Pattern of Linkage Disequilibrium (LD) is a major factor largely determining the power of association mapping studies. Along with nucleotide diversities and DNA polymorphism, knowledge of patterns of LD along the genome needs to be to known to effectively design association mapping studies. In this study, patterns of nucleotide diversity, population structure, LD was estimated in Norway spruce (Picea abies). The data used for this were 23 nuclear loci sequenced in around 90 individuals originating from natural populations of Norway spruce throughout the current distribution range in Sweden and Finland. The observed levels of nucleotide diversity are variable among loci varying between 0.002 and 0.008 if measured by average pairwise nucleotide diversity. Despite the samples stretching large part of Finland and Sweden there were no evidence for strong population structure. As in earlier studies LD decays fast with distance and the average pattern of the squared correlation of allele frequencies drops to less than 0.2 within 100bp. In order to put the data in perspective previously generated data sets were re-analyzed and compared to the inferred results.

Abstract Natural selection, mutation, recombination, demographic history and chance all have a role in evolution. In natural populations, the outcome of these forces is seen as adaptations, differences between geographic varieties, and as genetic diversity in populations—both at the phenotypic and molecular levels. In this thesis I wanted to examine the roles of the evolutionary forces shaping molecular genetic diversity in trees, with emphasis on a boreal conifer, Scots pine (Pinus sylvestris). Phylogeographic history and past population size changes have a dominant role in molecular diversity of P. sylvestris. The effect of the Last Glacial Maximum (37 000–16 000) was observed in the distribution of mitochondrial DNA variation. In contrast, nuclear DNA was not much affected by the last glacial period. Instead, more ancient demographic events that took place millions of years ago can still be observed in the variation of P. sylvestris nuclear DNA. Not much evidence of positive natural selection was found in pines or trees in general. This is in contrast to strong natural selection that is observed at the phenotypic level. Positive selection is difficult to prove, especially when the genome is still affected by demographic history. Mutation–drift equilibrium may rarely be reached in tree populations.

No description available.

<p>Availability of genome sequences for numerous bacterial species comprising of different bacterial strains allows elucidation of species and strain specific adaptations that facilitate their survival in widely fluctuating micro-environments and enhance their pathogenic potential. Different bacterial species use different strategies in their pathogenesis and the pathogenic potential of a bacterial species is dependent on its genomic complement of virulence factors. A bacterial virulence factor, within the context of this study, is defined as any endogenous protein product encoded by a gene that aids in the adhesion, invasion, colonization, persistence and pathogenesis of a bacterium within a host. Anecdotal evidence suggests that bacterial virulence genes are undergoing diversifying evolution to counteract the rapid adaptability of its host&rsquo / s immune defences. Genome sequences of pathogenic bacterial species and strains provide unique opportunities to study the action of diversifying selection operating on different classes of bacterial genes.</p>

<p>Availability of genome sequences for numerous bacterial species comprising of different bacterial strains allows elucidation of species and strain specific adaptations that facilitate their survival in widely fluctuating micro-environments and enhance their pathogenic potential. Different bacterial species use different strategies in their pathogenesis and the pathogenic potential of a bacterial species is dependent on its genomic complement of virulence factors. A bacterial virulence factor, within the context of this study, is defined as any endogenous protein product encoded by a gene that aids in the adhesion, invasion, colonization, persistence and pathogenesis of a bacterium within a host. Anecdotal evidence suggests that bacterial virulence genes are undergoing diversifying evolution to counteract the rapid adaptability of its host&rsquo / s immune defences. Genome sequences of pathogenic bacterial species and strains provide unique opportunities to study the action of diversifying selection operating on different classes of bacterial genes.</p>

Individuals vary from each other in their genetic content. Genetic diversity is at the core of the evolutionary theory. Rooted in a solid theoretical framework developed as early as the 1930s, current empirical observations of genomic diversity became possible due to technological advances. These measurements, originally based on a few gene sequences from several individuals, are becoming possible at the genome scale for entire populations. We can now explore how evolutionary forces shape diversity levels along different parts of the genome. In this thesis, I focus on the variation in levels of diversity within genomes using avian systems and in particular that of the collared flycatcher (Ficedula albicollis). First, I describe the variation in genetic diversity along the genome of the collared flycatcher and compare it to the amount of variation in diversity across individuals within the population. I provide guidelines on how a small number of makers can capture the extent of variability in a population. Second, I investigate the stability of the local levels of diversity in the genome across evolutionary time scales by comparing collared flycatcher to the hooded crow (Corvus (corone) corone). Third, I study how selection can maintain variation through pervasive evolutionary conflict between sexes. Lastly, I explore how shifts in genome-wide variant frequencies across few generations can be utilised to estimate the effective size of population.

Abstract The timing growth and reproduction are critical to the fitness of plants and animals. The timing also has an important role in local adaptation. Locally adapted plants may have different responses to photoperiod and other environmental cues and genes or alleles behind underlying differences may differ between populations. The molecular genetics and physiology of flowering of the plant molecular biology model organism Arabidopsis thaliana is being intensively studied, and this offers a good opportunity to study the genetic basis of flowering time variation in related non-model species. The closely related perennial species Arabidopsis lyrata provides an interesting comparison to A. thaliana because of its different ecology, mating system and life history. The influence of sampling designs on clustering methods was analyzed using simulations and microsatellite data in the selfing A. thaliana. It was found that sample size has a large effect on the resulting number of clusters and sampling too few individuals per locality could lead to a severe underestimation of the real number of subpopulations. Patterns of sequence variation in flowering time genes and association between polymorphisms at FRI (and FLC) and flowering time was studied in A. thaliana and in A. lyrata to find out whether the genes were responsible for flowering time differences between and within natural populations. In A. thaliana there was no significant association between polymorphisms at FLC and FRI and flowering time. In A. lyrata the FRI gene was polymorphic for an indel associated with flowering time variation within two Northern European populations, suggesting that the indel (or a linked polymorphism) was involved in flowering time variation. However, FRI did not explain the flowering time differences between A. lyrata populations, and other loci must be involved. Patterns of diversity and divergence at flowering time related loci were compared against a set of random reference loci to examine the roles of selection and demography. Sequence variation in the studied A. lyrata populations departed from the standard neutral equilibrium model and it has been influenced by recent historical events, most likely bottlenecks. The level of silent and synonymous polymorphisms in flowering time genes was highly reduced and this can be likely explained by selective sweeps at flowering time genes. / Tiivistelmä Kasveilla kukkimisen ajoittaminen suotuisaan ajankohtaan on hyvin tärkeää suvullisen lisääntymisen kannalta. Kukkimisen oikealla ajoituksella on myös tärkeä rooli kasvien sopeutumisessa paikallisiin olosuhteisiin. Kukkimisaikamuunteluun vaikuttavat useimmiten lukuisat geenit sekä ympäristötekijät, jotka voivat vaihdella alueellisesti ja populaatioiden välillä. Vaikka kukkimiseen ja kukkimisaikaan vaikuttavia tekijöitä tunnetaan jo hyvin, luonnonpopulaatioiden muuntelun ja paikallisen sopeutumisen geneettinen tausta on huonommin tunnettu. Väitöstutkimus keskittyy Arabidopsis-populaatioiden paikalliseen sopeutumiseen tarkastelemalla kukkimisajan muuntelua ja siihen vaikuttavia geeneettisiä tekijöitä. Tutkimuksessa käytetyt geneettiset aineistot perustuvat osin neutraaleihin merkkigeeneihin (mikrosatelliittimuunteluun), ja osin sekvenssien nukleotidimuunteluun. Väitöstutkimuksessa on simulointien avulla selvitetty populaatiosta analysoitavien yksilöiden lukumäärän merkitystä populaatiorakenteen selvittämisessä itsesiittoisella lituruoholla (Arabidopsis thaliana). Tulosten mukaan on hyvä analysoida useampia yksilöitä paikallisista populaatioista, sillä liian pienet otoskoot voivat johtaa ryhmien määrän aliarvioimiseen. Koalesenssisimulaatiot osoittavat idänpitkäpalon (Arabidopsis lyrata) populaatioiden poikkeavan tasapainotilasta ja populaatioissa tapahtuneen populaatiokoon muutoksia (ns. pullonkaulailmiö). Tutkimuksessa havaittiin sekvenssimuuntelun olevan alhaisempaa kukkimisaikageeneissä kuin referenssigeeneissä todennäköisesti positiivisen valinnan vaikutuksesta. Tutkimuksessa todettiin, että FRI geenissä tapahtuneet mutaatiot ovat kahdessa tutkitussa lajissa erilaisia luonteeltaan, mutta geenillä on kuitenkin samanlainen rooli kukkimisajan määräämisessä. Assosiaatiokokeissa lituruoholla ei Pohjois-Euroopan populaatioissa löydetty merkitsevää assosiaatiota FRI geenin ja kukkimisajan välillä, kun puolestaa idänpitkäpalolla FRI vaikutti kukkimisaikamuunteluun kahdessa pohjoisessa populaatiossa.

Philosophiae Doctor - PhD (Biotechnology) / Availability of genome sequences for numerous bacterial species comprising of different bacterial strains allows elucidation of species and strain specific adaptations that facilitate their survival in widely fluctuating micro-environments and enhance their pathogenic potential. Different bacterial species use different strategies in their pathogenesis and the pathogenic potential of a bacterial species is dependent on its genomic complement of virulence factors. A bacterial virulence factor, within the context of this study, is defined as any endogenous protein product encoded by a gene that aids in the adhesion, invasion, colonization, persistence and pathogenesis of a bacterium within a host. Anecdotal evidence suggests that bacterial virulence genes are undergoing diversifying evolution to counteract the rapid adaptability of its host&rsquo;s immune defences. Genome sequences of pathogenic bacterial species and strains provide unique opportunities to study the action of diversifying selection operating on different classes of bacterial genes. / South Africa

The aim of this thesis is to obtain a better understanding of mutation rates within as well as between the genomes of humans and chimpanzees using data generated by high throughput sequencers. I will start with a review of the field and an overview of the technologies and protocols used to generate and analyse high throughput sequencing data. I apply some of the discussed techniques to show that there is evidence of a selective advantage of pathogenic de novo mutations in the Fibroblast Growth Factor Receptor 3 gene in the male germ line of humans. Furthermore, I use some of the methods to generate a map of genome-wide sequence variation in Western chimpanzees. Ever since Darwin [Darwin, 1871] and Huxley [Huxley, 1863] postulated more than a century ago that African great apes are our closest living evolutionary relatives, the study of chimpanzee individuals is of great scientific interest from an evolutionary point of view, as comparisons between the genomes of human and chimpanzee offer the potential to help to understand the molecular basis for similarities and differences between the two species. I use the generated data to explore the breadth of the nucleotide diversity in the chimpanzee genome in order to shed light on whether or not the local variation in mutation rate has been conserved since the divergence of the two species and to place human nucleotide diversity into perspective with an evolutionary closely related species. I explore the relationship of nucleotide diversity in chimpanzees with specific large-scale genome features to reveal a number of highly significant correlations which explain over 40% of the observed variation. I use data from the 1000 Genomes Project to examine the occurrence of ancestral polymorphisms shared between human and chimpanzee on a genome-wide scale. These ancestral polymorphisms do not only influence fine-scale divergence rates across the genome in very closely related species, they are also good candidates for regions under balancing selection and thus, they are a useful tool to study long-time population demographics and speciation. Using these variants, I postulate that long-term balancing selection may be more common than previously believed. I conclude with a discussion of the results contained in the body of the thesis and suggest a number of areas for future research.

L'utilisation de variétés présentant des résistances quantitatives polygéniques est une pratique respectueuse de l'environnement et potentiellement durable pour lutter contre les bioagresseurs. Les résistances quantitatives sont cependant mal connues et encore peu exploitées. Via l'étude de l'interaction Capsicum spp. / Phytophthora capsici, les objectifs sont de (i) caractériser la diversité naturelle de l'hôte pour le phénotype quantitatif de résistance, (ii) décrire la diversité au QTL Pc5.1, déterminant majeur de la résistance, conservé chez les géniteurs et efficace à large spectre, et (iii) déterminer le profil d'évolution moléculaire aux gènes candidats de Pc5.1. L'évaluation du niveau de résistance de ressources génétiques de Capsicum spp. et du spectre de résistance d'un panel d'accessions a permis d'identifier de nouveaux géniteurs de forte résistance au spectre large et a fourni un set d'isolats différenciant les accessions selon leur spectre. Le polymorphisme à Pc5.1 a été révélé par séquençage haut débit. Globalement, Pc5.1 présente un polymorphisme nucléotidique plus élevé que le reste du génome. Les accessions résistantes sont très peu divergentes au QTL, signe d'une forte conservation intra- et inter-génique, alors que les accessions sensibles sont plus polymorphes. Aux gènes candidats, deux haplotypes majeurs ont été identifiés, l'un présent quasi exclusivement chez des accessions résistantes et l'autre chez des accessions sensibles, ce qui confirme la forte conservation du locus et la divergence entre résistants et sensibles. Le déséquilibre de liaison mesuré aux gènes candidats étant fort, surtout chez les C. annuum, 65% des polymorphismes sont significativement associés à la résistance. Cette étude a mis en évidence le caractère contraint de l'allèle de résistance à Pc5.1 et interroge sur l'origine et l'histoire évolutive du QTL, en relation avec sonefficacité à large spectre. Il semble qu'une localisation proche du centromère limite les recombinaisons au locus et que la divergence entre les sensibles et les résistants soit un événement ancien. La détermination de la nature moléculaire et de l'histoire évolutive de Pc5.1 sera poursuivie en approfondissant les analyses de divergence des séquences et en se focalisant sur la validation fonctionnelle des gènes candidats déjà en cours. / An environmentally friendly and potentially durable strategy to control diseases is the breeding for varieties displaying quantitative polygenic resistances. However a few is known about quantitative resistances, which are thus underexploited. Through the investigation of the Capsicum spp. / Phytophthora capsici interaction, this study aimed to (i) phenotype natural host diversity for the quantitative resistance, (ii) describe the nucleotide diversity at the QTL Pc5.1, a major determinant of resistance that is retrieved among genitors and is broad-spectrum, and (iii) explore the pattern of molecular evolution at Pc5.1 candidate genes. Through the phenotyping for level of resistance in Capsicum spp. genetic resources and spectrum of resistance in a sample of accessions, novel genitors displaying strong and broadspectrum resistance have been identified, and a set of isolates that differentiate accessions according to their resistance spectrum has been established. High-throughput sequencing has been exploited to identify polymorphisms at Pc5.1. Nucleotide diversity at Pc5.1 is higher than over the genome. Resistant accessions displayed low divergence thatindicates high intra- and inter-genic conservation, while susceptible accessions are more polymorphic than resistant ones. At the candidate genes, two major haplotypes have been identified, one being almost exclusively exhibited by resistant accessions and the other by susceptible ones, which reinforces the assessments that the QTL is highly conserved and that resistant and susceptible accessions are divergent. Linkage disequilibrium at candidate genes being high, particularly for C. annuum, 65% of polymorphisms are in significant association with resistance. By highlightingthe constraint pattern of selection at Pc5.1, this study wonders about the origin and the evolution history of the QTL, in relation to its broad-spectrum efficiency. A close proximity with the centromere region seems to restrict recombinations at the QTL, and divergence between resistant and susceptible may be an ancient event. The investigation of the molecular function and the pattern of evolution of Pc5.1 will be continued through in depth study of the acquired sequences and functional validation of candidate genes already ongoing.