Antibiotic resistance is critical to global health. This thesis examines the relationship between antibiotic resistance and genomic variations in E. coli from wastewater. E. coli is of interest as it causes urinary tract and other infections. Wastewater is a good source because it is a melting pot for E. coli from diverse origins. The research delves into two key aspects: including or excluding antibiotic resistance data and the level of granularity in representing genomic variations. The former is important because there is more genomic data than antibiotic resistance data. Consequently, relying solely on genomic data, this thesis studies positive selection in E. coli to identify mutations and genes favored by evolution. This study demonstrates the preferential selection of known antibiotic resistance genes and mutations, particularly mutations located on functionally important locations of outer membrane porins, and may hence have a direct effect on structure and function. Encouraged by these results, the study was expanded to include antibiotic resistance data and to examine genomic variations at three resolution levels: single mutations, unitigs (genome words) that may contain multiple mutations, and whole coding genome using machine learning classifier models that capture dependencies among multiple mutations and other genomic variations. Representation of single mutations detects well-known resistance mutations as well as potentially novel mechanisms related to biofilm formation and translation. By exploring larger genomic units such as genome words, the analysis confirms the findings from single mutations and additionally uncovers joint mutations in both known and novel genes. Finally, machine learning models, including AI language models, were trained to predict antibiotic resistance based on the whole coding genome. This achieved an accuracy of over 90% in predicting antibiotic resistance when sufficient data were available. Overall, this thesis unveils new antibiotic resistance mechanisms, conducts one of the largest studies of positive selection in E. coli, and stands out as one of the pioneering studies that utilizes AI language models for antibiotic resistance prediction.

No description available.

L'identification de régions génomiques cibles de la sélection naturelle positive permet de mieux comprendre notre passé évolutif et de trouver des variants génétiques fonctionnels importants. Puisque la fréquence des allèles sélectionnés augmente dans la population, la sélection laisse des traces sur les séquences d'ADN et ces empreintes sont détectées lorsque la variabilité génétique d'une région est différente de celle attendue sous neutralité sélective. On propose une nouvelle approche pour analyser les données de polymorphismes : le calcul des classes alléliques d’haplotypes (HAC), permettant d'évaluer la diversité globale des haplotypes en étudiant leur composition allélique. L'idée de l'approche est de déterminer si un site est sous sélection positive récente en comparant les distributions des HAC obtenues pour les deux allèles de ce site. Grâce à l'utilisation de données simulées, nous avons étudié ces distributions sous neutralité et sous sélection en testant l'effet de différents paramètres populationnels. Pour tester notre approche empiriquement, nous avons analysé la variation génétique au niveau du gène de lactase dans les trois populations inclues dans le projet HapMap. / Natural selection eliminates detrimental and favors advantageous phenotypes. This process leaves characteristic signatures in the underlying genomic segments that can be recognized through deviations in the allelic or in haplotypic frequency spectra. We introduce a new way of looking at the genomic single nucleotide polymorphisms : the haplotype allelic classes (HAC). The model combine segregating sites and haplotypic informations in order to reveal useful characteristics of the data, providing an identifiable signature of recent positive selection that can be detected by comparison with the background distribution. We compare the HAC distribution's partition between the haplotypes carrying the selected allele and the remaining ones. Coalescence simulations are used to study the distributions under standard population models assuming neutrality, demographic scenarios and selection models. To test, in practice, the performance of HAC and the derived statistic in capturing deviation from neutrality due to selection, we analyzed the genetic variation in the locus of lactase persistence in the three HapMap populations.

L’adénovirus possède plusieurs caractéristiques faisant de ce virus un candidat de choix pour la construction de vecteurs utiles dans les études de génomique fonctionnelle. Dans la majorité de ces applications, on a recours à un vecteur adénoviral de première génération délété de sa région E1. L’utilisation de vecteurs adénoviraux comprend deux maillons faibles : la construction du vecteur et la production subséquente de ce dernier. Le développement de méthodes alternatives est donc nécessaire pour renforcer ces deux maillons, permettant ainsi une utilisation étendue de ces vecteurs. Ce développement va s’articuler sur deux axes : l’ingénierie du vecteur de transfert pour la construction de l’adénovirus recombinant et l’ingénierie d’une lignée cellulaire pour la production du vecteur. En utilisant un vecteur de transfert adénoviral co-exprimant, à partir d’un promoteur régulable à la tétracycline, la protéase de l’adénovirus et une protéine de fluorescence verte (GFP) par l’intermédiaire d’un site d’entrée ribosomal interne (IRES), notre groupe a établi que la sélection positive, via l’expression ectopique de la protéase, est un processus efficace pour la création de librairie d’adénovirus recombinants. Par contre, la diversité atteinte dans ce premier système est relativement faible, environ 1 adénovirus recombinant par 1 000 cellules. Le travail effectué dans le cadre de cette thèse vise à construire un nouveau transfert de vecteur dans lequel l’expression de la protéase sera indépendante de celle du transgène permettant ainsi d’optimiser l’expression de la protéase. Ce travail d’optimisation a permis de réduire le phénomène de transcomplémentation du virus parental ce qui a fait grimper la diversité à 1 virus recombinant par 75 cellules. Ce système a été mis à l’épreuve en générerant une librairie adénovirale antisens dirigée contre la GFP. La diversité de cette librairie a été suffisante pour sélectionner un antisens réduisant de 75% l’expression de la GFP. L’amplification de ce vecteur adénoviral de première génération doit se faire dans une lignée cellulaire exprimant la région E1 telle que les cellules 293. Par contre, un adénovirus de première génération se répliquant dans les cellules 293 peut échanger, par recombinaison homologue, son transgène avec la région E1 de la cellule créant ainsi un adénovirus recombinant réplicatif (RCA), compromettant ainsi la pureté des stocks. Notre groupe a déjà breveté une lignée cellulaire A549 (BMAdE1) exprimant la région E1, mais qui ne peut pas recombiner avec le transgène du virus. Par contre, le niveau de réplication de l’adénovirus dans les BMAdE1 est sous-optimal, à peine 15-30% du niveau obtenu dans les cellules 293. Le travail fait dans le cadre de cette thèse a permis de mettre en évidence qu’une expression insuffisante d’E1B-55K était responsable de la mauvaise réplication du virus dans les BMAdE1. Nous avons produit de nouveaux clones à partir de la lignée parentale via une transduction avec un vecteur lentiviral exprimant E1B-55K. Nous avons confirmé que certains clones exprimaient une plus grande quantité d’E1B-55K et que ces clones amplifiaient de manière plus efficace un vecteur adénoviral de première génération. Ce clone a par la suite été adapté à la culture en suspension sans sérum. / The adenovirus has numerous interesting characteristics making this particular virus an ideal candidate for the construction of vector for conducting studies in functional genomics. The vast majority of those applications rely on a so-called “first-generation vector” in which the E1 region is replaced by a transgene. Despite all their advantages, there are 2 weak links associated with first-generation vector: the efficient construction of the actual vector and its production. Therefore, the development of alternative methods for construction and production is necessary to ensure their usefulness. The development will involve 2 axes: the reengineering of the transfer vector for the construction of recombinant adenovirus and the reengineering of the cell line capable of producing the vector. Using a transfer vector co-expressing the adenoviral protease (PS) gene and GFP by using an IRES under the control of a tetracycline-regulated promoter, our laboratory previously established the proof of concept that positive selection of recombinant adenovirus through ectopic expression of the PS gene was an efficient approach to generate adenoviral libraries. However, the diversity achieved was quite low, around 1 recombinant adenovirus per 1,000 cells. The goal of this thesis was to design a new transfer vector in which the PS expression was independent from the expression of the transgene in order to be able to optimize its expression independently. We also improved library diversity by lowering the amount of PS in order to reduce the the trans-complementation from the transfer vector. Using this method, at least 1 recombinant adenovirus per 75 cells was generated with 100% of the plaques being recombinant. This system was successfully used to generate an antisense library targeting GFP. The diversity of the library was high enough to allow the selection of an antisense that inhibited 75% of GFP expression. Amplification of those first-generation recombinant adenoviruses must take place in an E1-expressing cell such as 293 cells. However, when replicating in 293 cells, the recombinant adenovirus can exchange their transgene with the E1 region of the cell by homologous recombination, which results in the generation of a fully replicative adenovirus (RCA), a situation that compromises the purity of the viral preparation. Our laboratory has previously patented an A549 cell line expressing the E1 region and producing RCA-free recombinant adenovirus (BMAdE1). However, the replication of E1-deleted adenovirus in BMAdE1 cells was sub-optimal, in the range of 15-30% the level obtained in 293 cells. The work done in this thesis establishes that the low level of E1B-55K could be responsible for the lower productivity of BMAdE1 cells. Thus, we have derived new clones following lentiviral transduction in order to increase E1B-55K expression. Western blot confirmed that some clones expressed more E1B-55K than BMAdE1, and this correlated with a more robust replication of a recombinant adenovirus in those clones. This newly optimized BMAdE1 cell line was adapted to serum-free suspension culture.

Dans le cadre de cette thèse nous nous sommes intéressés à l'étude de l'évolution et de la variabilité génétique de la famille des butyrophilines (BTN), des récepteurs de la superfamille des immunoglobulines impliqués dans la régulation de la réponse immunitaire. Par une étude phylogénétique approfondie nous avons caractérisé chez les mammifères 14 groupes phylogénétiques résultant d'une série de duplications à partir de huit gènes ancestraux à la base des thériens. Par la suite, nous avons étudié l'évolution des BTN de la région CMH chez les primates et leur variabilité génétique dans les populations humaines par une analyse minutieuse des données de séquençage générées du projet 1000 Genomes pour plus de 1600 individus à travers le monde. Nous avons montré que l'évolution du gène BTNL2 est marquée par une pression de sélection positive diversifiante chez les mammifères qui est accompagnée chez les hominoïdes d'un niveau de polymorphisme élevé induisant la formation de variants tronqués de BTNL2. Chez l'homme, quatre lignages d'allèles ont été identifiés. Ils ont été maintenus à des fréquences intermédiaires par une forte sélection balancée. D'autre part, l'analyse phylogénétique détaillée du groupe BTN3 (BTN3A1, 3A2 et 3A3) a montré la présence d'une évolution concertée, caractérisée par une homogénéisation forte et récurrente de la région codant pour le peptide signale et le domaine IgV chez les hominoïdes, au cours de laquelle les séquences de 3A1 et 3A3 sont remplacées par la séquence de 3A2. Chez l'homme, ces gènes sont polymorphismes important avec plus de 46 allèles chacun, mais avec la présence d'une homogénéisation extrême des séquences du domaine IgV / In this thesis we were interested in studying the evolution and the genetic variability of the butyrophilin family (BTN), a family of immune receptors belonging to the immunoglobulin superfamily implicated in the regulation of immune response. Through a thorough phylogenetic study of the family we characterized 14 phylogenetic groups in mammals resulting from a series of duplications from eight ancestral genes at the base of therian. Thereafter, we studied the evolution of the BTN of the MHC region and their genetic variability in human populations by a careful analysis of sequencing data generated by the consortium 1000 Genomes for more than 1,600 individuals representing 26 populations worldwide. We have shown that the evolution of BTNL2 gene is marked by a positive diversifying selection in placental mammals. This selection pressure is accompanied in hominoids of a high level of polymorphism inducing the formation of truncated BTNL2 variants. In humans this high level of polymorphism results in the presence of four ancient allele lineages that are maintained at intermediate frequencies by a strong balancing selection. On the other hand, a detailed phylogenetic analysis of BTN3 group (BTN3A1, 3A2 and 3A3) showed that these genes evolve in hominoids in a concerted manner characterized by a strong and recurrent homogenization of the regions encoding for the peptide signal and the IgV domain in which the 3A1 and 3A3 sequences are replaced by the 3A2 sequence. In humans these genes are polymorphic with over 46 alleles each, but with the presence of extreme homogenization of IgV domain sequences

Plant pathogens have the ability to quickly overcome host resistance and shift to novel hosts. The (re)emergence of plant pathogens is a major concern in agriculture and in conservation of natural landscapes. The rapid adaptation to hosts and new environments depends on the genetic variability in pathogen populations. Despite of the importance of sugarcane for Brazilian agribusiness and the persistence of the smut pathogen Sporisorium scitamineum in most cropping areas, genetic variation studies are still missing for Brazilian isolates. In the chapters 1 and 2, molecular variability studies were performed for Brazilian and Argentine isolates of S. scitamineum, using molecular markers (AFLP, telRFLP) and sequencing (ITS and a candidate effector gene) strategies. No variation was found in ITS sequences. On the contrary, telRFLP marker generates almost a unique fingerprint for each strain. Two genetically distinct groups were formed by the joint analysis of the AFLP and telRFLP markers. The two groups were the same formed by haplotypes of a candidate effector gene. The presence of polymorphisms that causes non-synonymous mutations in a candidate effector gene potentially involved in the specific interaction with sugarcane may cause distinct performances on host genotypes. S. scitamineum is part of the highly diverse clade of Ustilaginomycetes fungi that includes several smut disease agents. Despite being phylogenetically close and present similar lifestyles, species of smut fungi have distinct and narrow host ranges. Hence, another objective in this thesis was to identify the genetic basis of host specialization in smut fungi using comparative genomics analyses. In chapter 3, the mating-type loci were described in S. scitamineum genome and compared among smut fungi. Transposable elements are the likely mechanism causing chromosomal rearrangements between mating-type loci. The presence of trans-specific polymorphisms at the genes encoding pheromone/receptor proteins suggests a hybridization potential among smut species. In the chapter 4, a broad comparative genomics analysis was performed among nine species of smut fungi infecting distinct hosts. The genetic basis of host specialization in smut fungi is complex and seems to involve a range of evolutionary processes, including gene gain/loss and episodic selection events. Species-specific effectors and positively selected genes will be good candidates for further characterization in regards to their role in host adaptation. / Fitopatógenos apresentam a habilidade de rapidamente suplantar os mecanismos de defesas da planta e adaptar-se a um novo hospedeiro. A (re)emergência de patógenos é uma das maiores preocupações na agricultura e na conservação de populações naturais. A rápida adaptação ao hospedeiro e a novos ambientes depende da variabilidade genética nas populações de patógenos. Apesar da importância da cana-de-açúcar para o agronegócio brasileiro e da persistência do patógeno Sporisorium scitamineum, o agente causal do carvão da cana-de-açúcar, na maioria das áreas canavieiras, estudos de variabilidade genética ainda não foram realizados para isolados brasileiros. Nos capítulos 1 e 2, estudos de variabilidade molecular foram realizados para isolados brasileiros e argentinos de S. scitamineum, usando marcadores moleculares (AFLP e telRFLP) e dados de sequenciamento (ITS e um gene candidato a efetor). Nenhum polimorfismo foi encontrado usando sequências ITS. Contrariamente, o marcador telRFLP gerou quase um fingerprint para cada linhagem. Dois grupos geneticamente distintos foram formados pela análise conjunta dos marcadores telRFLP e AFLP. Os dois grupos também foram formados pelos haplótipos obtidos pelo sequenciamento de um candidato a efetor. A presença de polimorfismos causando mutações não-sinônimas em um candidato a efetor pode acarretar em performances distintas em diferentes genótipos de cana-de-açúcar. S. scitamineum pertence à classe Ustilaginomycetes, a qual também abrange vários outros agentes causais de doenças do carvão. Apesar de filogeneticamente próximos e com estilo de vida similar, espécies de carvão apresentam uma faixa distinta e estreita de hospedeiros. Portanto, outro objetivo desta tese foi identificar a base genética da especialização ao hospedeiro por fungos causadores de carvão usando análises de genômica comparativa. No capítulo 3, os loci envolvidos na determinação do tipo de reação sexual (mating-type) foram caracterizados no genoma de S. scitamineum e comparados com sequências de outras espécies de carvão. Tranposons foram identificados como provável mecanismo de rearranjo cromossômico entre os loci de mating-type. Polimorfismos trans-específicos nos genes codificadores de feromônios e receptores sugerem o potencial de hibridização entre espécies de carvão. No capítulo 4, análises de genômica comparativa abrangendo nove espécies de carvão infectando hospedeiros distintos foram realizadas. A base genética da especialização ao hospedeiro em fungos causadores de carvão é complexa e parece envolver processos evolutivos de ganho/perda de genes e seleção positiva. Efetores espécie-específicos e sob seleção positiva são destacados como bons candidatos para serem caracterizados quanto ao papel que estabelecem na adaptação ao hospedeiro.

L'identification de régions génomiques cibles de la sélection naturelle positive permet de mieux comprendre notre passé évolutif et de trouver des variants génétiques fonctionnels importants. Puisque la fréquence des allèles sélectionnés augmente dans la population, la sélection laisse des traces sur les séquences d'ADN et ces empreintes sont détectées lorsque la variabilité génétique d'une région est différente de celle attendue sous neutralité sélective. On propose une nouvelle approche pour analyser les données de polymorphismes : le calcul des classes alléliques d’haplotypes (HAC), permettant d'évaluer la diversité globale des haplotypes en étudiant leur composition allélique. L'idée de l'approche est de déterminer si un site est sous sélection positive récente en comparant les distributions des HAC obtenues pour les deux allèles de ce site. Grâce à l'utilisation de données simulées, nous avons étudié ces distributions sous neutralité et sous sélection en testant l'effet de différents paramètres populationnels. Pour tester notre approche empiriquement, nous avons analysé la variation génétique au niveau du gène de lactase dans les trois populations inclues dans le projet HapMap. / Natural selection eliminates detrimental and favors advantageous phenotypes. This process leaves characteristic signatures in the underlying genomic segments that can be recognized through deviations in the allelic or in haplotypic frequency spectra. We introduce a new way of looking at the genomic single nucleotide polymorphisms : the haplotype allelic classes (HAC). The model combine segregating sites and haplotypic informations in order to reveal useful characteristics of the data, providing an identifiable signature of recent positive selection that can be detected by comparison with the background distribution. We compare the HAC distribution's partition between the haplotypes carrying the selected allele and the remaining ones. Coalescence simulations are used to study the distributions under standard population models assuming neutrality, demographic scenarios and selection models. To test, in practice, the performance of HAC and the derived statistic in capturing deviation from neutrality due to selection, we analyzed the genetic variation in the locus of lactase persistence in the three HapMap populations.

L’adénovirus possède plusieurs caractéristiques faisant de ce virus un candidat de choix pour la construction de vecteurs utiles dans les études de génomique fonctionnelle. Dans la majorité de ces applications, on a recours à un vecteur adénoviral de première génération délété de sa région E1. L’utilisation de vecteurs adénoviraux comprend deux maillons faibles : la construction du vecteur et la production subséquente de ce dernier. Le développement de méthodes alternatives est donc nécessaire pour renforcer ces deux maillons, permettant ainsi une utilisation étendue de ces vecteurs. Ce développement va s’articuler sur deux axes : l’ingénierie du vecteur de transfert pour la construction de l’adénovirus recombinant et l’ingénierie d’une lignée cellulaire pour la production du vecteur. En utilisant un vecteur de transfert adénoviral co-exprimant, à partir d’un promoteur régulable à la tétracycline, la protéase de l’adénovirus et une protéine de fluorescence verte (GFP) par l’intermédiaire d’un site d’entrée ribosomal interne (IRES), notre groupe a établi que la sélection positive, via l’expression ectopique de la protéase, est un processus efficace pour la création de librairie d’adénovirus recombinants. Par contre, la diversité atteinte dans ce premier système est relativement faible, environ 1 adénovirus recombinant par 1 000 cellules. Le travail effectué dans le cadre de cette thèse vise à construire un nouveau transfert de vecteur dans lequel l’expression de la protéase sera indépendante de celle du transgène permettant ainsi d’optimiser l’expression de la protéase. Ce travail d’optimisation a permis de réduire le phénomène de transcomplémentation du virus parental ce qui a fait grimper la diversité à 1 virus recombinant par 75 cellules. Ce système a été mis à l’épreuve en générerant une librairie adénovirale antisens dirigée contre la GFP. La diversité de cette librairie a été suffisante pour sélectionner un antisens réduisant de 75% l’expression de la GFP. L’amplification de ce vecteur adénoviral de première génération doit se faire dans une lignée cellulaire exprimant la région E1 telle que les cellules 293. Par contre, un adénovirus de première génération se répliquant dans les cellules 293 peut échanger, par recombinaison homologue, son transgène avec la région E1 de la cellule créant ainsi un adénovirus recombinant réplicatif (RCA), compromettant ainsi la pureté des stocks. Notre groupe a déjà breveté une lignée cellulaire A549 (BMAdE1) exprimant la région E1, mais qui ne peut pas recombiner avec le transgène du virus. Par contre, le niveau de réplication de l’adénovirus dans les BMAdE1 est sous-optimal, à peine 15-30% du niveau obtenu dans les cellules 293. Le travail fait dans le cadre de cette thèse a permis de mettre en évidence qu’une expression insuffisante d’E1B-55K était responsable de la mauvaise réplication du virus dans les BMAdE1. Nous avons produit de nouveaux clones à partir de la lignée parentale via une transduction avec un vecteur lentiviral exprimant E1B-55K. Nous avons confirmé que certains clones exprimaient une plus grande quantité d’E1B-55K et que ces clones amplifiaient de manière plus efficace un vecteur adénoviral de première génération. Ce clone a par la suite été adapté à la culture en suspension sans sérum. / The adenovirus has numerous interesting characteristics making this particular virus an ideal candidate for the construction of vector for conducting studies in functional genomics. The vast majority of those applications rely on a so-called “first-generation vector” in which the E1 region is replaced by a transgene. Despite all their advantages, there are 2 weak links associated with first-generation vector: the efficient construction of the actual vector and its production. Therefore, the development of alternative methods for construction and production is necessary to ensure their usefulness. The development will involve 2 axes: the reengineering of the transfer vector for the construction of recombinant adenovirus and the reengineering of the cell line capable of producing the vector. Using a transfer vector co-expressing the adenoviral protease (PS) gene and GFP by using an IRES under the control of a tetracycline-regulated promoter, our laboratory previously established the proof of concept that positive selection of recombinant adenovirus through ectopic expression of the PS gene was an efficient approach to generate adenoviral libraries. However, the diversity achieved was quite low, around 1 recombinant adenovirus per 1,000 cells. The goal of this thesis was to design a new transfer vector in which the PS expression was independent from the expression of the transgene in order to be able to optimize its expression independently. We also improved library diversity by lowering the amount of PS in order to reduce the the trans-complementation from the transfer vector. Using this method, at least 1 recombinant adenovirus per 75 cells was generated with 100% of the plaques being recombinant. This system was successfully used to generate an antisense library targeting GFP. The diversity of the library was high enough to allow the selection of an antisense that inhibited 75% of GFP expression. Amplification of those first-generation recombinant adenoviruses must take place in an E1-expressing cell such as 293 cells. However, when replicating in 293 cells, the recombinant adenovirus can exchange their transgene with the E1 region of the cell by homologous recombination, which results in the generation of a fully replicative adenovirus (RCA), a situation that compromises the purity of the viral preparation. Our laboratory has previously patented an A549 cell line expressing the E1 region and producing RCA-free recombinant adenovirus (BMAdE1). However, the replication of E1-deleted adenovirus in BMAdE1 cells was sub-optimal, in the range of 15-30% the level obtained in 293 cells. The work done in this thesis establishes that the low level of E1B-55K could be responsible for the lower productivity of BMAdE1 cells. Thus, we have derived new clones following lentiviral transduction in order to increase E1B-55K expression. Western blot confirmed that some clones expressed more E1B-55K than BMAdE1, and this correlated with a more robust replication of a recombinant adenovirus in those clones. This newly optimized BMAdE1 cell line was adapted to serum-free suspension culture.

Primates are one of the best characterized phylogenies with vast amounts of comparative data available, including genomic sequences, gene expression, and epigenetic modifications. Thus, they provide an ideal system to study sequence evolution, regulatory evolution, epigenetic evolution as well as their interplays. Comparative studies of primate genomes can also shed light on molecular basis of human-specific traits. This dissertation is mainly composed of three chapters studying human and non-human primate evolution. The first study investigated evolutionary rate difference between sex chromosome and autosomes across diverse primate species. The second study developed an unbiased approach without the need of prior information to identify genomic segments under accelerated evolution. The third study investigated interplay between genomic and epigenomic evolution of humans and chimpanzees. Research advance 1: evolutionary rates of the X chromosome are predicted to be different from those of autosomes. A theory based on neutral mutation predicts that the X chromosome evolves slower than autosomes (slow-X evolution) because the numbers of cell division differ between spermatogenesis and oogenesis. A theory based on natural selection predicts an opposite direction (fast-X evolution) because newly arising beneficial mutations on the autosomes are usually recessive or partially recessive and not exposed to natural selection. A strong slow-X evolution is also predicted to counteract the effect of fast-X evolution. In our research, we simultaneously studied slow-X evolution, fast-X evolution as well as their interaction in a phylogeny of diverse primates. We showed that slow-X evolution exists in all the examined species, although their degrees differ, possibly due to their different life history traits such as generation times. We showed that fast-X evolution is lineage-specific and provided evidences that fast-X evolution is more evident in species with relatively weak slow-X evolution. We discussed potential contribution of various degrees of slow-X evolution on the conflicting population genetic inferences about human demography. Research advance 2: human-specific traits have long been considered to reside in the genome. There has been a surge of interest to identify genomic regions with accelerated evolution rate in the human genome. However, these studies either rely on a priori knowledge or sliding windows of arbitrary sizes. My research provided an unbiased approach based on previously developed “maximal segment” algorithm to identify genomic segments with accelerated lineage-specific substitution rate. Under this framework, we identified a large number of human genomic segments with clustered human-specific substitutions (named “maximal segments” after the algorithm). Our identified human maximal segments cover a significant amount of previously identified human accelerated regions and overlap with genes enriched in developmental processes. We demonstrated that the underlying evolutionary forces driving the maximal segments included regionally increased mutation rate, biased gene conversion and positive selection. Research advance 3: DNA methylation is one of the most common epigenetic modifications and plays a significant role in gene regulation. How DNA methylation status varies on the evolutionary timescale is not well understood. In this study, we investigated the role of genetic changes in shaping DNA methylation divergence between humans and chimpanzees in their sperm and brain, separately. We find that for orthologous promoter regions, CpG dinucleotide content difference is negatively correlated with DNA methylation level difference in the sperm but not in the brain, which may be explained by the fact that CpG depleting mutations better reflect germline DNA methylation levels. For the aligned sites of orthologous promoter regions, sequence divergence is positively correlated with methylation divergence for both tissues. We showed that the evolution of DNA methylation can be affected by various genetic factors including transposable element insertions, CpG depleting mutations and CpG generating mutations.

No description available.