Un objectif central en biologie est de comprendre la relation entre le génotype et le phénotype. Afin de disséquer les bases génétiques de la diversité phénotypique, il est nécessaire de disposer d’une collection de données génomiques d’un grand nombre d’individus d’une même espèce. Dans ce but, mes travaux de thèse se basent sur l’étude des séquences génomiques ainsi que des données phénotypiques de 1011 isolats naturels de la levure Saccharomyces cerevisiae. Dans un premier temps, je me suis intéressé à la description de la variation génétique et phénotypique pour dresser un portrait précis de l’histoire évolutive de cette espèce. Les données de phénotypage nous ont permis de réaliser des études pangénomiques d’association génotype-phénotype avec une puissance jusque là inégalée chez Saccharomyces cerevisiae. Je me suis par la suite penché sur l’évaluation des paramètres influençant le pouvoir de détection d’une telle approche, d’en apprécier limites pour tenter de les contourner. / Elucidating the genetic origin of phenotypic diversity among individuals within the same species is essential to understand evolution. Using whole genome sequences of 1,011 Saccharomyces cerevisiae isolates, my work sought to describe intraspecific genetic variation and investigate of its phenotypic consequences. Doing so, I obtained a precise view of the evolutionary history of S. cerevisiae. Phenotypic characterization provided the opportunity to perform genotype-phenotype genome-wide association studies with unprecedented power. I then focused on the evaluation of the parameters influencing genome-wide association studies, the appreciation of the limits of such an approach, and ways to circumvent them.

The study of biological invasions is not only essential to regulate their vast potential for ecological and economical harm, they offer a unique opportunity to study adaptive evolution in the context of recent range expansions into novel environments. The North American invasion of the gypsy moth, Lymantria dispar L., since its introduction in 1869 to Massachusetts, has expanded westward to Minnesota, northward to Canada, and southward to North Carolina. Fluctuating range dynamics at the southern invasive edge are heavily influenced by heat exposure over their optimal (supraoptimal) during the larval stage of development. We coupled genomic sequencing with reciprocal transplant and laboratory-rearing experiments to examine the interactions of phenotypic, genetic, and environmental variation under selective supraoptimal regimes. We demonstrate that while there is no evidence to support local adaptation in the fitness-related physiological traits we measured, there are clear genomic patterns of adaptation due to differential survival in higher temperatures. Mapping of loci identified as contributing to local adaptation in a selective environment and those associated with phenotypic variation highlighted that variation in larval development time is partly driven by pleiotropic loci also affecting survival. Overall, I highlight the necessity and inferential power gained through replicating environmental conditions using both phenotypic and genome-wide analyses.

Comprendre comment les espèces s'adaptent à leur environnement est un des buts majeurs de la biologie évolutive. Il s'agit d'identifier les gènes responsables des caractères adaptatifs, mais aussi de comprendre les mécanismes généraux de l'adaptation, et des phénomènes empêchant une adaptation optimale. Les régions non-recombinantes sont particulières pour ces aspects. En effet, elles peuvent protéger de la recombinaison des combinaisons d'allèles favorables, et inversement, la suppression de recombinaison peut entraîner une dégénérescence, comme une accumulation de mutations délétères ou des pertes de gènes. Même les organismes à reproduction sexuée possèdent cependant souvent de larges régions non-recombinantes, associées à la détermination du sexe génétique ou du type sexuel. Dans cette thèse, j’ai ainsi étudié les traces d’adaptation et de dégénérescence dans des génomes de champignons pathogènes de plantes. Les champignons du complexe d'espèces Microbotryum violaceum, qui causent la maladie du charbon des anthères chez les Caryophyllacées et comptent des dizaines d'espèces spécifiques d’hôtes différents, sont d'excellents modèles pour l'étude des processus génomiques de l'adaptation. Ils possèdent de plus des chromosomes de types sexuels non-recombinants sur une partie de leur longueur. Pour étudier l'évolution des chromosomes de types sexuels, la dégénérescence et l'adaptation à l'hôte dans le complexe M. violaceum, nous avons adopté diverses approches de génomique. En utilisant la technologie PacBio, nous avons obtenu un assemblage complet des chromosomes de types sexuels pour l'espèce M. lychnidis-dioicae. Nous avons montré que la région non-recombinante s'étend sur 90 % des chromosomes de types sexuels, présente un niveau de réarrangements exceptionnel entre les deux types sexuels, et que des centaines de gènes sont présents à l'état hémizygote et ont donc probablement été perdus dans un type sexuel. De plus, la comparaison des génomes d'une douzaine d'espèces de M. violaceum a montré une accumulation de mutations non-synonymes et d'éléments transposables dans les chromosomes de types sexuels. Nous avons aussi étudié la dégénérescence dans le contexte de l'exposition aux radiations ionisantes, en analysant des populations de M. lychnidis-dioicae exposées à différents niveaux de radiation dans la région de Tchernobyl. Nous n'avons pas détecté d'augmentation du taux de mutations non-synonymes par rapport au groupe témoin, ce qui suggère que le champignon est radio-résistant ou que la sélection est plus forte dans la région de Tchernobyl. Enfin, pour étudier l'adaptation à l’hôte, nous avons reséquencé des dizaines des génomes de deux espèces sœurs de M. violaceum. L'analyse du polymorphisme a révélé des balayages sélectifs tout le long des génomes et à des localisations différentes entre les deux espèces. Nous avons identifié un certain nombre de gènes candidats pour l'adaptation à l’hôte dans ces régions de balayages sélectifs, sur la base de leur expression in planta et de leurs annotations. Les gènes sur-exprimés dans la plante montraient d’autre part un taux de substitutions non-synonymes entre les deux espèces sœurs plus élevé que les autres gènes, ce qui suggère qu’une bonne partie pourrait être impliquée dans l'adaptation à l’hôte. Ces travaux ouvrent la voie à une comparaison des génomes de différentes espèces du complexe M. violaceum, d’une part pour reconstituer l'histoire de la suppression de recombinaison dans les chromosomes de types sexuels, et d’autre part pour étudier les bases génétiques de l'adaptation à différents hôtes dans un complexe d’espèces phylogénétiquement proches. / Understanding how species adapt to their environment is a major goal in evolutionary biology. Scientists aim to identity the genes underlying key adaptive traits, but also to understand more broadly adaptive processes and phenomena that allow or prevent optimal adaptation. Non-recombining regions are particular for these aspects. They can indeed protect adaptive combinations of alleles from recombination, and conversely, suppressed recombination can lead to degeneration, such as accumulation of deleterious mutations or genes losses. Even sexually-reproducing organisms often possess large non-recombining regions associated with sex ou mating-type determination. In this thesis, I therefore studied signatures of adaptation and degeneration in genomes of plant pathogenic fungi. Fungi of the species complex Microbotryum violaceum, with dozens of host-specific sibling species causing anther-smut disease in the Caryophyllaceae family, are particularly good models for addressing the question of the genomic processes involved in host adaptation. Moreover, they possess size-dimorphic, partly non-recombining mating-type chromosomes. To study the evolution of mating-type chromosomes, degeneration and host-adaptation in the M. violaceum species complex, we used a genomic approach. Using PacBio sequencing, we obtained a complete assembly of the mating-type chromosomes of the species M. lychnidis-dioicae. We showed that the non-recombining regions span 90 % of the mating-type chromosomes, exhibit an exceptional level of rearrangements between the two mating-types, and that hundreds of genes are in a hemizygous state and were therefore probably lost in one of the two mating-type chromosomes. Moreover, comparing a dozen of species of the M. violaceum complex revealed an accumulation of non-synonymous substitutions and of transposable elements in mating-type chromosomes. We also studied degeneration in the context of ionizing radiations, by analysing populations of M. lychnidis-dioicae exposed to different radiation levels in the Chernobyl area. We did not detect any increase in the rate of non-synonymous mutations compared to the control group or with radiation, which suggests that the fungi is radio-resistant or that selection is higher in the Chernobyl area. Lastly, we resequenced dozens of genomes of two sibling species of M. violaceum in order to study host adaptation. Analysing polymorphism patterns, we found several selective sweeps along the genome, at different locations in the two species. We identified candidate genes for host-adaptation in the regions of selective sweeps, based on their expression pattern and on their putative functions. In addition, genes up-regulated in planta exhibited a higher rate of non-synonymous substitutions than other genes, suggesting that many of them are likely involved in host adaptation. This work paves the way to a larger comparison of genomes of different species of the M. violaceum species complex, in order to reconstruct the history of recombination suppression on the mating-type chromosomes on the one hand, and to study the genetic bases of adaptation to different hosts in a complex of phylogenetically close species on the other hand.

Subalpine larch (Larix lyallii Parl.) has a narrow ecological niche at timberline in the Cascade Range and the Rocky Mountains of western North America. Demographic factors, including a long generation time (average 500 years) and a late arrival at sexual maturity (100-200 years), make it unlikely that this species will be able to adapt to predicted climate change. A better understanding of genetic structure and genetic diversity is necessary in order to effectively manage this species for future generations. Foliage from 62 populations of subalpine larch was collected in order to elucidate the range-wide population genomics of the species. DNA was extracted and a next-generation sequencing method, restriction site associated DNA sequencing (RAD-seq), was used to generate genome-wide single nucleotide polymorphism (SNP) marker data. Three genetically differentiated clusters were identified via principal components analysis, a discriminant analysis of principal components and Bayesian STRUCTURE analysis: the Cascade Range, the southern Rocky Mountains and the northern Rocky Mountains. A monophyletic group in the central Rocky Mountains was also identified in a dendrogram of genetic distance but this group had weak bootstrap support (49%), meaning genetic differentiation depends on relatively few genetic variants. Genetically differentiated groups should be prioritized for future management and conservation efforts. Negative values of Tajima’s D and preferred demographic scenarios generated by coalescent simulations indicated that 15 populations all have a recent history of expansion. Genetic diversity within these populations was found to be moderate (HO = 0.15 – 0.20), inbreeding coefficients were found to be high (FIS = 0.15 – 0.25) and genetic differentiation among populations was found to be high (average FST = 0.18). These results indicated that fragmentation driven by Holocene warming may have resulted in reduced effective population sizes. Smaller populations experience stronger genetic drift and an increased likelihood of inbreeding, which may hinder an adaptive response to natural selection. Still, parameter estimates for preferred demographic scenarios suggested a minimum effective population size of around 20,000 individuals, which is not considered small by most conservationists. A final study of 18 populations found local adaptation to cold temperature in the northern portion of the species range. In all seasons, populations from the northern Rocky Mountains had significantly higher cold tolerance than populations from the central Canadian Rocky Mountains and the northern Cascades. Winter cold tolerance showed strong clines associated with the frost-free period and degree days below zero. These two climate variables explained 65% of the explainable variance in phenotype when redundancy analysis models were conditioned on geography. Seven SNPs were identified that explained a significant portion of the variance in winter cold tolerance. Range-wide, additional SNPs were identified as FST outliers and/or as significantly correlated with environmental gradients, even after correcting for neutral genetic structure. Together, the results of this work indicate that dispersal, neutral evolutionary processes and natural selection have all played important roles in shaping patterns of genetic variation across the natural range of subalpine larch. All of these factors should be considered during the development of management and conservation strategies for this high-elevation conifer species. / Graduate

No description available.

Yes / Buruli ulcer is a neglected tropical disease of skin and subcutaneous tissue caused by infection with the pathogen Mycobacterium ulcerans. Many critical issues for disease control, such as understanding the mode of transmission and identifying source reservoirs of M. ulcerans, are still largely unknown. Here, we used genomics to reconstruct in detail the evolutionary trajectory and dynamics of M. ulcerans populations at a central African scale and at smaller geographical village scales. Whole-genome sequencing (WGS) data were analyzed from 179 M. ulcerans strains isolated from all Buruli ulcer foci in the Democratic Republic of the Congo, The Republic of Congo, and Angola that have ever yielded positive M. ulcerans cultures. We used both temporal associations and the study of the mycobacterial demographic history to estimate the contribution of humans as a reservoir in Buruli ulcer transmission. Our phylogeographic analysis revealed one almost exclusively predominant sublineage of M. ulcerans that arose in Central Africa and proliferated in its different regions of endemicity during the Age of Discovery. We observed how the best sampled endemic hot spot, the Songololo territory, became an area of endemicity while the region was being colonized by Belgium (1880s). We furthermore identified temporal parallels between the observed past population fluxes of M. ulcerans from the Songololo territory and the timing of health policy changes toward control of the Buruli ulcer epidemic in that region. These findings suggest that an intervention based on detecting and treating human cases in an area of endemicity might be sufficient to break disease transmission chains, irrespective of other reservoirs of the bacterium.

Sociability is an individual’s tendency to associate with conspecifics in a non-aggressive manner. Sociability can manifest in the formation of social groups that can reduce predation risk and increase feeding success. Studies of social behaviour in insects are typically through the lens of classically know social insects, however many insect species that have been long thought as non-social have been shown to exhibit social behaviour, in particular Drosophila. A previous experiment evolved lineages of high and low sociable fruit flies (Drosophila melanogaster) following 25 generations of artificial selection, after which RNA and DNA was extracted and sequenced. The main goal of this thesis was to integrate analyses of differential gene expression, transcript usage and population genomics to investigate the genetic architecture of sociability in Drosophila. I developed a pipeline to perform differential gene expression analysis by modelling gene expression using a generalized linear mixed-effect model. Here I found a total of 327 genes differentially expressed and 174 genes differentially expressed between the low and high sociable lineages. Next, I developed a pipeline to perform differential transcript usage analysis using a generalized linear mixed-effect model to model transcript usage. I found 619 genes to have transcripts with differential usage and 190 genes to have transcripts with differential usage between the low and high sociable lineages. Lastly, I developed a pipeline for population genomics to identify regions of the genome under selection. I identified genes that are likely under selection and the overlap between these genes and genes/transcripts found to be differentially expressed/used. Overall, I identified potential genes that are involved in the genetic architecture of sociability and can be further candidate tested. / Thesis / Master of Science (MSc)

A fundamental goal in biological research is to gain an understanding of the evolutionary processes and genetic elements that drive speciation. Genes responsible for reproductive isolation in young divergent lineages are particularly poorly known. In this thesis, the speciation genetics of carrion (Corvus (corone) corone) and hooded (C. (corone) cornix) crows were studied. These taxa differ strikingly in colouration and meet in a narrow hybrid zone in Europe, yet appear to be very similar genetically. A major component of reproductive isolation is social selection on colour differences. First, we investigated the genetic basis of plumage divergence between carrion and hooded crows using a candidate gene approach. Nucleotide divergence was confirmed to be low, while there was no evidence for any of the sequenced genes to be associated with colour differences. Second, we performed a simulation study to assess the performance of RNA-seq, a relatively novel approach that we later employed ourselves. We asked how variation in transcriptome complexity and bioinformatic workflow affected the accuracy of gene expression profiling. We generally found reassuring robustness and made a number of specific recommendations. Third, we compared the corticosterone stress response of carrion and hooded crows. In accordance with the hypothesis that the degree of melanization and physiological traits are correlated due to pleiotropy, we found a higher stress response in hooded crows, and detected possibly associated gene expression in pituitary. Fourth, we investigated genomic divergence by assembling a hooded crow reference genome followed by whole-genome resequencing of four European population samples. Northern European carrion crows were more similar to hooded crows than to Spanish carrion crows, pointing towards rampant introgression far beyond the hybrid zone. Nevertheless, several narrow genomic regions harboured high between-taxon divergence and were potentially associated with phenotypic traits. Fifth, we compared whole-transcriptome gene expression profiles between crows, focusing on skin with developing feathers. We used a design that allowed to differentiate between taxon-specific, colour-specific and body patterning effects. Widespread underexpression of genes in the melanogenesis pathway was associated with grey colour, and we detected several genes that may contribute to colour divergence in this system.

This thesis explores the role mutualist pollinators and their symbionts play in the genetic structuring and speciation of their host plants along an elevational gradient in Papua New Guinea. Using the fig and fig-wasp mutualism as a model system, we employed high-throughput sequencing techniques to explore fine-scale population genomics of both fig and wasps along their elevational range. We found there to be clear lowland and highland clustering of tree populations along the gradient, often with a mid-elevation contact zone. In the case of the pollinating wasps, we retrieved the same clustering except in this case, the genetic difference between clusters was high enough as to consider them as separate species. This result supports evidence from other studies challenging the cospeciation paradigm of one wasp species per fig species. In addition, we explore ecological traits which may promote, or at least, maintain, reproductive isolation between fig (sub)species along with behavioural preference tests from pollinating wasps. In order to further investigate the mechanisms promoting wasp speciation along the gradient, we describe Wolbachia infection status as well as strain type. Wolbachia-induced cytoplasmic incompatibility (CI) is often invoked as a possible speciation agent since it can rapidly provoke and maintain reproductive isolation between otherwise freely interbreeding insect populations. Finally, we explore non-pollinating fig wasp (NPFW) diversity along the gradient for a subset of our focal species. Our study reveals that there is a tight relationship between NPFW diversity and host species, and a mid-elevation peak.

D’après un rapport de l’OMS, la tuberculose reste en 2015 l’une des 10 premières causes de décès à l’échelle mondiale. De ce fait, en matière de santé, éradiquer la maladie à l’horizon 2030 est un des objectifs majeurs fixés par les Nations Unies. La bactérie responsable de cette infection, Mycobacterium tuberculosis, est un pathogène obligatoire dont l’origine et l’évolution sont intrinsèquement liées à celles de son hôte principal, Homo sapiens. En effet, les souches actuelles de tuberculose présentent, tout comme l’homme, une forte structure phylogénétique, trace de leur origine géographique. Les pays pauvres et en développement sont les plus touchés par l’épidémie globale, favorisée par des systèmes de santé défaillants et une haute prévalence du VIH. Les pays occidentaux ne sont pas épargnés, menacés par l’émergence de souches de plus en plus résistantes aux antibiotiques provenant en grande partie de l’ex URSS. Au cours de cette thèse, j’analyse l’histoire évolutive, la propagation et l’acquisition de résistances aux antibiotiques de plusieurs épidémies de tuberculose en me basant sur des données génétiques et génomiques. Dans un premier temps je m’intéresse aux effets d’une campagne nationale de traitements en Asie Centrale sur le développement de souches multi-résistantes et met également en lumière le rôle clef de certaines mutations dans le succès des clones présentés. Ainsi cette campagne a été partiellement mise en échec par la présence de souches pré-résistantes, grâce à la survenue de mutations avant même la mise en place des traitements antibiotiques. Par la suite je me suis focalisé sur un clade particulier de souches multi-résistantes, le clone Russe W148. Je présente sa dispersion géographique et temporelle à travers l’Eurasie et démontre l’importance des mutations compensatoires dans son succès épidémique. De plus, la tuberculose ne touche pas seulement les hommes mais infecte également plusieurs autres mammifères. Afin d’appréhender les contraintes adaptatives accompagnants ces changements d’hôtes, j’ai effectué divers tests de sélection dans le but d’identifier les gènes impliqués. Pour finir, nous avons développé un indice souche spécifique, permettant de mesurer le succès épidémique de celles-ci à un niveau individuel. Dans le cadre d’études épidémiologiques, cette mesure peut être croisée avec des informations sur le patient, la souche ou même socio-économiques. / According to a 2015 WHO report, tuberculosis remains one of the top 10 causes of death worldwide. Despite considerable efforts by the United Nations to eradicate the disease by 2030, a global TB epidemic still persists. Its causative agent, the bacterium Mycobacterium tuberculosis, an obligate pathogen, has been plaguing humanity since it originated, and has coevolved with its main host, Homo sapiens, over thousands of years. Contemporary tuberculosis strains exhibit a structured phylogeographic pattern, carrying the genetic print of their geographic origin. The Koch bacillus infects and kills in large numbers, in poor and developing countries, where fragile health care systems, combined with high HIV prevalence, facilitate epidemic spread. In western countries, the major current threats are the multiplication and propagation of antibiotic resistant strains (MDR/XDR) coming predominantly from former Soviet republics. In this thesis, I unravel the evolutionary history, propagation, and acquisition of drug resistance-conferring mutations in different settings, by implementing multiple genetic and genomic data sets. First, focusing on Central Asia, using whole genome sequencing and Bayesian statistics, I assess the effects of a treatment campaign on the development of MDR strains and highlight key mutations in successful strains. More importantly, the success of DOTs campaigns was compromised by the genetic make-up of these outbreak clades (pre-treatment low frequency resistance SNPs). Special attention was also given to a particular outbreak of MDR strains, i.e. the Russian W148 clone. I present its westward spatial and temporal propagation at a continental scale during the last century, and underline the key contribution of compensatory mutations in its epidemic success. However, tuberculosis does not only infect humans, but also has experienced successive mammalian host jumps. To decipher the adaptive constraints accompanying such secondary events, a systemic gene screen with selection signature-detecting algorithms was implemented to identify putative targets during diversifying selection. Finally, novel mathematical tools and indices that reflect the epidemicity of a strain were developed, jumping from a population-driven approach to a strain specific one, with broader epidemiological applications. This allows us to correlate strain fitness with patient, lineage, and socio-economic information.