Brettanomyces bruxellensis est un microorganisme qui est considéré comme la cause majeure des défauts microbiologiques du vin. L’importance de cette levure à l’échelle industrielle est liée au fait qu’elle est isolée à partir de substrats différents tels que la bière, le kombucha, les molasses utilisées pour la production de bioéthanol et autres. Ce projet a pour objectif d’étudier la diversité génétique de l’espèce en se basant sur une large population d’isolats provenant de niches écologiques et géographiques variées. Pour ce faire, une méthode de génotypage robuste (analyse microsatellite) a été optimisée et appliquée sur la population, mettant en évidence la coexistence de populations diploïdes et triploïdes à l’échelle globale. Puis, la relation entre regroupement génétique et traits physiologiques a été explorée. Notamment, l'étude de la tolérance aux sulfites a été effectuée sur un sous-ensemble de souches représentatif de la population. Les résultats obtenus mettent en évidence un lien entre groupes génétiques et comportement vis-à-vis des sulfites. Des expériences de compétition en présence de dioxyde de soufre montrent un avantage sélectif des souches tolérantes aux sulfites par rapport aux souches sensibles, suggérant ainsi une adaptation spécifique au principal antiseptique utilisé en œnologie. Ce travail contribue à une meilleure connaissance de cette levure d’altération du vin en termes de diversité génétique et phénotypique et permet d’émettre des hypothèses sur les stratégies évolutives d'adaptation au milieu anthropique de cette espèce modèle non conventionnelle. / Brettanomyces bruxellensis is a microorganism described as the first cause of microbial spoilage of wine. Its industrial relevance is highlighted by the fact that this yeast is isolated from different substrates such as beer, kombucha, bioethanol fermentation molasses and others. This project aims to explore the genetic diversity of the species by studying a large population of isolates from various geographical and ecological niches. For this purpose, a robust genotyping method (microsatellite analysis) was optimized and applied on the population, thus highlighting the coexistence of diploid and triploid populations worldwide. Further, the relation between genotypic clustering and physiological traits was studied. Namely, sulphite tolerance assay was performed on a subset of strains representative of the total population. The results reveal a link between genetic group and growth profile in the presence of sulphur dioxide. Competition experiments in presence of sulphites highlight a selective advantage of sulphite tolerant strains compared to sulphite sensitive ones, thus suggesting a specific adaptation to the main antimicrobial used in winemaking. This work contributes to a deeper understanding of this wine spoilage microorganism in means of genetic and phenotypic diversity and sheds light on putative evolutionary strategies for adaptation to human related environment of this non-conventional model yeast species.

Repeated polyploidization events are thought to be among the most important causes of sympatric speciation throughout evolutionary time. Changes in phenology and trait expressions that arise in polyploids have been shown to affect plant interactions with insect herbivores and pollinators. If these interactions are changed, selection subsequent to the polyploidization event could contribute to further divergence, or increased similarity, of cytotypes. This study was conducted to investigate plant interactions with insect herbivores and pollinators and patterns of selection in tetraploid and octoploid Cardamine pratensis L. (Brassicaceae), and to answer the following questions: i) Is there phenotypic selection on flowering phenology and number of flowers? ii) Is pollen limitation or herbivory most important for variation in reproductive output? iii) During what stages of ovary and ovule development do variation in fitness mainly arise? iv) Can the intensity of interactions be linked to phenology and number of flowers, suggesting that selection is mediated by pollen limitation or herbivory? v) Do intensity of interactions, and of interaction-mediated selection, differ between ploidy levels? From a combination of an observational study of herbivory and a hand pollination experiment, selection was found for earlier flowering in both subspecies. Intensity of herbivory was an important determinant of plant reproductive success, while hand pollination had little effect. Positive effects of flowering time on intensity of herbivory suggest that selection for earlier flowering was mediated by herbivores. Tetraploids initiated flowering later and suffered from more intense herbivory than did octoploids. The direction of selection was similar in both subspecies. However, differences strength of selection and intensity of herbivory suggest that there is a possibility of selection for their further divergence. / Polyploidisering anses vara en av de viktigaste orsakerna till artbildning inom populationer. Skillnader i blomningskaraktärer, såsom fenologi och blomantal, som uppstår i och med polyploidiseringen har visat sig påverka växters interaktioner med såväl pollinatörer som herbivorer. Förändringar i växt-insektsinteraktioner till följd av polyploidiseringen kan leda till selektion för ökade skillnader, eller likheter, mellan cytotyper. Studiens syfte var att undersöka växters interaktioner med insekter i form av pollinatörer och herbivorer, samt att undersöka selektionsmönster hos tetraploida och oktoploida Cardamine pratensis L. (Brassicaceae). Jag ville även besvara följande frågor: i) Sker selektion på blomningstid och blomantal? ii) Vilken växt-insektsinteraktion är viktigast för variation i reproduktionsframgång? iii) Under vilka utvecklingsstadier uppstår den största variationen i fitness? iv) Kan intensiteten av interaktionerna kopplas till blomningsfenologi och blomantal, vilket skulle indikera att selektion förmedlas genom pollenbegränsning eller herbivori? v) Skiljer sig styrkan av interaktionerna, och av interaktionsförmedlad selektion, mellan ploidinivåer? Studien utformades som en kombination av en observationsstudie av herbivori och ett handpollineringsexperiment, och jag fann selektion för tidigare blomning hos de två underarterna. Reproduktionsframgång styrdes av herbivori snarare än pollenbegränsing. Förlust av potentiell fitness genom att fröämnen inte utvecklades till frön var den faktor som starkast påverkade variation i fitness, och detta var också den fas i utvecklingen som bidrog i störst utsträckning till kvantitativ förlust av fitness. Ett positivt samband mellan blomningsfenologi och herbivoriintensitet indikerar att selektion för blomningstid var förmedlad av herbivorer. Tetraploider blommade senare och utsattes för mer intensiva herbivorattacker än oktoploider. Detta, samt skillnader i selektionsstyrka, indikerar att selektion skulle kunna leda till ökad divergens av underarterna.

The main drivers of microevolution in the genus Sorbus are interspecific hybridisation and polyploidy. The fate of new hybrid and polyploid taxa is determined by their mode of reproduction. Especially apomixis could be very advantageous for these new taxa. The S. aria agg. (subg. Aria) plays an important role within the genus since its members are involved in all hybridisation events and thereby is responsible for the substantial part of variation of the genus. Flow cytometry, molecular markers and multivariate morphological analyses were employed to evaluate the processes generating the variability in the S. aria group. Three ploidy levels were detected among species from subg. Aria in the Czech Republic. All of them could be found in the South Moravia, whereas only tetraploids occur in the Bohemia region. Moreover, most of the Czech taxa (5 out of 7) grow also only in the South Moravia which is therefore considered as a centre of diversity of the genus Sorbus in the Czech Republic. Flow cytometry seed screen revealed 7 modes of reproduction among the individuals from S. aria agg. A wide range of sexual and apomictic types of reproduction including reduced and unreduced gametes was detected. All of the diploid individuals are completely sexual. Among polyploid taxa, most of the species are...

Genetic composition of hybrid zones often reflects geographical and ecological gradients. Hybrid zone of Arabidopsis lyrata and A. arenosa in Central Europe can be convenient model system for testing such hypothesis. These are well circumscribed but still interfertile, and their offspring is fully fertile. Besides repeated hybridisation events, the current state is complicated by the autopolyploidisation events of one of the parents, namely A. lyrata, which is present in the area studied both as diploid and tetraploid. This hybrid zone was already described in previous publications, which showed certain gradient of introgression. Moreover, the area of the hybrid zone represents a transition between Alpine and Pannonian climate along an altitudinal gradient leading from the Prealps to the lowland Wienerwald. The current thesis is the as yet most detailed study of this hybrid zone both in respect of number of studied populations and the amount of data acquired using the methods of RAD Sequencing, multivariate morphometrics and flow cytometry. The analysis of genetic data showed a gradient of introgression, where parental populations are placed at opposite ends, whereas genetically intermediate hybrids are placed in its centre. Analysis of the genome size showed an additional gradient, where hybrids...

Mixed-ploidy populations, consisting of multiple cytotypes, are an optimal system for studying genome doubling consequences in plants. The role of frequency dependent selection, known as minority cytotype exclusion principle, is very important in them, but there are many factors limiting this selection. In my thesis, I evaluate the changes in cytotype frequencies and pattern in permanent plots in natural mixed-ploidy populations of three plant species - Butomus umbellatus, Knautia serpentinicola and Tripleurospermum inodorum and I also experimentally analyze partial aspects of frequency dependent selection towards minority cytotype in artificially established mixed-ploidy arrays of two plant species - Arabidopsis arenosa and Tripleurospermum inodorum. Varied changes in frequencies of minority cytotype ware revealed in permanent plots. Usually there was decrease, but in two plots there was increase in minority cytotype frequency and in one case it became dominant. Observed changes depend on initial frequencies of minority cytotype in populations, biological properties of species and particular environment of permanent plot. Relative indexes describing the frequency and the strength of disturbances and also the amount of soil nutrients was used to compare the environment of permanent plots across...

A lot of the research has been made in the field of plant polyploidy since the discovery of this phenomenon. However, the more we know, the more questions arise. Overall, the most insistent questions remain: How did the polyploids arise and become established? Is it advantageous to be polyploid? We chose a perennial herb Vicia cracca L. to study the causes and consequences of polyploidisation on microevolution of a diploid-tetraploid complex in central European conditions. First, evidence from both flow cytometry and molecular markers (allozymes, DNA sequences, microsatellites) confirmed a hypothesised autopolyploid origin of tetraploids. Based on allozymes, we proved that tetraploids are genetically richer than diploid ancestors. However, we showed that the conclusions depend on statistics used for genetic variation measurements. Nevertheless, tetraploids of V. cracca suffered lesser reduction in seed production after artificial selfing than diploids. We thus infer that they profit from multiple allele dosage, which can mask deleterious alleles. We also corroborated an existence of a central European contact zone of diploids and tetraploids and discovered two other contact zones in south-western and south- eastern Europe. The central European contact zone with several mixed-ploidy populations served us as...

The western North American species of the genus Geranium have never been satisfactorily clarified. The perennial, indigenous species of this interesting group have been particularly confusing. One important reason for confusion in this group is the fact that the taxonomic probems of the perennial species have never been studied from the genetic point of view. A sound delimitation of specific and subspecific boundaries and phylogenetic relationships cannot be achieved without the application of cyto-genetic principles. In respect to the cytological phase of this study, the author has placed emphasis on chromosome numbers in order to show evidences for and possible origin of polyploidy. Detailed chromosome morphology has not been attempted because of the very small size of the chromosomes. This study has been limited to the Wasatch region. this area respresents a natural geographical unit which is small enough to permit a detailed field study of the group and yet provide a wide range of habitats, both ecologic and geographic. This region forms the western front of the Rocky Mountain province and extendes 200 miles south from the great bend in the Bear river at Soda springs, Idaho, to the pass south of Mt. Nebo and east of Nephi, Utah.

A lot of the research has been made in the field of plant polyploidy since the discovery of this phenomenon. However, the more we know, the more questions arise. Overall, the most insistent questions remain: How did the polyploids arise and become established? Is it advantageous to be polyploid? We chose a perennial herb Vicia cracca L. to study the causes and consequences of polyploidisation on microevolution of a diploid-tetraploid complex in central European conditions. First, evidence from both flow cytometry and molecular markers (allozymes, DNA sequences, microsatellites) confirmed a hypothesised autopolyploid origin of tetraploids. Based on allozymes, we proved that tetraploids are genetically richer than diploid ancestors. However, we showed that the conclusions depend on statistics used for genetic variation measurements. Nevertheless, tetraploids of V. cracca suffered lesser reduction in seed production after artificial selfing than diploids. We thus infer that they profit from multiple allele dosage, which can mask deleterious alleles. We also corroborated an existence of a central European contact zone of diploids and tetraploids and discovered two other contact zones in south-western and south- eastern Europe. The central European contact zone with several mixed-ploidy populations served us as...

Like many angiosperms, Brassica rapa underwent several rounds of whole genome duplication during its evolutionary history. Brassica rapa is particularly valuable for studying genome evolution because it also experienced whole genome triplication shortly after it diverged from the common ancestor it shares with Arabidopsis thaliana about 17-20 million years ago. While many B. rapa genes appear resistant to paralog retention, close to 50% of B. rapa genes have retained multiple, paralogous loci for millions of years and appear to be multi-copy tolerant. Based on previous studies, gene function may contribute to the selective pressure driving certain genes back to singleton status. It is suspected that other factors, such as gene expression patterns, also play a role in determining the fate of genes following whole genome triplication. Published RNA-seq data was used to determine if gene expression patterns influence the retention of extra gene copies. It is hypothesized that retention of genes in duplicate and triplicate is more likely if those genes are expressed in a tissue-specific manner, as opposed to being expressed globally across all tissues. This study shows that genes expressed specifically in flowers and roots in B. rapa are more resistant to fractionation than globally expressed genes following whole genome triplication. In particular, there appears to have been selection on genes expressed specifically in flower tissues to retain higher copy numbers and for all three copies to exhibit the same flower-specific expression pattern. Future research to determine if these observations in Brassica rapa are consistent with other angiosperms that have undergone recent whole genome duplication would confirm that retention of flower-specific-expressed genes is a general feature in plant genome evolution and not specific to B. rapa.

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