BACKGROUND:Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes.RESULTS:Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the duplication arose as a result of NAHR using L1 elements as substrates. L1 and ERVII retrotransposons are considerably denser in the Abp regions than in one Mb flanking regions, while other repeat types are depleted in the Abp regions compared to flanking regions. L1 retrotransposons preferentially accumulated in the Abp gene regions after lineage separation and roughly followed the pattern of Abp gene expansion. By contrast, the proportion of shared vs. lineage-specific ERVII repeats in the Abp region resembles the rest of the genome.CONCLUSIONS:We confirmed the role of L1 repeats in Abp gene duplication with the identification of recombinant L1Md_T elements at the edges of the most recent mouse Abp gene duplication. High densities of L1 and ERVII repeats were found in the Abp gene region with abrupt transitions at the region boundaries, suggesting that their higher densities are tightly associated with Abp gene duplication. We observed that the major accumulation of L1 elements occurred after the split of the mouse and rat lineages and that there is a striking overlap between the timing of L1 accumulation and expansion of the Abp gene family in the mouse genome. Establishing a link between the accumulation of L1 elements and the expansion of the Abp gene family and identification of an NAHR-related breakpoint in the most recent duplication are the main contributions of our study.

This project aimed to reanalyse two large historical data sets from two different locations in New Zealand (Fiordland in the South Island and Pureora Forest Park in the North Island). The data describe populations of mice (Mus musculus), rats (Rattus rattus and R. norvegicus), and stoats (Mustela erminea) collected using standard monitoring techniques from five distinct types of forest habitat. The new analysis methods selected were an index of patchiness and Site Occupancy analysis. The objectives of the analysis were (1) to evaluate whether the patchiness index and Site Occupancy analysis methods might contribute to improved protocols for monitoring small mammal populations in the future, and (2) to use formal tests of five hypotheses to evaluate two of the assumptions made by the conventional density index often used in small mammal studies. I describe the results of the analyses for each species, including any problems encountered (such as the inability of the Site Occupancy method to analyse very sparse data sets). I also describe the results pooled from each of the two study locations and potential consequences for small mammal monitoring and control. This analysis has suggested that in most cases the density index is not a rigorous measure of small mammal populations. However, both the index of patchiness and Site Occupancy analysis provided useful, new information about these populations of rodents and stoats, despite the fact that these historical data sets were not designed for use with modern methods of analysis. Please note: some figures and tables were printed separately and added to the thesis as unnumbered pages. These can be found in the file 03Plates_and_Tables.pdf.

The PRDM9 (PR domain containing 9) protein is an epigenetic factor that trimethylates lysine 4 of histone H3 and thereby determines the future meiotic double-strand breaks - sites important for proper segregation of homologous chromosomes. Males of the Mus musculus domesticus (Mmd) origin with homozygous deletion in Prdm9 (Prdm9-/- ) are sterile with a complete arrest in meiotic prophase I, in contrast to the same mutant males of the M. m. musculus (Mmm) subspecies. The aim of this diploma thesis was to identify the genomic loci responsible for the phenotypic difference of these Prdm9-/- males. The major research tool was a population of 182 Mmm x Mmd Prdm9-/- males. The mapping method of quantitative trait loci (QTLs) was based on relating the genotypes of single-nucleotide and microsatellite polymorphisms to the observed phenotypes. At least two QTLs on Chr X were identified. The Mmm alleles of these QTLs reduced fertility of Prdm9-/- males. Both QTLs were confirmed and narrowed down using two types of subconsomic strains. It was not possible to confirm other QTLs, particularly on autosomes. This QTL mapping is the first step towards the identification of genes that modify the resulting phenotype of Prdm9-/- animals. This identification should help designing studies of human infertility that...

Hybrid zones provide a valuable opportunity to study the process of speciation in real time. Untested combinations of genes from diverging populations come to the contact here causing a breakdown of genetic interactions and giving rise to reproductive isolation. Two house mouse subspecies (Mus musculus musculus/Mus musculus domesticus) form a narrow zone of secondary contact across Central Europe which is thought to be maintained by a balance between selection against unfit hybrids and dispersion of individuals. During my PhD study my collaborators and I used an array of ~ 1400 SNP markers to study patterns of introgression on a genome-wide scale across two/three house mouse hybrid zone transects. Our aim was to identify the genomic regions putatively harboring genes which are involved in the reproductive isolation between the two subspecies, characterize their distribution in mouse genome and assess genomic features associated with them. We were able to confirm on a genome-wide scale the importance of the X chromosome in the evolution of reproductive isolation. This chromosome exhibited introgression corresponding to strong negative epistasis and the patterns were consistent between transects pointing out to a common basis of reproductive isolation playing a role in two transects. Contrary to the...

The aim of my thesis was to identify proteins involved in chemical communication and especially those that are involved in sexual signalling. Volatile chemical signals are transported with lipocalins in their beta-barrel structure to present their ligands to receptors or out of the body. Thus, I focused on the identification of these proteins in saliva and vaginal secretion of the house mouse using proteomic and transcriptomic approaches. Due to a cyclic manner of reproduction and its hormonal control, I have also focused on the role of estradiol on sperm phenotype in the laboratory mouse. We have identified an elevated sexual dimorphism in several lipocalins (i.e. 10 out of 20) in the saliva proteome where they may play a role in sexual signalling (i.e. similar to their described roles in the mouse urine). Interestingly, vaginal secretion also contains lipocalins and they rise from proestrus to estrus and remain steady during metestrus. Such variation provides evidence that they serve sexual signalling, however, due to their elevated levels during metestrus it is most likely that their ligands function as signals and not the proteins themselves. On the level of sperm phenotype, we have provided evidence, that experimental concentrations of estradiol have differential effects on sperm. This is due...

Comprendre quels mécanismes contrôlent la variabilité phénotypique et comment ces mécanismes influencent et contraignent la divergence interspécifique est un objectif important en biologie de l'Evolution. Dans cette thèse, nous avons essayé d'étudier comment l'histoire phylogénétique, la génétique, l'environnement, et le développement influencent l'évolution d'une structure morphologique complexe, en utilisant la mandibule de la souris domestique comme modèle.Afin d'étudier les processus qui contrôlent la variation phénotypique, des analyses de génétique quantitative ont été réalisées sur un pedigree obtenu à partir des individus sauvages d'une population de la souris domestique. Les descendants ont été divisés en deux, l'un suit un régime alimentaire dur et l'autre un régime alimentaire mou, pour que l'effet de la plasticité phénotypique puisse être considérée. On montre que le développement et les contraintes épigénétiques pourraient changer l'architecture génétique des traits morphologiques dans une population. En outre, les résultats suggèrent que la plasticité phénotypique pourrait être adaptative dans certaines conditions environnementales, mais pas dans d'autres.Ensuite, on a utilisé la mandibule de la souris domestique pour étudier les patrons de l'évolution morphologique des populations de cette espèce dans un contexte phylogéographique. Les résultats suggèrent que la divergence morphologique chez la souris domestique a suivi la différenciation génétique. On a aussi trouvé que la variation morphologique a augmenté au cours de l'expansion des sous-espèces sans qu'une convergence significative n'accompagne l'évolution vers le commensalisme avec l'homme. Finalement on a déterminé si l'hypothèse d'évolution de la mandibule sous l'effet de la dérive génétique peut expliquer la diversification morphologique au cours de la divergence et d'expansion de la souris domestique. Les résultats rejettent cette hypothèse et plaident en faveur d'autres forces évolutives telles que la sélection.Nos résultats, dans leur ensemble, montre une origine multifactorielle de la variation et permettent de mieux comprendre la diversification morphologique des populations et des sous-espèces de la souris domestique. / A major goal of evolutionary biology is to understand which mechanisms monitor phenotypic variation and how this variation can generate species diversity. In this thesis we tried to investigate how phylogenetic, genetic, environmental, and development influence the evolution of a complex morphological structure using house mouse mandible as a model.In order to study the processes monitoring phenotypic variation, quantitative genetic analyses were performed on a pedigree of wild captured specimens of house mouse. The progenies were divided into two groups followed two different diets (soft and hard), so that the effect of phenotypic plasticity can be regarded. We show that developmental and epigenetic factors could influence the genetic architecture of morphological traits in a population. Moreover, the results suggest that phenotypic plasticity might be adaptive in some environmental conditions but not in the others.We then used the house mouse mandible in order to study the patterns of morphologic evolution of the populations of this species in a phylogeographic context. Our results show that morphological divergence in the house mouse was followed the genetic differentiation. We also found that morphological variation was increased during the expansion of house mouse subspecies without a significant convergence due to commensalism with human. Finally, we investigated whether the hypothesis of genetic drift could explain the morphological diversification during the divergence and expansion of the house mouse. The results reject this hypothesis and argue for the interfering of other evolutionary forces like selection.Our results, all in all, show a multifactorial origin for phenotypic variation and permit us to better understand the morphological divergence of the population of the subspecies of house mouse.

Understanding the genetic basis of reproductive isolation is the ultimate goal of the study of speciation. Here I present the results of a study of gene flow and its barriers at sex chromosome markers across the central European portion of the hybrid zone between two house mouse subspecies, Mus musculus musculus and M. m. domesticus. We identified strong introgression of Y musculus chromosome into the domesticus area accompanied by a perturbation of the census sex ratio. In addition, we detected stochastic effects that can distort results of hybrid zone studies. Finally, we confirmed a strong effect of sex chromosomes on reproductive isolation and hence their important role in the process of speciation.

The production of haploid sperm is a precondition for sexual reproduction of males. PRDM9 protein is a histone methyltransferase which localizes sites of meiotic recombination in many mammals. Mouse males of the C57BL/6J (B6) strain deficient for Prdm9 (Prdm9-/- ) are sterile, while Prdm9-/- males of PWD/Ph (PWD) strain have reduced sperm count. The comparison of the distribution of trimethylation of histone 3 on lysine 36 (H3K36me3) in genome of Prdm9-/- males of these two strains will help to determine the role of this epigenetic modification on meiotic recombination and fertility of Prdm9-/- males. The second part of this thesis is focused on transgenic males. Male offspring from the first generation of B6 female and PWD male crosses (B6PF1) have reduced fertility parameters due to incompatibility of Prdm9 alleles. The fertility parameters of B6PF1 hybrids carrying CHORI-34-289M8 or RP24-346I22 transgene are even lower. The candidate gene, which participates in the reduction of fertility of the transgenic B6PF1 hybrids, was determined as the proteasome subunit encoding gene Psmb1, because its relative transcription level best correlates with sperm count. The reason of lowered fertility thus might be a defect in proteasome assembly. The investigation of the fitness of transgenic animals is...

L'étude comparative de l'architecture des génomes mammaliens a révélé l'association des séquences répétées et des réarrangements. Cette thèse porte sur la dynamique et le rôle dans les remaniements de deux types de séquences répétées: les clusters ribosomiques et les satellites. Ces séquences sont analysées par une approche cytogénomique (FISH, CO-FISH) dans le genre Mus connu pour sa diversité chromosomique, et pour lequel les phylogénies moléculaires et chromosomiques sont disponibles.1) La distribution chromosomique des clusters ribosomiques, établie chez 19 espèces, a permis de reconstruire les états ancestraux des clusters. Cette analyse montre que les clusters (24%) sont associés à des points de cassures, mais présentent également une grande labilité en l'absence de réarrangements. De plus, une forte association entre les clusters et les centromères est mise en évidence. 2) Le sous-genre Mus se caractérise par un caryotype très conservé excepté chez une sous-espèce de la souris domestique (M. musculus domesticus), qui est connue pour son extraordinaire radiation chromosomique impliquant les séquences satellites du centromère. Afin de rechercher les spécificités génomiques responsables de ce patron d'évolution contrasté, la dynamique évolutive des séquences satellites a été analysée chez 11 taxons. Révélant des différences qualitatives entre taxons, cette étude a permis de proposer un scénario évolutif de ces séquences. Toutefois, aucune des caractéristiques étudiées (composition, orientation) n'est propre à M. m. domesticus, et ne permet de rendre compte de sa plasticité chromosomique. De même, chez cette dernière, aucun lien entre la quantité de séquences satellites et la fréquence d'implication des chromosomes dans les réarrangements n'est mis en évidence.Cette étude confirme que les séquences répétées participent à l'évolution chromosomique, mais ne constituent pas à elles seules l'élément clef de cette dernière. / Comparative analyses of the architecture of mammalian genomes have highlighted the association between repetitive sequences and rearrangements. This thesis focuses on the evolutionary dynamics of two repeat sequences (ribosomal clusters and satellites) and explores their role in chromosomal change. These sequences are analyzed by a cytogenomic approach (FISH, CO-FISH) in the genus Mus that is known for its chromosomal diversity and for which molecular and chromosomal phylogenies are available.1) The chromosomal distribution of ribosomal clusters, established in 19 species, allowed us to reconstruct the ancestral states of clusters. This analysis demonstrated that 24% of clusters were associated with breakpoints, whereas others showed high lability in the absence of rearrangements. Moreover, a strong association between clusters and centromeres was retrieved.2) The subgenus Mus is characterized by a highly conserved karyotype except for one subspecies of the house mouse (M. musculus domesticus), that displays an extraordinary chromosomal radiation involving centromeric satellite sequences. To determine the genomic traits related to this difference in rate, the evolutionary dynamics of satellite sequences was analyzed in 11 taxa. From the qualitative differences evidenced between taxa, an evolutionary scenario of these sequences is proposed. None of the studied features (composition, orientation) of these sequences was found to be specific to M. m. domesticus, and could explain its chromosomal plasticity. Similarly, in the latter, no relationship between satellite sequence quantity and the rearrangement frequency of chromosomes was found.This study confirms that although repeated sequences are involved in chromosomal evolution, they aren't in themselves the key element of the latter.

Contrary to the classical mouse inbred strains with unnatural genetic variability, wild-derived strains offer a more suitable model for evolutionary immunology. Toll-like receptors (TLRs) belong to initial detectors of invading pathogens. Although TLRs recognise conserved structures they were shown to be polymorphic. This polymorphism is associated with various diseases. In my thesis, I describe variability of Tlr1, 2 and 6 in 24 inbred strains derived from two subspecies of house mouse (Mus m. musculus and M. m. domesticus). These Tlrs exhibit different levels in variability among the strains. In Tlr1 the polymorphic sites are spread along the whole exodomain. Tlr6 is quite conserved (a lower amount of substitutions located far from the binding region and with minor modifications in the amino acid residue properties). Tlr2, on the contrary, contains some substitutions with substantial alternations of residue properties that are located within or nearby the binding region and the subspecies differ at these sites. All alleles of M. m. domesticus and M. m. musculus, except for Tlr1 PWD, Tlr2 STAIL, are phylogenetically separated. The strains and the subspecies vary in the production of IL-1β, IL-12 a NO after stimulation by TLR1, 2 and 6 ligands. This trend is, however, presumably influenced by the effect of...