Viruses constitute the vast majority of all biological entities in the biosphere and represent one of the biggest reservoirs of undetected genetic diversity on Earth. Of all the viral particles inhabiting the ocean, phages are the most abundant and can affect the overall microbial composition of marine ecosystems and the dynamics of global biogeochemical cycles. The interaction between prokaryotic cells and their phages is among the oldest and most intertwined host-parasite relationships on the planet. It has been extensively studied by culture, molecular biology, and experimental evolution. However, due to the difficulties of culture with environmental samples, only a few studies have analyzed the mechanisms of phage-host interaction in the marine environment. Here, we have studied the genes involved in viral host recognition and their evolutionary dynamics by focusing on two species of the marine copiotrophic bacterium Alteromonas and several phages infecting them. We described the genomic and morphological characterization of the first Alteromonas phage belonging to the Myoviridae family (Alteromonas myovirus V22) that was isolated in coastal waters of the Mediterranean Sea, and we identified its receptor-binding protein (RBP) used for host recognition by combining fluorescence microscopy and spectrometry. In addition, using size-exclusion chromatography, we showed how this protein required co-expression with a downstream protein to be functional, which later was identified as a new type of intermolecular chaperone crucial for RBP maturation. We also identified a conserved host recognition module in V22 and other unrelated alterophages belonging to different viral families and with completely different morphologies, suggesting horizontal gene transfer between the ancestors of these phages. Furthermore, we described the first coevolution study of a host-parasite system performed with Alteromonas using a metagenomics-like approach. Finally, we analyzed the micro- and macrodiversity of an alterophage population that was able to survive over a long period of time and showed remarkable genomic stability, indicating stable interactions over time between phage-host recognition structures. Overall, this study has contributed to extend the knowledge of known phage-host recognition mechanisms present in the marine ecosystem and has provided a first glimpse of the evolutionary dynamics in phages infecting Alteromonas.

Meiosis is functionally conserved across eukaryotes, thus not expected to vary considerably among different species, and even less so among lineages within a species. However, recent studies showed that this is not necessarily the case in Arabidopsis arenosa. Genome scanning identified an excess differentiation in meiosis genes between A. arenosa diploids and tetraploids, interpreted as meiosis adaptation to the whole genome duplication in tetraploids and differentiation was also found between two diploid lineages. Thus, I present a population-based analysis of positive selection acting on meiosis proteins across multiple lineages of A. arenosa. I showed that meiosis proteins were under positive selection in all diploid lineages, mainly in the Pannonian and South-eastern Carpathian lineage. The evidence for positive selection in diploid lineages suggested differential pathways of meiosis adaptations in the species, probably reflecting the necessity to adapt to local environments, among all to temperature. The highest enrichment of amino acid substitutions (AASs) under positive selection was identified in tetraploids, in consistence with previous genome-scan results. As several interacting meiosis proteins were under positive selection in the same A. arenosa lineage, I hypothesize that the close...

The topic of semestral thesis is methods to detect selection in DNA sequences. In the begining of the thesis we will describe molecular evolution. It will be written what made the evolution and how the evolution is shown. Moreover there are gen mutations and mechanisms of diffuse and fixation. It will be defined what pozitive, negative and neutral selection is. The thesis is focused on evolution distance of synonymous and nonsynonymous substitution. There will be described three methods – Nei-Gojobori, Li-Wu-Luo and Comeron. All these methods will be described with mathematic formulas. There will be statistic test to decide what kind of selection ti is – there will be used z-test. In the practical part, there will be information about developed software what counts selection pressure from sequences from databazes in format GenBank and it shows parts where selection is. The software will be used for two data sets with two different genetic codes. The result will be discussed. We will discuss results of all three methods of selection pressure and influence of input parametrs.

This thesis investigates the molecular evolutionary and macroevolutionary consequences of flight loss in insects. Chapter 2 tests the hypothesis that flightless groups have smaller effective population sizes than related flighted groups, expected to result in a consistent pattern of increased non-synonymous to synonymous ratios in flightless lineages due to the greater effect of genetic drift in smaller populations. Chapter 3 tests the hypothesis that reduced dispersal and species-level traits such as range size associated with flightlessness increase extinction rates, which over the long term will counteract increased speciation rates in flightless lineages, leading to lower net diversification. The wide-spread loss of flight in insects has led to increased molecular evolutionary rates and is associated with decreased long-term net diversification. I demonstrate that the fundamental trait of dispersal ability has shaped two forms of diversity—molecular and species—in the largest group of animals, and that microevolutionary and macroevolutionary patterns do not necessarily mirror each other. / Generously funded by NSERC with a Canada Graduate Scholarship and the Government of Ontario with an Ontario Graduate Scholarship to T. Fatima Mitterboeck; NSERC with a Discovery Grant to Dr. Sarah J. Adamowicz

Inspired by Gould, who claimed life would be arriving at a different outcome each time it were allowed to run from the same beginning, I have attempted to determine the repeatability of the adaptive course of one Pseudomonas fluorescens lineage. In addition, my study aimed to establish whether the likelihood of parallel evolution of the two synonymous single-nucleotide substitutions was contingent upon a prior motility-impairing deletion or a prior increase in fitness. Further, the study was designed to provide empirical data addressing the long-standing question of the effect of starting fitness on the ensuing rate of adaptation. Although no exact replay of the initial evolutionary trajectory was observed, I have demonstrated that gtsB, but not gtsC gene, is likely to be a mutational hotspot under the low glucose with a recovery of two undescribed mutations in gtsB. My data are consistent with a notion that substitutions in gtsB may be contingent upon Δ35kB(fliJ-PFLU4466) motility-impairing deletion, but not the fitness increase associated with it. Finally, the features of the adaptive landscape of P. fluorescens in the minimal glucose provide languid support for Fisher’s hypothesis of a decrease in adaptation rate with the rise in the starting fitness. Taken together, these original results reinforce the non-negligible role of history in shaping the outcomes of biological evolution and call for caution in attempting a formulation of rigid predictive models of evolutionary change. Inspiré par les travaux de Stephen J. Gould qui affirmait que la vie sur terre arriverait à une forme différente si elle repartait à zéro, je présente ici mes travaux où je teste la reproductibilité du cours adaptatif d’une lignée expérimentale de Pseudomonas fluorescens. L’objectif de cette étude était de déterminer si la probabilité que deux mutations synonymes évoluent en parallèle est affectée par la présence d’une délétion affectant la motilité de la bactérie ou de l’augmentation de la valeur sélective de celle-ci. De plus, le design expérimental de cette étude permet de tester si la valeur sélective initiale d’une population affecte le taux d’adaptation de cette même population. Bien d’une reproductibilité exacte du cours adaptatif initial ne fut pas observée, je démontre que le gène gtsB est probablement un « hotspot »mutationnel permettant l’adaptation à de bas niveau de glucose, ayant trouvé deux mutations dans ce site; alors que le gène gtsC ne l’est pas. Mes données sont également conséquentes avec le fait que les mutation dans le gène gtsB dépendent de l’effet de la délétion Δ35kB(fliJ-PFLU4466) affectant la motilité de la bactérie, mais non de l’augmentation de la valeur sélective qui y est associée. Finalement, la forme du plateau adaptative associé à de bas niveaux de glucose chez P. fluorescens supporte l’hypothèse émise par Fisher qui stipule que le taux d’adaptation d’un organisme diminue avec la valeur sélective initiale qui y est associée. L’ensemble de ces résultats supporte le rôle non-négligeable de l’histoire de vie d’une population en ce qui attrait à l’évolution future de cette même population. Aussi, ces résultats appelle à la prudence quand vient le temps de formuler des modèles prédictifs des changements évolutifs d’une population.

Inspired by Gould, who claimed life would be arriving at a different outcome each time it were allowed to run from the same beginning, I have attempted to determine the repeatability of the adaptive course of one Pseudomonas fluorescens lineage. In addition, my study aimed to establish whether the likelihood of parallel evolution of the two synonymous single-nucleotide substitutions was contingent upon a prior motility-impairing deletion or a prior increase in fitness. Further, the study was designed to provide empirical data addressing the long-standing question of the effect of starting fitness on the ensuing rate of adaptation. Although no exact replay of the initial evolutionary trajectory was observed, I have demonstrated that gtsB, but not gtsC gene, is likely to be a mutational hotspot under the low glucose with a recovery of two undescribed mutations in gtsB. My data are consistent with a notion that substitutions in gtsB may be contingent upon Δ35kB(fliJ-PFLU4466) motility-impairing deletion, but not the fitness increase associated with it. Finally, the features of the adaptive landscape of P. fluorescens in the minimal glucose provide languid support for Fisher’s hypothesis of a decrease in adaptation rate with the rise in the starting fitness. Taken together, these original results reinforce the non-negligible role of history in shaping the outcomes of biological evolution and call for caution in attempting a formulation of rigid predictive models of evolutionary change. Inspiré par les travaux de Stephen J. Gould qui affirmait que la vie sur terre arriverait à une forme différente si elle repartait à zéro, je présente ici mes travaux où je teste la reproductibilité du cours adaptatif d’une lignée expérimentale de Pseudomonas fluorescens. L’objectif de cette étude était de déterminer si la probabilité que deux mutations synonymes évoluent en parallèle est affectée par la présence d’une délétion affectant la motilité de la bactérie ou de l’augmentation de la valeur sélective de celle-ci. De plus, le design expérimental de cette étude permet de tester si la valeur sélective initiale d’une population affecte le taux d’adaptation de cette même population. Bien d’une reproductibilité exacte du cours adaptatif initial ne fut pas observée, je démontre que le gène gtsB est probablement un « hotspot »mutationnel permettant l’adaptation à de bas niveau de glucose, ayant trouvé deux mutations dans ce site; alors que le gène gtsC ne l’est pas. Mes données sont également conséquentes avec le fait que les mutation dans le gène gtsB dépendent de l’effet de la délétion Δ35kB(fliJ-PFLU4466) affectant la motilité de la bactérie, mais non de l’augmentation de la valeur sélective qui y est associée. Finalement, la forme du plateau adaptative associé à de bas niveaux de glucose chez P. fluorescens supporte l’hypothèse émise par Fisher qui stipule que le taux d’adaptation d’un organisme diminue avec la valeur sélective initiale qui y est associée. L’ensemble de ces résultats supporte le rôle non-négligeable de l’histoire de vie d’une population en ce qui attrait à l’évolution future de cette même population. Aussi, ces résultats appelle à la prudence quand vient le temps de formuler des modèles prédictifs des changements évolutifs d’une population.