are required to fully understand the processes driving speciation and provide the underlying data required for fisheries management.

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Tomaz, Adriano Cirino. "Genetic divergence and resistance of sugarcane genotypes to Diatraea saccharalis." Universidade Federal de Viçosa, 2014. http://www.locus.ufv.br/handle/123456789/7746.

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A broca-da-cana Diatraea saccharalis Fab. (Lepidoptera: Crambidae) é a principal praga da cana-de-açúcar no Brasil. No entanto, apesar da importância dessa praga, não há métodos precisos para comparação da resistência de genótipos e seleção de genótipos resistentes a serem aplicado por programas de melhoramento genético de cana-de-açúcar. Esse estudo foi conduzido para determinar um método para comparar injúria causada por broca-da-cana no colmo de genótipos de cana-de-açúcar em casa-de- vegetação, investigar características de resistência presentes na folha, superfície e interior do colmo de seis genótipos de cana-de-açúcar e a relação entre esses fatores de resistência. Adicionalmente, foi feito um estudo sobre divergência genética de genótipos de cana-de-açúcar para resistência à broca-da-cana através do uso de análises de agrupamento. A infestação de plantas individuais (não em touceiras) com sete meses de idade com 20 lagartas (3o ou 4o instar) por planta para avaliação do comprimento de galerias foi adequada para comparar a injúria entre genótipos. Os genótipos SP803280, RB928064 e RB835486 apresentaram as menores injúrias no colmo enquanto o genótipo SP891115 apresentou a maior injúria. As lagartas gastaram mais tempo para penetrar nos colmos do genótipo SP803280 em relação ao genótipo SP891115, indicando que esse genótipo apresenta alguma característica na superfície do colmo que atrasa a entrada da lagarta. As lagartas nos últimos instares apresentaram o menor ganho de massa ao se alimentarem no interior do colmo do genótipo SP813250, indicando que esse genótipo apresenta algum fator de resistência afetando o desenvolvimento da larva dentro do colmo. As análises de correlação entre os fatores de resistência indicam que o tempo gasto pelas lagartas para entrar no colmo das plantas está mais diretamente relacionado com a injúria no colmo do que a alimentação das lagartas no interior do colmo. Os genótipos RB867515 e SP891115 causaram a mais alta mortalidade de lagartas novas durante o período em que se alimentam na folha, indicando que a presença de fatores de antibiose na folha desses genótipos. As análises de agrupamento dividiram os genótipos em três grupos indicando divergência genética entre os genótipos.
The sugarcane stalk borer Diatraea saccharalis Fab. (Lepidoptera: Crambidae) is the most important pest of sugarcane in Brazil. However, despite the importance of this pest, there is a lack of efficient methods to compare the resistance of genotypes and select resistant sugarcane genotypes to be employed by sugarcane breeding programs. This study was conducted to determine a greenhouse method to compare stalk damage among sugarcane genotypes, investigate resistance factors present in the leaves, stalk surface and within the stalks of six Brazilian sugarcane cultivars and the relationship among these resistance factors. In addition, we assessed the genetic divergence of sugarcane genotypes to borer resistance by using cluster analysis. The infestation of 7- month-old single plants with 20 larvae (3rd - 4th instar) per plant for assessment of tunnel length was proved adequate to compare stalk damage among sugarcane genotypes. The genotypes SP803280, RB928064 and RB835486 had the lowest stalk damage while SP891115 had the highest damage. The larvae spent more time to enter the stalk of the genotype SP803280 compared to SP891115, indicating that this genotype has some resistance trait in stalk surface delaying the larvae entrance in the stalk. Late-stages larvae feeding in the stalk of SP813250 had the lowest weight gain indicating that this genotype present some resistance factor affecting larval development within the stalks. Correlation analysis among resistance factors indicated that the time spent by larvae to enter the stalk is more related to stalk damage than the larval feeding within the stalks. The genotypes RB867515 and SP891115 caused the highest mortality of early-stage larvae feeding on the leaves, which indicate the presence of antibiotic factors in the leaves of these genotypes. Cluster analysis divided the genotypes in three groups, indicating the genetic dissimilarity between genotypes. The results from this study may contribute in selection of resistant clones and choice of genitors for crossings in sugarcane breeding programs.

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Lavin, Patrick A. "Adaptive divergence and the evolution of trophic diversity in the threespine stickleback." Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/24837.

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Five populations of the threespine stickleback, Gasterosteous aculeatus,from the upper Cowichan River system (Vancouver Island, British Columbia) were surveyed to assess interpopulation levels of variability in trophic morphology. Phenotypic divergence is assumed to be a post-glacial event. Nine characters were scored; eight were related to feeding and the ninth character was lateral plate number. All populations surveyed were the low plate morph; however populations of Gasterosteus in lakes lacking piscivorous fish had significantly fewer lateral plates than populations in lakes with predatory fish species. Three trophic 'morphotypes' were identified, each associated with one of three lake environments. Populations inhabiting benthic dominated environments ('benthic morph') were found to possess reduced gill raker number and reduced gill raker length but increased upper jaw length relative to populations from lentic environments ('limnetic morph'). An intermediate morph may also exist and is characterized by a morphology suitable to either trophic regime. Analysis of stomach contents showed diet type (benthic or limnetic) to be significantly dependent on morph. The functional significance of differences in trophic morphology was investigated in three feeding experiments using a representative population from each morphotype. The longer jaw of the benthic and intermediate morphs allowed them to ingest a larger benthic prey than the limnetic. No behavioural component to benthic foraging success between populations was identified, although increased jaw length shortened the time spent manipulating prey. Both the intermediate and limnetic morphs were better foragers on an experimental limnetic prey than was the benthic. Head length, snout length, gill raker density and gill raker number were strongly correlated with limnetic foraging success. The quantitative genetics governing the eight trophic characters were investigated using the same three representative populations. Broad sense estimates of character heritabilities ranged from 0.132 to 0.677; all estimates were significant. Character genetic correlations were reasonably strong (0.3 ≤ |rG| ≤ 0.9), while character correlations arising through environment tended to be lower. Cluster analyses of the genetic correlation matrices defined two character suites, the first grouped measures of head shape, the second grouped measures of gill raker structure. The patterns of genetic correlations suggest the three populations are distinct races. Selection gradients for divergence between morphotype indicated that directional selection had operated hardest on head length, snout length, gill raker number, head depth and upper jaw length; hence selection has operated to modify characters related to food size. The benthic-limnetic and intermediate-limnetic morphs were separated by the greatest selection distance while the intermediate-benthic morphs were separated by the shortest selection distance. These results support the conclusion that directional selection, arising from trophic resource differences between lakes, has organized interpopulation variability for Gasterosteus within the upper Cowichan drainage. The racial distinction of each population coupled with the functional significance of some components of trophic morphology indicate that at least the benthic and limnetic morphs must be considered 'ecotypes'.
Science, Faculty of
Zoology, Department of
Graduate

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18

Paul, Richard E. L. "The genetic diversity of Plasmodium falciparum." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318788.

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Townsend, S. J. "Genetic diversity and domestication in sheep." Thesis, University of East Anglia, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368146.

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20

Williams, Louise Jane. "Recombinational mechanisms in human genetic diversity." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342483.

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Rogers, Emma Jayne. "Haplotype evolution and human genetic diversity." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342507.

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Ritz, Liliane R. "Genetic diversity in the tribe Bovini /." [S.l.] : [s.n.], 1997. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.

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Schmid, Marianne. "Genetic diversity in Swiss cattle breeds /." [S.l.] : [s.n.], 1998. http://www.stub.unibe.ch/html/haupt/datenbanken/diss/bestell.html.

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Wilder, Natalie Louise. "Correlating KSHV strain divergence with cellular genetic markers in Jewish populations." Thesis, University College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.404903.

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Fimusanmi, Julie. "Diversity and divergence : perspectives on inclusion through sport for ethnic minority young people." Thesis, Loughborough University, 2010. https://dspace.lboro.ac.uk/2134/7020.

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This thesis examines the perceived benefits of sport for ethnic minority young people in the context of social exclusion. The broad constructs of social exclusion, are examined whilst drawing together evidence of how individuals experience exclusion in contemporary Britain. Throughout reference is made specifically to a broad spectrum of ethnic minorities and the experiences they endure due to the distinctive combination of socio-economic factors and race. The claim that sport has the potential to address social exclusion through empowering individuals and creating community cohesion is examined. The link between education and exclusion is regarded as one of the key determinants with the potential to either positively or adversely affect the likelihood of ethnic minorities becoming excluded (Parekh, 2000). Therefore understanding the relationship between education and exclusion is key in examining the claim that sport can be used to address social exclusion in a group who are more likely to be excluded from both sport and education in the first place. In order to achieve the research aim a mixed method approach was utilised. By combining a flavour of grounded theory modelling, plus adopting a critical realist stance, provided an opportunity for the subject matter to be recorded and analysed in order to gain an understanding of social life and interaction. The research was carried out within the Arches School Sports Partnership in north Sheffield. By contextualising the programme, it was possible to investigate the young peoples responses and understandings of the sport within these parameters, identify and interview key stakeholders, sports deliverers and community practitioners. Additionally the views of the young people from a range of ethnic minorities were sought through a questionnaire and more detailed interviews. The results of the study illustrated the diverse range of views expressed by individuals. The ethnic minority young people revealed a greater degree of diversity in relation to hyphenated identities, which was closely linked to role or place of religion in their lives, particularly for the Muslims. All of the young people, regardless of their ethnicity, perceived exclusion as part of their lives in one form or another, which was expressed in diverse first-hand experiences, stemming from anti-social behaviour. Their perceptions of the use of sport to tackle wider social issues was the most negative response of all those interviewed. Whilst they believed there is a correlation between sport and social exclusion, and, along with other structured activities, could potentially positively affect their lives, in that if they had more to do in their spare time they would they be less susceptible to being involved in anti-social behaviour and thereby being excluded from society. The adults demonstrated a range in levels of knowledge and understanding of exclusion and how it may affect young people. However, whilst the deliverers were very positive about sport s potential use, citing a strong positive correlation between involvement in sport and improved behaviour management they believed multi-agency working and a variety of different agendas, were a potential conflict to successful outcomes from all young people. In comparison community practitioners were very knowledgeable about exclusion issues and generally positive of sport's potential use, though were keen to promote a multi-agency approach in order to achieve success, and expressed scepticism about sport being used as a purely diversionary tactic In addition to diversity within each group, there were also differences between the perceptions of understandings of young people and adults, demonstrating the degree of diversity in the research findings.

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Henry, Amanda Ann (Shaffer). "Clarkia genetic basis of sister species divergence Clarkia concinna x Clarkia breweri /." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/henry/HenryA0806.pdf.

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Terrinoni, Emanuela. "Genetic basis of phenotypic divergence between British populations of Fragaria vasca L." Thesis, University of Reading, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555835.

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The application of map-based investigations into plant genome architecture has featured the use of Ouantitative Trait loci (OTl) analysis to investigate gene function, the genetics of species divergence and for breeding purposes. To date, however, there has been comparatively little progress on the genetics underlying adaptive intra-specific variation. The present study investigates the genetic basis of phenotypic divergence between plants of wild populations of the alpine strawberry, Fragaria vesca, growing in geographically dispersed parts of the United Kingdom. A series of populations centred around Rogart, the Northern Highlands, Scotland occupy habitats seasonally dominated by bracken (Pteridium aquiiinum) and are characterised by a compact, dwarf habit. Another set of five populations in the extreme south-west of England (Padstow, Cornwall) were found in oak- beech woodland margins and are typified by a more bushy, erect habit. Morphometric analysis in a common garden experiment and genetic distance analysis established that this phenotypic variation has an underlying genetic basis. This was then tnvestlqated further using a map-based approach. An F2 progeny was created between phenotypically and genetically divergent paranetal clones from Cornwall (male parent) and the Northern Highlands (female parent). The F1 offspring were selfed to generate a mapping F2 population. Male and female linkage maps were created from this population using both AFlP and SSR markers. Both maps span seven linkage groups, corresponding to the base chromosome number of the genus Fragaria. The maps cover a genetic distance of 294.1 cM and 351 cM respectively. O'Tl, analysis was performed and a total of ten OTls were identified for six morphological traits. All traits for which a OTl was detected are leaf traits. A cluster of OTls was detected on linkage group VI of the female map, indicating that either single genes found in that genomic region have pleiotropic effects or that several linked genes contribute to each trait. The identification of a putative Scottish ecotype of Fragaria vesca has therefore established that OTl analysis is a valid tool for the study of adaptive changes at the intra-specific level.

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Cheikh, Al Bassatneh Marwan. "Diversité taxonomique, phylogénétique et fonctionnelle en région méditerranéenne : congruence ou divergence ?" Thesis, Aix-Marseille, 2019. http://www.theses.fr/2019AIXM0499.

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Les objectifs de la thèse sont d’analyser la biodiversité en région méditerranéenne européenne aux niveaux taxonomique, phylogénétique et fonctionnel et comprendre pourquoi ces différentes estimations de la biodiversité sont convergentes ou pas dans un contexte spatialisé et comment divers facteurs de l'environnement peuvent expliquer cette convergence ou son absence. Dans ce contexte, la thèse s’est d’abord focalisée sur la réalisation de nouveaux arbres phylogénétiques de la flore arborée méditerranéenne intégrant les espèces endémiques de cette région, permettant d’augmenter significativement la résolution des phylogénies en cours. Puis, à partir de cette phylogénie, il a été ensuite estimé les indices de diversité phylogénétique à différentes échelles (pays, îles, zones biogéographiques) pour les comparer à d’autres indices de la biodiversité (fonctionnelle et taxonomique) et pour étudier corrélativement l’impact de variables environnementales sur ces différents indices de biodiversité
The objectives of the thesis are to analyze biodiversity in the European Mediterranean region at the taxonomic, phylogenetic and functional levels and understand why these different estimates of biodiversity are convergent or not in a spatialized context and how various environmental factors may explain this convergence or its absence.In this context, the thesis first focused on generating new phylogenetic trees of Mediterranean trees integrating the endemic species of this region, to increase significantly the resolution of current phylogenies. Then, using these phylogenies, indices of phylogenetic diversity were estimated at different scales (country, island, biogeographic zone) and compared with other indices of biodiversity (functional and taxonomic) and to correlatively study the impact of environmental variables on these different biodiversity indices

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Gardner, Michelle. "Genetic diversity of " brain genes" across worldwide." Doctoral thesis, Universitat Pompeu Fabra, 2007. http://hdl.handle.net/10803/7169.

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El treball presentat en aquesta tesi és un estudi de la diversitat genètica en un conjunt de gens implicats en funcions neurològiques ("Gens cerebrals"). Hom ha examinat vint-i-dos gens implicats en els sistemes de neurotransmissió dopaminèrgic, serotoninèrgic i glutamatèrgic.
L'objectiu de l'estudi té dos vessants: per una banda l'anàlisi de la diversitat genètica en un conjunt de gens implicats en malaltia humana, en aquest cas en malaltia psiquiàtrica, en poblacions humanes mundials, amb la intenció d'assentar les bases per propers esforços de mapatge genètic; i per altra banda analitzar la diversitat genètica en aquest conjunt de gens per tal de descobrir evidències d'esdeveniments històrics, incloent possibles evidències de selecció.
The work presented in this thesis is a study of the genetic variation in a set of genes related to neurological function ('Brain genes'). Twenty two genes are examined, all of which are involved in either the Dopaminergic, Serotonergic or the Glutamatergic systems of neurotransmission.
The objective of the study has two aspects: on the one hand the analysis of genetic variation in a set of genes which are implicated in human disease, in this case psychiatric disease, across global human populations, towards the end of providing some new insight for gene mapping efforts, and on the other hand the study of genetic variation in this set of genes may reveal traces of the population history events undergone, including possible evidence for selection.

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Wilkinson, Samantha. "Genetic diversity and structure of livestock breeds." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/6488.

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This thesis addresses the genetic characterisation of livestock breeds, a key aspect of the long-term future breed preservation and, thus, of primary interest for animal breeders and management in the industry. First, the genetic diversity and structure of breeds were investigated. The application of individual-based population genetic approaches at characterising genetic structure was assessed using the British pig breeds. All approaches, except for Principle Component Analysis (PCA), found that the breeds were distinct genetic populations. Bayesian genotypic clustering tools agreed that breeds had little individual genetic admixture. However, inconsistent results were observed between the Bayesian methods. Primarily, BAPS detected finer genetic differentiation than other approaches, producing biologically credible genetic populations. BAPS also detected substructure in the British Meishan, consistent with prior known population information. In contrast, STRUCTURE detected substructure in the British Saddleback breed that could not wholly be explained. Further analysis of the British Saddleback revealed that the genetic subdivision did not reflect its historical origin (union of Essex pig and Wessex Saddleback) but was associated with herds. The Rainbarrow appeared to be moderately differentiated from the other herds, and relatively lower allelic diversity and higher individual inbreeding, a possible result of certain breeding strategies. The genetic structure and diversity of the British traditional chicken breeds was also characterised. The breeds were found to be highly distinctive populations with moderately high levels of within-breed genetic diversity. However, majority of the breeds had an observed heterozygote deficit. Although individuals clustered to their origin for some of the breeds, genetic subdivision of individuals was observed in some breeds. For two breeds the inferred genetic subpopulations were associated with morphological varieties, but in others they were associated with flock supplier. As with the British Saddleback breed, gene flow between flocks within the chicken breeds should be enhanced to maintain current levels of genetic diversity. Second, the thesis focused on breed identification through the assignment of individuals to breed origin. Dense genome-wide assays provide an opportunity to develop tailor-made panels for food authentication, especially for verifying traditional breed-labelled products. In European cattle breeds, the prior selection of informative markers produced higher correct individual identification than panels of randomly selected markers. Selecting breed informative markers was more powerful using delta (allele frequency difference) and Wright's FST (allele frequency variation), than PCA. However, no further gain in power of assignment was achieved by sampling in excess of 200 markers. The power of assignment and number of markers required was dependent on the levels of breed genetic distinctiveness. Use of dense genome-wide assays and marker selection was further assessed in the British pig breeds. With delta, it was found that 96 informative SNP markers were sufficient for breed differentiation, with the exception of Landrace and Welsh pair. Assignment of individuals to breed origin was high and few individuals were falsely assigned, especially for the traditional breeds. The probability that a sample of a presumed origin actually originated from that breed was high in the traditional breeds. Validation of the 96-SNP panel using independent test samples of known origin and market samples revealed a high level of breed label conformity.

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Gustafson, Steven Matt. "An analysis of diversity in genetic programming." Thesis, University of Nottingham, 2004. http://eprints.nottingham.ac.uk/10057/.

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Genetic programming is a metaheuristic search method that uses a population of variable-length computer programs and a search strategy based on biological evolution. The idea of automatic programming has long been a goal of artificial intelligence, and genetic programming presents an intuitive method for automatically evolving programs. However, this method is not without some potential drawbacks. Search using procedural representations can be complex and inefficient. In addition, variable sized solutions can become unnecessarily large and difficult to interpret. The goal of this thesis is to understand the dynamics of genetic programming that encourages efficient and effective search. Toward this goal, the research focuses on an important property of genetic programming search: the population. The population is related to many key aspects of the genetic programming algorithm. In this programme of research, diversity is used to describe and analyse populations and their effect on search. A series of empirical investigations are carried out to better understand the genetic programming algorithm. The research begins by studying the relationship between diversity and search. The effect of increased population diversity and a metaphor of search are then examined. This is followed by an investigation into the phenomenon of increased solution size and problem difficulty. The research concludes by examining the role of diverse individuals, particularly the ability of diverse individuals to affect the search process and ways of improving the genetic programming algorithm. This thesis makes the following contributions: (1) An analysis shows the complexity of the issues of diversity and the relationship between diversity and fitness, (2) The genetic programming search process is characterised by using the concept of genetic lineages and the sampling of structures and behaviours, (3) A causal model of the varied rates of solution size increase is presented, (4) A new, tunable problem demonstrates the contribution of different population members during search, and (5) An island model is proposed to improve the search by speciating dissimilar individuals into better-suited environments. Currently, genetic programming is applied to a wide range of problems under many varied contexts. From artificial intelligence to operations research, the results presented in this thesis will benefit population-based search methods, methods based on the concepts of evolution and search methods using variable-length representations.

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Clarke, Stephen James. "Genetic diversity in nativeIrish oak and ash." Thesis, Queen's University Belfast, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397902.

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Mauricio, Isabel Larguinho. "Genetic diversity in the Leishmania donovani complex." Thesis, London School of Hygiene and Tropical Medicine (University of London), 2000. http://researchonline.lshtm.ac.uk/682281/.

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The Leishmania donovani complex comprises four described species: L. donovani, L. archibaldi, L. infantum and L. chagasi. L. chagasi is the only New World species and has been considered similar to L. infantum, although some authors insist on maintenance of its independent species status. L. donovani has at least two major epidemiological subgroups whose relationships are poorly understood. In this thesis, molecular biological techniques were used to investigate the taxonomy and phylogenetic relationships within the L. donovani complex, with isoenzyme analysis (lEA) as reference technique. Random amplification of polymorphic DNA (RAPD) was used to provide anonymous genetic markers which allowed overall comparisons of genomes. Selected target genes and intergenic regions were also amplified by the polymerase chain reaction (PCR), namely the major surface protease (msp or gp63), the mini-exon and the ribosomal internal transcribed spacer (ITS). PCR products of intergenic regions between msp genes (ITG/CS and ITG/L), mini-exon and ITS were analysed by restriction fragment length polymorphism (RFLP). Phylogenies generated from each of the methods were compared with that of IEA. L. infantum and L. chagasi were found to be synonymous, whilst L. donovani was found to be more polymorphic than L. infantum and a fourth possible species in the complex, L. archibaldi, was not supported. Six genetic groups of strains were identified in the L. donovani complex, based on all DNA based analyses, which agreed with IEA typing. Pooled data from RFLP and RAPD analyses generated robust phylogenies which were congruent with ITG/CS RFLP and msp DNA sequence based phylogenies, but not with lEA phylogenies. The evolutionary history of the L. donovani complex is analysed in the light of the present results. The diverse typing methods were also evaluated and genetic markers suggested, that are applicable to classification and typing of L. donovani species and strains.

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Soto, Esteban. "Genetic and virulence diversity of Flavobacterium columnare." Master's thesis, Mississippi State : Mississippi State University, 2007. http://library.msstate.edu/etd/show.asp?etd=etd-05292007-091752.

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Palo, Jukka. "Genetic diversity and phylogeography of landlocked seals." Helsinki : University of Helsinki, 2003. http://ethesis.helsinki.fi/julkaisut/mat/ekolo/vk/palo/.

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Moody, Jonathan. "Genetic diversity in the processing and transcriptomic diversity in the targeting of microRNAs." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/25409.

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MicroRNAs are short RNA molecules that are central to the regulation of many cellular and developmental pathways. They are processed in several stages from structured precursors in the nucleus, into mature microRNAs in the cytoplasm where they direct protein complexes to regulate gene expression through, often imperfect base-pairing with target messenger RNAs. The broad aim of this project is to better understand how polymorphisms and new mutations can disrupt microRNA processing and targeting, and ultimately define their contributions to human disease. I have taken two approaches towards this. The first approach is to comprehensively identify the microRNA targets by developing and applying a novel computational pipeline to identify microRNA binding events genome-wide in RNA-RNA interaction datasets. I use this to examine the transcriptomic diversity of microRNA binding, finding microRNA binding events along the full length of protein coding transcripts and with a variety of non-coding RNAs. This reveals enrichment for non-canonical microRNA binding at promoters and intronic regions around splice sites, and identifies highly spatially clustered binding sites within transcripts that may be acting as competitive endogenous RNAs to compete for microRNAs, effectively sequestering them. Using statistical models and new cell fractionated RNA-seq data, I rank the features of microRNAs and their binding sites which contribute to the strength and specificity of their interaction to provide a better understanding of the major determinants of microRNA targeting. The second approach is to directly identify DNA sequence changes in microRNA precursors that alter processing efficiency affecting mature microRNA abundance which are routinely overlooked in the search for disease or trait associated causal variants. I have systematically screened public datasets for both rare and common polymorphisms that overlap microRNA precursors and are correlated with mature microRNA levels as measured in short RNA sequencing. I use these eQTL SNPs to examine the most important microRNA precursor regions and sequence motifs. Several of these SNPs have been observed as risk factors in cancer or other clinically relevant traits, and correlated with microRNA processing efficiency. I demonstrate that a specific DNA change which is known to be important in the development of some cancers, is located in a microRNA precursor and affects the balance of its two products, miR-146a-3p and miR-146a-5p, that can be produced from that single precursor providing new insights into the mechanisms of microRNA production and the aspects of genetic mis-regulation that result in cancer. I find further examples of common human polymorphisms that appear to affect microRNA production from their precursors, several of these variants are independently implicated in human immune disease, cancer susceptibility and associated with other complex traits. As they exhibit a molecular phenotype and immediately lead to mechanistic hypotheses of trait causality that can be tested, these variants could provide a route into the frequently intractable problem of mechanistically linking non-coding genetic variation to human phenotypes. Applying similar studies to patient DNA has revealed rare and unique DNA changes that are now candidates for causing human disease that are being subject to follow-up experimental studies. Collectively this work has started to define which sequences changes in microRNAs are likely to disrupt their function and provides a paradigm for the analysis of microRNA sequence variants in human genetic disease.

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Steury, Robert. "Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback." Thesis, University of Oregon, 2019. http://hdl.handle.net/1794/24561.

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Studying the microbiome in natural populations could improve our understanding of the biological factors that influence microbiome variation. If host genetic variation is important in microbiota assembly, then understanding genetic divergence among natural populations could be informative. Despite advances in sequencing technology, we have not yet taken full advantage of this technology in natural populations. Here we integrate genome-wide population genomic and microbiome analyses in wild threespine stickleback (Gasterosteus aculeatus) fish distributed throughout western Oregon, USA. We found that gut microbiome varied in diversity and composition more among than within wild host populations. Furthermore, this among population variation was better explained by host population genetic divergence than by environment and geography. We also identified a subset of gut microbial taxa that were most strongly sorted both across environments and across genetically divergent populations. We believe this study contributes generalizable methods and findings in host systems. This thesis includes supplemental materials.
2021-04-30

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Graham, Elaine Brigid. "Genetic diversity and crossing relationships of Lycopersicon chilense /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.

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Larsson, Pär. "The genetic composition and diversity of Francisella tularensis." Doctoral thesis, Umeå University, Clinical Microbiology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1139.

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Francisella tularensis is the causative agent of the debilitating, sometimes fatal zoonotic disease tularemia. To date, little information has been available on the genetic makeup of this pathogen, its evolution, and the genetic differences which characterize subspecific lineages. These are the main areas addressed in this thesis.

The work indicated a high degree of genetic conservation of F. tularensis, both on the sequence level as determined by sequencing and on the compositional level, determined by array-based comparative genomic hybridizations (aCGH). One striking finding was that subsp. mediasiatica was most similar to subsp. tularensis, despite their natural confinement to Central Asia and North America, respectively. All genetic Regions of Difference RD found by aCGH distinguishing lineages were had resulted from repeat-mediated excision of DNA. This was used to identify additional RDs. Such data along with a multiple locus sequence analysis suggested an evolutionary scenario for F. tularensis.

Based on genomic information, a novel typing scheme for F. tularensis was furthermore devised and evaluated. This method provided increased robustness compared to previously used methods for F. tularensis typing, while retaining a capacity for high resolution.

Finally, the genomic sequence of the highly virulent F. tularensis strain SCHU S4 was determined and analysed. Evidenced by numerous pseudogenes and disrupted metabolic pathways, the bacterium appears to be undergoing a genome reduction process whereby a large proportion of the genetic capacity gradually is lost. It is likely that F. tularensis has irreversibly has evolved into an obligate host-dependent bacterium, incapable of a free-living existence. Unexpectedly, the bacterium was found to be devoid of common virulence mechanisms such as classic toxins, or type III and IV secretion systems. Instead, the virulence of this bacterium is probably largely the result of specific and unusual mechanisms.

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Uimaniemi, L. (Leena). "Maintenance of genetic diversity in four taiga specialists." Doctoral thesis, University of Oulu, 2004. http://urn.fi/urn:isbn:9514274105.

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Abstract Genetic diversity in three taiga specialists – the Siberian tit (Parus cinctus), the Siberian jay (Perisoreus infaustus) and the Siberian flying squirrel (Pteromys volans) – was assessed by comparing DNA sequence variation across the mitochondrial control region and allele frequencies of microsatellites from samples collected from Fennoscandia and Siberia. Population sizes of these species have declined in association with fragmentation and loss of suitable forest habitat due to modern forestry practices in Fennoscandia. The red squirrel (Sciurus vulgaris) served as a reference for the flying squirrel. Genetic differentiation among species studied ranged from a panmictic population in the Siberian tit to that of the strong differentiation of populations (θST = 53%) in the flying squirrel in Finland. MtDNA and microsatellite data, together with assignment studies, showed the Siberian jay population to be significantly genetically structured and supported the existence of a metapopulation like structuring in Fennoscandia. Division of genetic variation among flying squirrel populations along the ancient shoreline of the Littorina Lymnea Sea stage of the Baltic Sea (7000 BP) and two geographically associated branches in the minimum spanning network supported a two-way colonisation history for the species. The Finnish inland appears to have been colonised from the east in association with the arrival of Norway spruce. At the same time, Coastal Finland was colonised from the south-east through the Karelian Isthmus. Gene flow of the species appeared female biased and restricted. Species exhibiting more restrictive dispersal characteristics and habitat requirements possessed stronger population genetic structure than those with opposite characteristics. Growth or contractions in population size leave characteristic signatures in mtDNA that can be studied by comparing different sequence diversity estimates among populations. I applied this method to the species studied. Significant differences in nucleotide diversities indicated restrictions in gene flow among populations in all species studied. Half of the Siberian jay populations gave a signal of population size bottleneck. All the species studied showed differences in their population genetic structures across their entire distribution ranges consistent with the multirefugia model, most likely to be attributable to differences in their ecological characteristics and Pleistocene histories.

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Larsson, Pär. "The genetic composition and diversity of Francisella tularensis /." Umeå : Umeå universitet, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1139.

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Ismail, Mohamed. "Molecular genetic diversity among natural populations of Populus." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/26273.

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Genetic diversity is a key factor in species survival, evolution, and adaptation. It also reveals species genetic structure and provides insights into how different demographic forces shape species genetic variability. Although, black cottonwood (Populus trichocarpa Torr. & Gray) is the first tree to have its genome completely sequenced; however, information regarding its natural genetic diversity and population structure is lacking. I have investigated the extent of genetic diversity within and among 38 natural populations of P. trichocarpa sampled across British Columbia using 10 nuclear (nuSSR) and 12 chloroplast microsatellite (cpSSR) markers. CpSSR represents two haplotypes, clustering as northern and southern groups; however, a Bayesian population structure analysis suggested the presence of three highly admixed groups supported by low population differentiation (low FST and RST). Monmonier’s spatial analysis suggested the presence of one genetic discontinuity dividing the studied area into northern and southern regions. These findings indicated that P. trichocarpa might have originated from two, northern and southern, glacial refugia that have experienced moderate contact through extensive gene flow. Nucleotide diversity for 10 candidate-gene loci involved in adaptive, defence, and housekeeping functions was abundant and varied across loci, with the majority showing neutral variations. Linkage disequilibrium (LD), decays rapidly to r² ≈ 0.18 within 700 base pairs (bp). Comparing the nucleotide diversity between P. trichocarpa and P. balsamifera L. to the Eurasian P. tremula L. indicated that the two North American species had lower diversity (θw range 0.002 to 0.004) than the Eurasian poplar (θw = 0.005). The estimated time of divergence between the two North American and the Eurasian species indicated that the latter was five- to six-fold older compared to the two former species. The substitution rate was lower in North American species (0.4 x 10-⁸ per year) compared to the Eurasian poplar (2 x 10-⁸). Different association genetics models produced strikingly different results after the inclusion or exclusion of population structure, highlighting the importance of proper model construction.

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May, Shoshanna. "Fitness and genetic diversity in Bufo calamita populations." Thesis, University of Sussex, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.505908.

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The aims of this DPhil were the characterisation of major histocompatibility complex class II β loci in the amphibian species Bufo calamita, determination of fitness of four Bufo calamita populations and measurement of genetic diversity at both microsatellite loci and MHC class II β loci. The genetic diversity at microsatellite loci is considered to be neutral to selection and the genetic diversity seen at MHC loci is adaptive. Fitness in the four populations was measured using the known larval fitness traits age at metamorphosis, growth rates and survival. A 114 base pair section of MHC class II loci was characterised in this study. It was shown here that the diversity at neutral microsatellite markers was negatively correlated with adaptive MHC class II variation. No correlation was found between microsatellite HE and the larval fitness traits growth rate, survival and age at metamorphosis. However, MHC class II diversity was found to be associated with survival, and individuals that were heterozygous at both MHC loci had a significantly higher chance of survival than individuals homozygous at one or both of the two loci. A separate part of this DPhil project was the population genetics of six Irish Bufo calamita populations. The genetic structure was investigated using nine polymorphic microsatellite markers. It was found that all populations had similar and moderate levels of genetic diversity, comparable with those on the coast of north-west England. Toad populations were substantially differentiated, implying little migration between sites within historical times. Phylogenetics and estimates of divergence times supported the hypothesis that populations on the north coast of Dingle separated from those around Castlemaine Harbour many thousands of years ago, and are not recent introductions.

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Craven, Kelly D. "COEVOLUTION AND GENETIC DIVERSITY IN GRASS-ENDOPHYTE SYMBIOSES." UKnowledge, 2003. http://uknowledge.uky.edu/gradschool_diss/431.

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Symbioses between cool-season grasses (Subfamily Pooideae) and endophytic fungi in the genera Epichlo and Neotyphodium straddle a continuum of interactions from antagonistic to highly mutualistic. Although these two genera of endophytes are closely related, Neotyphodium endophytes are strictly seed-transmitted and provide many physiological and defensive benefits to their hosts, while Epichlo spp. have an obligately sexual contagious stage wherein host inflorescences are replaced by fungal sexual structures (stromata), effectively sterilizing the plant. Between these two extremes of interactions are Epichlo spp. with a mixed strategy, where some grass tillers are sterilized while others develop normally and yield healthy endophyte-infected seeds. These symbioses offer a unique opportunity to dissect evolutionary mechanisms that may drive movement along this continuum. The research presented characterizes distinct hybridization processes in endophytes and grasses that result in the generation of astounding genetic diversity for the symbiosis. Interspecific hybridization via hyphal anatomosis is a common feature of Neotyphodium endophytes, and may promote mutualism by combining suites of defensive alkaloid genes and ameliorating the adverse evolutionary effects of an asexual lifestyle. My results demonstrate that several genetically distinct hybrid endophytes infect grass species in tribe Poeae. Further, I show that a highly mutualistic asexual endophyte infecting tall fescue (=Festuca arundinaceum Schreb.), Neotyphodium coenophialum, also infects two closely related and interfertile relatives of this host. My findings suggest that this seed-borne endophyte may have been introgressed into these grasses through sexual grass hybridization events. These findings highlight interspecific hybridization as a means of generating tremendous genetic variability in both endophytes and their hosts, thus magnifying the adaptive evolutionary potential of these symbioses. Further, I establish a phylogenetic framework for grasses naturally harboring Epichlo and Neotyphodium endophytes. I show that patterns of genetic divergence among grass lineages are emulated by those of their fungal symbionts. These results suggest that endophytes have co-evolved with grasses in subfamily Pooideae, and may have played a critical role in the evolutionary success and radiation of this group of grasses.

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Cooper, Fiona Mary Phillips. "Geographic distribution and genetic diversity of black poplar." Thesis, University of Nottingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246878.

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Massawe, Festo J. "Phenotypic and genetic diversity in Bambara groundnut landraces." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342048.

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Ward-Rainey, Naomi Louise. "Genetic diversity in members of the order Planctomycetales." Thesis, University of Warwick, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390026.

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Savage, Anne Margaret. "Genetic diversity and photosynthetic characteristics of zooxanthellae (Symbiodinium)." Thesis, University of York, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369298.

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49

Harris, Kathryn Ann. "Genetic diversity and evolution of hepatitis C virus." Thesis, Open University, 2000. http://oro.open.ac.uk/58053/.

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Inter- and intra-host Hey variation was investigated. First. a polymerase chain reactionrestriction fragment length polymorphism procedure was used to assign genotypes and subtypes to Hey infecting 567 individuals (comprising haemophilia patients, blood donors, intravenous drug users, attenders of antenatal and genito-urinary medicine clinics and chronic liver disease patients) from England and Wales. The majority of infections were associated with types 3a, 1 a and 1 b, and genotype distributions were generally similar in different sub-populations. Only 1 % of individuals were identified as being infected with more than one subtype. The intra-host variability of Hey in a selection of haemophilia patients, blood donors and intravenous drug users was then studied. For each individual, peR clones derived from the NS5b and 5' non-coding regions of the Hey genome were screened for sequence differences by denaturing gradient gel electrophoresis (DGGE) and nucleotide sequencing. The complexity and diversity of Hey quasi species, though differing between individuals, could not be correlated with the risk group to which the study patients belonged. Furthermore, no mixed genotype or subtype infections were identified. Thus the hypothesis that multiply exposed individuals are infected with a greater variety of HCY variants could not be substantiated. The DGGE procedure was further used to investigate the hypothesis that HCY genetic evolution occurs uniformly in patients during the acute phase of infection. Changes in diversity in the HCY hypervariable region 1 in individuals undergoing seroconversion were observed to differ between patients, thereby negating that hypothesis. Moreover, in a given individual, Hey could be subjected to either positive or negative selective pressure. Thus, factors other than the acute-phase host response determine the course of Hey genetic evolution.

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Yang, N. "Population history and genetic diversity in the Americas." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/668017/.

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This thesis aims to provide insights into the evolutionary history of populations from the Americas by studying patterns of genetic diversity in uniparental (Y-chromosome and mtDNA) and in biparental (X-chromosome and autosomes) marker systems in Native Americans and in populations of mixed ancestry (i.e. “Mestizos”) from Latin American countries. A novel aspect of this work, relative to previous studies, is that the same population samples were examined for all marker systems, thus allowing a more direct contrast of results obtained with the different markers used. I obtained in the laboratory the complete D-loop sequences (~1,200 bp) of 327 Native American mtDNAs from 22 populations sampled across the Americas and in 211 Mestizo individuals from 13 urban centres. I also genotyped 3 SNPs and 11 microsatellites on the Y-chromosome for 220 male individuals available. These data were analyzed together with unpublished data for 38 X-chromosome and 6 Y-chromosome STRs (collected by the Marshfield Foundation, USA) and with published data for 678 autosomal STRs obtained in the same population samples (Wang et al. 2007). Both, the Native and Mestizo populations show evidence of higher admixture with the Y-chromosome than with the mtDNA data. This indicates that admixture in these populations has been sex-biased and involved predominantly Native American women and immigrant men. This sex-biased admixture has thus influenced in a similar way the genetic makeup of both Native and Mestizo populations, which differ only in the extent of this admixture. Population structure analysis also indicates that the mtDNA lineages found in the Mestizo are of local origin, confirming the earlier proposal of a regional “genetic continuity” between Mestizo and native populations. This means that the Mestizo can, to some extent, allow the analysis of Native populations that do not exist anymore. For subsequent analyses I therefore considered the Native American mtDNA and Y-chromosome lineages identified in Mestizo populations as samples of from these presently unavailable native populations. These data demonstrate a lower diversity and higher differentiation among American populations, relative to other continental populations. In addition, a pattern of North to South decrease in population diversity (and increasing population differentiation) is observed across the American continent. These findings agree with the proposal that Native American ancestors came to the New World through the Bering Strait. These data also point to an important role of the coasts as facilitators of migration during the initial colonization of the continent. Phylogenetic, genetic structure and principal component analyses are broadly consistent with the geographic distribution of the populations examined and their proposed linguistic affinity. In addition, these data point to a differentiated demographic history between the various populations examined. Signals of population expansion were detected in the Meso American and Andean populations while populations from East and North West South American appear to have undergone population contractions.

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Dissertations / Theses on the topic 'Genetic diversity and divergence'

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