Добірка наукової літератури з теми "Genomic incompatibilities"

The role of genomic balance in accumulating species hybrid incompatibilities is discussed. Aneuploidy has been shown to produce more global modulations than polyploidy with the responsible genes being transcription factors and signaling components involved in molecular complexes, illustrating a stoichiometric component to gene expression. Genomic imbalance is usually detrimental to the organism and in many cases results in lethality. Here, it is proposed that once gene flow is prevented between or within populations by various speciation initiating processes, the stoichiometric relationship of members of macromolecular complexes can change via compensatory drift with the eventual result of newly established functional balances. However, when these new relationships are brought together in interspecific hybrids, detrimental consequences will occur. We suggest that these detrimental interactions contribute to hybrid incompatibilities.

Reproductive isolation is central to speciation, but interspecific crosses between two closely related species can produce viable and fertile hybrids. Two different species of tunicates in the same ascidian genus, Ciona robusta and Ciona intestinalis, can produce hybrids. However, wild sympatric populations display limited gene flow, suggesting the existence of obstacles to interspecific reproduction that remain unknown. Here, we took advantage of a closed culture system to cross C. robusta with C. intestinalis and established F1 and F2 hybrids. We monitored post-embryonic development, survival, and sexual maturation to characterize the genetic basis of simple traits, and further probe the physiological mechanisms underlying reproductive isolation. Partial viability of first and second generation hybrids suggested that both pre- and postzygotic mechanisms contributed to genomic incompatibilities in hybrids. We observed asymmetric fitness, whereby the C. intestinalis maternal lines fared more poorly in our system, pointing to maternal origins of species-specific sensitivity. We discuss the possibility that asymmetrical second generation inviability and infertility emerge from interspecific incompatibilities between the nuclear and mitochondrial genomes, or other maternal effect genes. This work paves the way to quantitative genetic approaches to study the mechanisms underlying genomic incompatibilities and other complex traits in the genome-enabled Ciona model.

Polyploidy is much rarer in animals than in plants but it is not known why. The outcome of combining two genomes in vertebrates remains unpredictable, especially because polyploidization seldom shows positive effects and more often results in lethal consequences because viable gametes fail to form during meiosis. Fortunately, the goldfish (maternal) × common carp (paternal) hybrids have reproduced successfully up to generation 22, and this hybrid lineage permits an investigation into the genomics of hybridization and tetraploidization. The first two generations of these hybrids are diploids, and subsequent generations are tetraploids. Liver transcriptomes from four generations and their progenitors reveal chimeric genes (>9%) and mutations of orthologous genes. Characterizations of 18 randomly chosen genes from genomic DNA and cDNA confirm the chimera. Some of the chimeric and differentially expressed genes relate to mutagenesis, repair, and cancer-related pathways in 2nF1. Erroneous DNA excision between homologous parental genes may drive the high percentage of chimeric genes, or even more potential mechanisms may result in this phenomenon. Meanwhile, diploid offspring show paternal-biased expression, yet tetraploids show maternal-biased expression. These discoveries reveal that fast and unstable changes are mainly deleterious at the level of transcriptomes although some offspring still survive their genomic abnormalities. In addition, the synthetic effect of genome shock might have resulted in greatly reduced viability of 2nF2 hybrid offspring. The goldfish × common carp hybrids constitute an ideal system for unveiling the consequences of intergenomic interactions in hybrid vertebrate genomes and their fertility.

Abstract Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers.

Abstract The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

The past few years have seen considerable advances in speciation research, but whether drift or adaptation is more likely to lead to genetic incompatibilities remains unknown. Some of the answers will probably come from not only studying incompatibilities between well-established species, but also from investigating incipient speciation events, to learn more about speciation as an evolutionary process. The genus Arabidopsis , which includes the widely used Arabidopsis thaliana , provides a useful set of model species for studying many aspects of population divergence. The genus contains both self-incompatible and incompatible species, providing a platform for studying the impact of mating system changes on genetic differentiation. Another important path to plant speciation is via formation of polyploids, and this can be investigated in the young allotetraploid species A. arenosa . Finally, there are many cases of intraspecific incompatibilities in A. thaliana , and recent progress has been made in discovering the genes underlying both F 1 and F 2 breakdown. In the near future, all these studies will be greatly empowered by complete genome sequences not only for all members of this relatively small genus, but also for many different individuals within each species.

Speciation may occur when the genomes of two populations accumulate genetic incompatibilities and/or chromosomal rearrangements that prevent inter-breeding in nature. Chromosome stability is critical for survival and faithful transmission of the genome, and hybridization can compromise this. However, the role of chromosomal stability on hybrid incompatibilities has rarely been tested in recently diverged populations. Here, we test for chromosomal instability in hybrids between nascent species, the ‘dwarf’ and ‘normal’ lake whitefish ( Coregonus clupeaformis ). We examined chromosomes in pure embryos, and healthy and malformed backcross embryos. While pure individuals displayed chromosome numbers corresponding to the expected diploid number (2 n = 80), healthy backcrosses showed evidence of mitotic instability through an increased variance of chromosome numbers within an individual. In malformed backcrosses, extensive aneuploidy corresponding to multiples of the haploid number (1 n = 40, 2 n = 80, 3 n = 120) was found, suggesting meiotic breakdown in their F 1 parent. However, no detectable chromosome rearrangements between parental forms were identified. Genomic instability through aneuploidy thus appears to contribute to reproductive isolation between dwarf and normal lake whitefish, despite their very recent divergence (approx. 15–20 000 generations). Our data suggest that genetic incompatibilities may accumulate early during speciation and limit hybridization between nascent species.

Transposable elements (TEs) play an important role in shaping genomic organization and structure, and may cause dramatic changes in phenotypes. Despite the genetic load they may impose on their host and their importance in microevolutionary processes such as adaptation and speciation, the number of population genetics studies focused on TEs has been rather limited so far compared to single nucleotide polymorphisms (SNPs). Here, we review the current knowledge about the dynamics of transposable elements at recent evolutionary time scales, and discuss the mechanisms that condition their abundance and frequency. We first discuss non-adaptive mechanisms such as purifying selection and the variable rates of transposition and elimination, and then focus on positive and balancing selection, to finally conclude on the potential role of TEs in causing genomic incompatibilities and eventually speciation. We also suggest possible ways to better model TEs dynamics in a population genomics context by incorporating recent advances in TEs into the rich information provided by SNPs about the demography, selection, and intrinsic properties of genomes.

Previous work has demonstrated that genomic incompatibilities work together with ecologically divergent selection to promote and maintain reproductive isolation between incipient species (dwarf and normal) of lake whitefish ( Coregonus clupeaformis (Mitchill, 1818)). Whitefish spawn in groups with external fertilization, which creates conditions for strong sperm competition. In this study, we asked whether reduced sperm performance in hybrids from whitefish species-pair matings might contribute to postzygotic isolating mechanisms between these taxa. We examined two sperm traits, sperm swimming speed and flagellum length, in pure dwarf and normal whitefish and in their F1 and backcross hybrids. We observed significantly reduced sperm swimming speed in backcross but not in F1 hybrids. Sperm flagellum length was not significantly correlated with sperm swimming speed. These results demonstrate that F1 hybrids formed in nature should be capable of the same fertilization success as the parental species during sperm competition, everything else being equal. However, reduced sperm performance in the backcross generation is consistent with other evidence suggesting that genomic incompatibilities create a range of negative fitness effects in post-F1 whitefish hybrids and provides evidence for an additional postzygotic isolation mechanism involved in the incipient speciation of sympatric dwarf and normal whitefish.

Cette thèse a contribué, en utilisant le séquençage haut débit de génomes, à la compréhension de l’histoire de la divergence conduisant à la spéciation, et des causes et conséquences des échanges génétiques entre espèces.Ce travail a contribué au développement des ressources génomiques pour étudier la génomique des populations de lièvres, en produisant le premier assemblage de novo d’un génome de lièvre (Lepus timidus), et en évaluant son utilité en comparaison au génome de référence du lapin, préalablement disponible. Nous avons aussi produit le premier transcriptome de L. timidus, le plus complet de ceux disponibles pour les lièvres. En combinaison avec des données publiées sur L. europaeus, nous avons trouvé les différences fixées entre les deux espèces, qui peuvent être utilisées pour construire des outils pour étudier les échanges interspécifiques dans les zones d’hybridation.Nous avons contribué à la compréhension de l’introgression massive documentée du génome mitochondrial de L. timidus vers L. granatensis dans la péninsule ibérique, en reconstituant l’évolution démographique post-glaciaire de cette dernière à partir de la variation génétique actuelle. Nous avons démontré que cette introgression s’est faite à la faveur de l’envahissement du territoire de l’espèce donneuse par la receveuse, soulignant l’importance de la démographie et de la biogéographie pour favoriser l’introgression.A partir de séquences de génomes complets, nous avons étudié la différenciation et le re-mélange en Iran, la région d’origine des trois sous-espèces connues de souris domestique (Mus musculus domesticus, musculus et castaneus), source de leur expansion au reste de l’Eurasie, conduisant à leurs distributions parapatriques actuelles. Nous avons découvert au centre de l’Iran une population différenciée de ces trois sous-espèces, et inféré qu’elle résulte d’un mélange passé entre M. m. domesticus (environ 40%) et une population apparentée à M. m. musculus. Les lignées domesticus et musculus se sont donc largement mélangées à proximité de leur région d’origine, mais apparaissent isolées suite à leurs expansions géographiques indépendantes vers l’Europe, où elles forment une zone de tension étroite, un patron évocateur d’une espèce en anneau. Ceci offre un modèle exceptionnel pour étudier l’évolution et les déterminants de l’isolement reproductif entre ces sous-espèces. Nos analyses suggèrent un avantage sélectif du chromosome Y de la lignée musculus dans ce contexte de mélange en Iran central.Nous avons aussi découvert au NW de l’Iran une population d’origine majoritairement domesticus, avec des contributions de ses deux voisins (musculus et Iran central), mais qui a fixé une lignée de chromosome Y de la branche musculus. Nous trouvons que cette introgression massive de Y est accompagnée par la co-introgression de gènes impliqués dans la fertilité mâle, particulièrement sur le chromosome X. Nous avons testé le lien potentiel de cette invasion de Y avec une course aux armements entre le X et le Y qui pourrait biaiser les sex-ratios, et ainsi pu aborder la question du rôle des conflits génétiques comme promoteurs de l’introgression. Entre sous-espèces, nous avons trouvé une corrélation entre les nombres de copies Y et X de familles ampliconiques (gènes Sly/Slx) dont l’interaction est connue pour contrôler le sex-ratio de manière antagoniste en fonction de la dose. Plus de copies dans la lignée musculus suggère des propriétés distortrices plus fortes. Toutefois nous argumentons que ce conflit X-Y n’est pas le moteur de l’invasion du Y, qui résulterait plutôt d’un avantage intrinsèque du Y musculus en situation de mélange entre sous-espèces. La propension du Y musculus à envahir les régions où musculus se mélange avec d’autres sous-espèces semble générale et observée dans d’autres régions géographiques. Le conflit entraînerait la co-introgression ou la coévolution des régions ampliconiques du X dans les zones de mélange
The present thesis has contributed, using high throughput genome sequencing, to understanding the history of divergence leading to speciation, and the causes and consequences of genetic exchanges between species, in hares and mice.First, this work has contributed to the development of the genomic resources available to study hare population genomics, by providing the first de novo assembly of a hare genome (for the mountain hare, Lepus timidus), and assessing its utility as compared to the rabbit assembly, previously available. We have also generated the first mountain hare transcriptome, and the most complete among the currently available Lepus transcriptomes. In combination with published data on the European brown hare (L. europaeus), we pinpointed candidate fixed differences between the two species that can be used to build genotyping tools to monitor gene exchange in contact zones.Second, we have contributed to the understanding of the documented massive introgression of the mitochondrial genome from the mountain hare to the Iberian hare (L. granatensis) in Iberia, by reconstructing the post-glacial demographic dynamics of the latter species using Single Nucleotide Polymorphism data. We demonstrated that this introgression occurred at the favor of the invasive replacement of the donor species by the recipient one during the last deglaciation, thus showing the importance of demographic and biogeographic history in driving introgression.Third, using whole genome sequencing, we studied genetic differentiation and admixture in Iran, the region of origin of the three described house mouse subspecies (M. m. domesticus, musculus and castaneus), source of their expansion to the rest of Eurasia, leading to their present parapatric distributions. We discovered in Central Iran a population that is differentiated from these three subspecies, and inferred that it results from an ancient admixture between M. m. domesticus (about 40%) and a population related to M. m. musculus. The domesticus and musculus lineages thus admixed extensively close to their region of origin, but appear genetically isolated after their independent geographical expansions to Europe, where they form a narrow tension zone, a pattern evocative of a ring species. This offers an exceptional model to further study the evolution and determinants of reproductive isolation between these subspecies. Our analyses also suggest a selective advantage of non-domesticus Y chromosome in this context of admixture in Central Iran.We also discovered in North Western Iran a population that is mostly of domesticus origin, with inferred admixture from its geographical neighbours (musculus and central Iran), but which has fixed a Y chromosome lineage related to that of musculus. We show that this massive Y introgression is accompanied by co-introgression of genes with functions related to male fertility, especially on the X chromosome. We tested the potential link of this Y invasion with an arms-race between the X and Y chromosomes that could bias sex-ratio, and therefore address the question of the potential role of genetic conflicts in promoting introgression. Among subspecies we found a correlation between copy numbers of Y and X ampliconic families (Sly/Slx genes) whose interaction is known to control sex chromosome transmission in a dosage dependent manner. Higher copy numbers in the musculus lineage suggest stronger distortion properties. We however argue that this X-Y conflict is not the cause of massive Y introgression, which would rather reflect an intrinsic advantage of the musculus Y lineage in zones of admixture between the subspecies. The ability of the musculus Y chromosome to invade zones where musculus admixes with other subspecies seems to be a ubiquitous pattern, observed in other geographic regions. The conflict would rather cause co-introgression or co-evolution of the X ampliconic region in admixed populations

Cette thèse a contribué, en utilisant le séquençage haut débit de génomes, à la compréhension de l’histoire de la divergence conduisant à la spéciation, et des causes et conséquences des échanges génétiques entre espèces.Ce travail a contribué au développement des ressources génomiques pour étudier la génomique des populations de lièvres, en produisant le premier assemblage de novo d’un génome de lièvre (Lepus timidus), et en évaluant son utilité en comparaison au génome de référence du lapin, préalablement disponible. Nous avons aussi produit le premier transcriptome de L. timidus, le plus complet de ceux disponibles pour les lièvres. En combinaison avec des données publiées sur L. europaeus, nous avons trouvé les différences fixées entre les deux espèces, qui peuvent être utilisées pour construire des outils pour étudier les échanges interspécifiques dans les zones d’hybridation.Nous avons contribué à la compréhension de l’introgression massive documentée du génome mitochondrial de L. timidus vers L. granatensis dans la péninsule ibérique, en reconstituant l’évolution démographique post-glaciaire de cette dernière à partir de la variation génétique actuelle. Nous avons démontré que cette introgression s’est faite à la faveur de l’envahissement du territoire de l’espèce donneuse par la receveuse, soulignant l’importance de la démographie et de la biogéographie pour favoriser l’introgression.A partir de séquences de génomes complets, nous avons étudié la différenciation et le re-mélange en Iran, la région d’origine des trois sous-espèces connues de souris domestique (Mus musculus domesticus, musculus et castaneus), source de leur expansion au reste de l’Eurasie, conduisant à leurs distributions parapatriques actuelles. Nous avons découvert au centre de l’Iran une population différenciée de ces trois sous-espèces, et inféré qu’elle résulte d’un mélange passé entre M. m. domesticus (environ 40%) et une population apparentée à M. m. musculus. Les lignées domesticus et musculus se sont donc largement mélangées à proximité de leur région d’origine, mais apparaissent isolées suite à leurs expansions géographiques indépendantes vers l’Europe, où elles forment une zone de tension étroite, un patron évocateur d’une espèce en anneau. Ceci offre un modèle exceptionnel pour étudier l’évolution et les déterminants de l’isolement reproductif entre ces sous-espèces. Nos analyses suggèrent un avantage sélectif du chromosome Y de la lignée musculus dans ce contexte de mélange en Iran central.Nous avons aussi découvert au NW de l’Iran une population d’origine majoritairement domesticus, avec des contributions de ses deux voisins (musculus et Iran central), mais qui a fixé une lignée de chromosome Y de la branche musculus. Nous trouvons que cette introgression massive de Y est accompagnée par la co-introgression de gènes impliqués dans la fertilité mâle, particulièrement sur le chromosome X. Nous avons testé le lien potentiel de cette invasion de Y avec une course aux armements entre le X et le Y qui pourrait biaiser les sex-ratios, et ainsi pu aborder la question du rôle des conflits génétiques comme promoteurs de l’introgression. Entre sous-espèces, nous avons trouvé une corrélation entre les nombres de copies Y et X de familles ampliconiques (gènes Sly/Slx) dont l’interaction est connue pour contrôler le sex-ratio de manière antagoniste en fonction de la dose. Plus de copies dans la lignée musculus suggère des propriétés distortrices plus fortes. Toutefois nous argumentons que ce conflit X-Y n’est pas le moteur de l’invasion du Y, qui résulterait plutôt d’un avantage intrinsèque du Y musculus en situation de mélange entre sous-espèces. La propension du Y musculus à envahir les régions où musculus se mélange avec d’autres sous-espèces semble générale et observée dans d’autres régions géographiques. Le conflit entraînerait la co-introgression ou la coévolution des régions ampliconiques du X dans les zones de mélange
The present thesis has contributed, using high throughput genome sequencing, to understanding the history of divergence leading to speciation, and the causes and consequences of genetic exchanges between species, in hares and mice.First, this work has contributed to the development of the genomic resources available to study hare population genomics, by providing the first de novo assembly of a hare genome (for the mountain hare, Lepus timidus), and assessing its utility as compared to the rabbit assembly, previously available. We have also generated the first mountain hare transcriptome, and the most complete among the currently available Lepus transcriptomes. In combination with published data on the European brown hare (L. europaeus), we pinpointed candidate fixed differences between the two species that can be used to build genotyping tools to monitor gene exchange in contact zones.Second, we have contributed to the understanding of the documented massive introgression of the mitochondrial genome from the mountain hare to the Iberian hare (L. granatensis) in Iberia, by reconstructing the post-glacial demographic dynamics of the latter species using Single Nucleotide Polymorphism data. We demonstrated that this introgression occurred at the favor of the invasive replacement of the donor species by the recipient one during the last deglaciation, thus showing the importance of demographic and biogeographic history in driving introgression.Third, using whole genome sequencing, we studied genetic differentiation and admixture in Iran, the region of origin of the three described house mouse subspecies (M. m. domesticus, musculus and castaneus), source of their expansion to the rest of Eurasia, leading to their present parapatric distributions. We discovered in Central Iran a population that is differentiated from these three subspecies, and inferred that it results from an ancient admixture between M. m. domesticus (about 40%) and a population related to M. m. musculus. The domesticus and musculus lineages thus admixed extensively close to their region of origin, but appear genetically isolated after their independent geographical expansions to Europe, where they form a narrow tension zone, a pattern evocative of a ring species. This offers an exceptional model to further study the evolution and determinants of reproductive isolation between these subspecies. Our analyses also suggest a selective advantage of non-domesticus Y chromosome in this context of admixture in Central Iran.We also discovered in North Western Iran a population that is mostly of domesticus origin, with inferred admixture from its geographical neighbours (musculus and central Iran), but which has fixed a Y chromosome lineage related to that of musculus. We show that this massive Y introgression is accompanied by co-introgression of genes with functions related to male fertility, especially on the X chromosome. We tested the potential link of this Y invasion with an arms-race between the X and Y chromosomes that could bias sex-ratio, and therefore address the question of the potential role of genetic conflicts in promoting introgression. Among subspecies we found a correlation between copy numbers of Y and X ampliconic families (Sly/Slx genes) whose interaction is known to control sex chromosome transmission in a dosage dependent manner. Higher copy numbers in the musculus lineage suggest stronger distortion properties. We however argue that this X-Y conflict is not the cause of massive Y introgression, which would rather reflect an intrinsic advantage of the musculus Y lineage in zones of admixture between the subspecies. The ability of the musculus Y chromosome to invade zones where musculus admixes with other subspecies seems to be a ubiquitous pattern, observed in other geographic regions. The conflict would rather cause co-introgression or co-evolution of the X ampliconic region in admixed populations

Afin de comprendre le processus de spéciation, il est nécessaire d'appréhender les patrons de flux géniques entre espèces naissantes et le rôle de la sélection dans leur détermination. C'est ce que tente d'aborder cette thèse en utilisant comme modèle deux sous-espèces de la souris domestique, Mus musculus. Nous avons reconstitué l'histoire de leur différenciation sur la base du polymorphisme de séquence à 60 locus autosomaux. La simulation du coalescent de ces locus sous plusieurs scenarios historiques nous a permis d'inférer, via une méthode ABC (Approximate Bayesian Computation), une divergence ancienne des sous-espèces (1,5Ma). Elle fut suivie d'une longue phase d'isolement (1,2Ma) précédant une phase d'échanges génétiques débutant bien avant la formation de la zone hybride européenne actuelle. La phase d'isolement a été assez longue pour expliquer une grande partie des incompatibilités génétiques observées actuellement. Les flux génétiques anciens et prolongés pourraient avoir favorisé le renforcement comportemental de l'isolement reproductif. Nous étudions aussi la relation entre le mode d'évolution de 77 régions génomiques autosomales et leur comportement d'introgression à travers une zone hybride. Le taux de recombinaison locale semble déterminer en partie les introgressions symétriques et limitées de certains locus. Toutefois tel n'est pas le cas pour 40% des locus, qui présentent une introgression asymétrique dans l'une ou l'autre direction. Nous proposons que l'introgression coté musculus soit majoritairement contrôlée par la sélection et que l'introgression coté domesticus soit influencée par un déplacement de la zone hybride vers le territoire musculus
Understanding the speciation process requires to appraise patterns of gene flow between incipient speices as well as the role of selection in their determination. This thesis attempts to do so using two subspecies of the house mouse, Mus musculus, as a model. We inferred the history of their differentiation based on sequence polymorphism data at 60 autosomal loci. By simulating the coalescent of these loci under several historical scenarios we were able to infer, using an ABC (Approximate Bayesian Computation) method, an ancient divergence of the subspecies (1.5 MY). This was followed by a long period of isolation (1.2 MY) preceding a phase of genetic exchanges that started well before the formation of the present European hybrid zone. The isolation phase lasted long enough to explain a majority of the present genetic incompatibilities. Ancient and lasting gene flow could have favoured a behavioural reinforcement of reproductive isolation. We a lso studied the relationship between the mode of evolution of 77 autosomal genomic regions and their introgression patterns across a hybrid zone. Local recombination rates variations seem to partly account for the patterns observed at some loci with limited and symmetrical introgression. However such is not the case for 40% of the the loci showing asymmetrical introgression in on direction or the other. domesticus results from a movement of the hybrid zone from domesticus to musculus

Le feu bactérien et le psylle causent d’importantes pertes économiques dans les zones de production du poirier dans le monde entier. Le développement de nouvelles variétés de poirier résistantes à ces bio-agresseurs constitue un enjeu majeur dans le cadre d’un programme de lutte intégrée. L’objectif de ce projet de thèse est l'étude du déterminisme génétique de la résistance vis-à-vis de ces deux bio-agresseurs. La thèse a été réalisée dans le cadre d’une collaboration internationale entre Fondazione Edmund Mach (Italie), Institut de Recherches en Horticulture et Semences (France) et Plant & Food Research (Nouvelle-Zélande). Une descendance interspécifique de poirier T003 x ‘Moonglow’ a été développée avec pour objectif de cumuler les résistances au feu bactérien et au psylle provenant de variétés asiatiques et européennes de Pyrus. Deux cartes génétiques ont été élaborées pour T003 et ‘Moonglow’ sur la base de marqueurs SNP (Single Nucleotide Polymorphism) et SSR (microsatellite), et la cartographie de QTLs (Quantitative Trait Loci) a permis de démontrer le déterminisme polygénique de la résistance à ces bio-agresseurs. Une sélection assistée par marqueurs (MAS) peut donc être engagée pour ces deux caractères. Des incompatibilités génétiques ont aussi été observées dans une partie de la descendance, ce qui a permis de cartographier pour la première fois chez le poirier les zones du génome liées au phénomène de « nécrose hybride ». Le développement de marqueurs liés aux gènes létaux devrait permettre aux sélectionneurs d’éviter les combinaisons incompatibles en croisement qui peuvent impacter certains caractères agronomiques co-ségrégant avec ces gènes létaux
The goal of this PhD project was to study the genetic architecture of pear resistance to two of its most significant diseases and pests, fire blight and psylla, which cause severe yield losses in all the main pear production regions worldwide. The development of new pear varieties with resistance against these two biotic stresses is of major interest for Integrated Pest Management. This project was designed in a joint collaboration among Fondazione Edmund Mach (Italy), Institut de Recherches en Horticulture et Semences (France) and Plant & Food Research (New-Zealand). The interspecific pear F1 progeny T003 x ‘Moonglow’ was developed with the purpose of cumulating resistances to fire blight and psylla deriving from Asian and European pear cultivars. Single nucleotide polymorphism (SNP) and simple sequence repeat (SSR)-based genetic maps were built for T003 and ‘Moonglow’. Quantitative Trait Loci (QTLs) were detected for the resistances, demonstrating their polygenic nature. Marker-assisted selection (MAS) can now be applied for these two traits. Furthermore, the segregating population exhibited genetic incompatibilities, and the genomic regions associated with hybrid necrosis were mapped for the first time in pear. Development of molecular markers linked to the lethal genes should allow breeders to avoid crosses leading to incompatible combinations that could affect the expression of important agronomic traits co-segregating with these genes

This chapter could as well be titled “Population Genomics,” although many aspects of population genomics are integrated throughout the other chapters. It includes estimates of mutational variance and standing variance, phenotypic evolution under directional selection as measured by the linear selection gradient, and phenotypic evolution under stabilizing selection. It explores the strengths and limitations of genome-wide association studies of quantitative trait loci (QTLs) and expression (eQTLs) to detect genetic influencing complex traits in natural populations and genetic risk factors for complex diseases such as heart disease or diabetes. The number of genes affecting complex traits is considered, as well as evidence bearing on the issue of whether complex diseases are primarily affected by a very large number of genes, almost all of small effect, and how this bears on direct-to-consumer and over-the-counter genetic testing. The population genomics of adaptation is considered, including drug resistance, domestication, and local selection versus gene flow. The chapter concludes with the population genomics of speciation as illustrated by reinforcement of mating barriers, the reproducibility of phenotypic and genetic changes, and the accumulation of genetic incompatibilities.

Genetic variation among individuals within populations and among populations can be assessed at the chromosomal, protein, or DNA sequence level. The best tool or approach depends on the question being asked. Variation in the number or structure of chromosomes can result in reproductive incompatibilities and reduced fitness that influences the success of conservation efforts. Differences in amino acid sequence that alter the electrophoretic mobility of proteins, termed allozymes, were widely used to measure genetic variation and population differentiation on a gene-by-gene basis prior to advances in DNA sequencing. Mitochondria and chloroplasts contain circular DNA molecules that are usually inherited from one parent and are useful for assessing population history and structure. Most studies of genetic variation now rely on the analysis of single nucleotide polymorphisms (SNPs)—variations in nucleotides at a single location within the genome—to understand both selectively neutral and adaptive processes.