L’abricotier cultivé (Prunus armeniaca L.) appartient au genre Prunus, de la sous-famille des Prunoideae qui comprend la totalité des arbres fruitiers à noyaux de la famille des Rosaceae. Il fait partie de la section taxonomique Armeniaca (Lam.) Koch. qui se présente comme un complexe d’espèces diploïdes, inter-fertiles avec un génome d’environ 200-220 Mbp (n=8). La section Armeniaca comprend deux espèces cultivées, P. armeniaca (fruitière) et P. mume (ornementale) ; mais également cinq espèces encore disponibles à l’état sauvage en Asie Centrale et en Asie du Nord-Est, le plus souvent en altitude. Dans ce contexte, mon travail de thèse vise à mieux comprendre les différents processus de l’histoire évolutive d’une espèce fruitière pérenne et comment ceux-ci influent sur la variabilité et la structuration génétique de l’espèce cultivée. Ceci inclut son adaptation à de multiples et changeantes conditions environnementales mais également à l’action de l’Homme au travers de la domestication, de la sélection et de l’amélioration génétique et son effet sur l’architecture génomique de l’abricotier.Dans un premier temps, des études de diversité réalisées à l’aide de marqueurs moléculaires de type microsatellites ont été réalisées chez l’abricotier et ses espèces apparentées, sauvages, afin de clarifier les généalogies et révéler les processus évolutifs qui sont à l’origine de la forme cultivée, fruitière. Notre étude de phylogéographie nous a permis de détecter des groupes génétiques différenciés résultant de l’histoire climatique passée de la planète mais également d’hybridation interspécifique et de flux de gènes récurrent entre individus sauvages et domestiques. Plusieurs événements indépendants de domestication ont ainsi été mis en évidence, ils sont à l’origine de l’abricotier cultivé en Occident, en Chine et en Asie Centrale.La même approche a été utilisée dans un second temps afin de décrire la diversité et la structuration génétique de P. brigantina Vill., la seule espèce européenne de la section Armeniaca, ce qui nous a conduit à préciser sa classification dans le genre Prunus.Enfin dans la troisième partie de cette thèse, la diversité génétique a cette fois été étudiée à l’échelle du génome complet de l’abricotier. L’objectif ici était de rechercher les régions génomiques permettant de différencier les groupes domestiques, européens et chinois, des populations sauvages d’Asie Centrale. Ces zones de forte différenciation dans les génomes correspondent à des signatures de balayages sélectifs. Nous avons ainsi identifié plus de 1700 régions génomiques comme cibles probables de l’adaptation et de la domestication de l’abricotier, pour lesquelles 136 présentaient un fort degré de similarité pour tous les cultivars d’abricotiers indiquant 56 régions génomiques de domestication homologues, non-chevauchantes. Pour 48 de ces régions, nous disposons d’annotations fonctionnelles qui permettent de déterminer les gènes sous sélection et leur fonction. Il apparaît que la plupart de ces gènes sont connus pour affecter l’expression de phénotypes liés 1) à la réponse aux pathogènes et au stress abiotique, 2) à la qualité du fruit ainsi qu’au 3) contrôle moléculaire de la floraison et de la transition entre période végétative et reproductive. Ce résultat constitue un premier pas vers la compréhension des mécanismes responsables du processus de domestication chez une espèce fruitière, pérenne. Il montre que des évènements de domestication indépendants ont impliqué des régions génomiques homologues. Les travaux aÌ venir devront également permettre de préciser les cibles génétiques des processus adaptatifs chez cette espèce fruitière, pérenne, et de fournir des cibles pour les programmes d’amélioration génétique de l’abricotier dans un contexte de changements climatiques. / Nowadays, increasing attention is focused on perennial crop species and their wild relatives. The domestication of perennials is expected to follow different processes than annuals, and there is limited knowledge about how perennial plant species evolve in response to human intervention or changing environmental conditions. Indeed, the diversity of perennial species results from a series of mechanisms of evolution, which include natural and artificial selection, gene flow between wild and cultivated compartments, and dynamics of dispersion at large scales, often over long periods. Unraveling the evolutionary history and domestication processes of long-lived tree species is expected to provide insights into the potential differences and similarities between annual and perennial species, and furtherly to facilitate breeding efforts for traits of interest.In the current PhD thesis, we focused on apricot species, Prunus armeniaca L., and its related species from the section Armeniaca (Lam.) Koch.. We characterized genetic diversity and variability and addressed a few important questions related to fruit tree origin, evolution and domestication, and further identified candidate genes and loci underlying important agronomic traits that have been under selection during domestication.Our microsatellite data and approximate Bayesian computation revealed that the wild species P. armeniaca and P. sibirica diverged ca. 8 to 16 Mya ago, followed by interspecific hybridization leading to a new, isolated species, in Western China. We also showed that the European and Chinese apricots were domesticated independently either both from the Central Asian wild progenitor or from the hybrid species.Following the same strategy, we studied the genetic diversity and structuration of the only European Armeniaca species, P. brigantina Vill. and thus questioned its classification among the genus Prunus.Finally, taking advantage of the de novo assembly of a high-quality apricot reference genome and of extensive resequencing data, we focused on how selection has influenced genomic architecture in apricot (P. armeniaca). To test for common or distinct signatures of selection, we took advantage of the parallel history of domestication in the European and Chinese apricots and compared with their wild, Central Asian progenitor. We detected evidence for artificial selection at a genome-wide scale, both for European and Chinese apricots, with a significant number of homologous genomic signatures of domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes. We also identified signatures of selection which could be associated with local adaptation in either wild or cultivated apricots.Therefore, a better knowledge on apricot evolutionary history combined with comparative population genomics enables the identification and utilization of adaptive and domestication traits that are important for apricot cultivation, It is expected to provide an unprecedented opportunity to identify the genetic basis of long-lived perennials’ adaptation and domestication.

Les variants structuraux génomiques (SVs) composent une large part du polymorphisme observable entre les individus mais leurs impacts sur les processus micro-évolutifs restent mal connus et leur étude à large échelle est rare.La première partie de ce manuscrit est une étude de la bibliographie portant sur les SVs décrits chez les animaux domestiques. Cette partie met en avant l'importance des SVs dans la modification des gènes ou de leur régulation, impactant un grand nombre de traits sélectionnés lors de la domestication, en lien avec la productivité, la morphologie ou encore le comportement.Basée sur l’étude de données de reséquençage de 500 génomes complets de petits ruminants sauvages et domestiques, la seconde partie, ciblant trois SVs décrits dans la bibliographie, a permis (i) de réfuter l’hypothèse d’amplification en lien avec la domestication des copies endogènes protectrices du retrovirus JSRV situées dans la région 6q13 du mouton, (ii) d’identifier des duplications entourant et affectant le gène ASIP qui seraient impliquées dans les modifications de coloration du pelage en lien avec la domestication des petits ruminants, ainsi que (iii) de montrer un potentiel rôle adaptatif d'un haplotype du locus de la beta-globine lié au climat aride chez le mouton.La troisième partie se base sur une recherche sans a priori de l’ensemble des SVs présents dans des génomes complets. Au travers du développement d’une méthode de détection des SVs et de son application, cette partie permet de décrire environ 50k et 20k SVs dans les génomes des Ovis et des Capra. Parmi ces SVs, 135 chez Ovis et 70 chez Capra semblent liés à la domestication et affectent des gènes impliqués dans l’amélioration, l’immunité, la reproduction ou la survie. De plus, les distributions de 130 SVs pour les moutons et 35 SVs pour les chèvres covarient avec des variables environnementales au Maroc. Certains affectent des gènes impliqués dans la morphologie, l’immunité et le métabolisme.Ce travail met ainsi en avant de nombreux variants qui peuvent impacter des gènes et qui ont pu être ciblés lors la domestication initiale, des étapes d’amélioration ultérieure ou de l’adaptation locale des petits ruminants. Il démontre l'importance de prendre en compte les variants structuraux dans les études génomiques visant à décrire les bases génétiques de la domestication. / Genomic structural variations (SVs) account for a large part of the polymorphism between individuals, but their impacts on micro-evolutionary processes remain poorly known and large-scale studies are scarce.The first part of this manuscript is a bibliographic study of SVs in domestic animals. This part highlights the importance of SVs in modifying genes or their regulation, impacting a large number of traits selected during domestication and linked to productivity, morphology or behaviour.Based on the study of resequenced data from 500 whole genomes of wild and domestic small ruminants, the second part, targeting three SVs described in the bibliography, allowed (i) to refute the hypothesis of a link between the domestication of sheep and the amplification of endogenous protective copies of the JSRV retrovirus located in the 6q13 region, l, (ii) to identify duplications surrounding and affecting the ASIP gene that could be involved in the coat color changes related to the domestication of small ruminants, as well as (iii) highlight a potential adaptive role to arid climate of an haplotype of beta-globin locus in sheep.In the third part, we conducted a whole genome survey of SVs . Through the development of a SVs detection method and its application, we could detect about 50k and 20k SVs in Ovis and Capra. Of these SVs, 135 and 70 in Ovis and Capra, respectively, appear to be linked with domestication and affect genes involved in improvement, immunity, reproduction or survival. In addition, in Morocco, the distributions of 130 SVs for sheep and 35 SVs for goats covariate with environmental variables. Some of them affect genes involved in morphology, immunity and metabolism.This work highlights that many variants impacting genes might have been targeted during initial domestication and subsequent improvement steps or during the local adaptation of sheep and goats. It demonstrates the importance of considering structural variants in genomic studies to describe the genetic basis of domestication.

The Domestication Syndrome Hypothesis posits that domesticated animal species exhibit a shared set of traits encompassing behavioral, physiological, and morphological characteristics. While this hypothesis has garnered significant attention, the evidence supporting its universality remains limited, particularly in species such as dogs and cattle. In this dissertation, I examined the Domestication Syndrome Hypothesis in mixed breed pet and shelter dogs as well as Holstein dairy heifers. This investigation focused on behavioral responses, physiological reactivity, and Domestication Syndrome Hypothesis-associated morphological variables in relation to human interaction. First, I explored the behavioral responses of Holstein dairy heifers representing a range of white spotting phenotypes towards people and handling, and their physiological response towards handling during an industry-standard palpation procedure. Additionally, I explored three pigmentation variables (coat color/pattern, eumelanin pigmentation, and white spotting) in dogs residing in a known stressful environment, an animal shelter. I assessed their baseline in-shelter cortisol and their cortisol response to an intervention in which they left the shelter to spend time with people. Lastly, I investigated citizen science behavioral surveys of owned mixed breed dogs to determine potential correlations between white spotting or ear set and various behavioral factors, including human sociability and aggression. Altogether, I found partial support for the Domestication Syndrome Hypothesis: some results aligned with the expectations of the Domestication Syndrome Hypothesis and some did not. Notably, in Holstein dairy heifers, I observed that less white spotting predicted a greater increase in cortisol levels and a higher rate of stepping in response to palpation, results that support the premises of the Domestication Syndrome Hypothesis. Moreover, in owned mixed breed pet dogs, I found that human sociability positively correlated with white spotting and floppier ears and that decreased arousal, decreased aggression, and increased proximity-seeking correlated with floppier ears, further supporting the Hypothesis. However, many of the correlations predicted by the Hypothesis were not statistically significant or exhibited an opposite direction to what was expected. For instance, more extensive white spotting in Holsteins predicted a higher rate of vocalization during palpation, pigmentation did not significantly predict cortisol levels in shelter dogs, and in owned mixed breed dogs playfulness and biddability negatively correlated with white spotting while biddability negatively correlated with floppier ears. Prior research on the Domestication Syndrome Hypothesis in dogs did not find covariation between domestication-associated behavioral and morphological traits, which the researchers suggest may have been driven by modern breeding practices; this confound could have also impacted my studies. Together, the results – both supportive and contradictory – included in this dissertation contribute to our understanding of the Domestication Syndrome Hypothesis. Further research is needed to reconcile these inconsistencies and explore the underlying mechanisms behind the observed relationships. By expanding sample sizes, using more standardized study designs, and investigating causative mechanisms, future studies can enhance our knowledge of the Domestication Syndrome Hypothesis and its implications in the domestication process of animals. / Doctor of Philosophy / The Domestication Syndrome Hypothesis suggests that domesticated animals share common traits in their behavior, physiology, and physical appearance. However, the evidence supporting this idea is limited, especially in dogs and cattle. In this dissertation, I studied mixed breed pet and shelter dogs, as well as Holstein dairy heifers, to explore the Domestication Syndrome Hypothesis. I looked at how these animals behaved and how their stress hormone levels changed when interacting with humans. For the dairy heifers, I focused on their responses to being handled during a routine procedure called a palpation. In dogs, I examined three aspects of their physical appearance related to the hypothesis: coat color/pattern, the color of their noses, and how much white fur they had. I also assessed their stress hormone levels while in the shelter and when they had a chance to spend time with people outside the shelter. Additionally, I collected information from surveys of mixed breed dogs owned by the public to see if their appearance was linked to their behavior. Altogether, my findings partially support the Domestication Syndrome Hypothesis: some results matched the expectations of the Domestication Syndrome Hypothesis and some did not. For example, I found that Holstein heifers with more black fur had higher stress hormone levels and moved their feet more when palpated, which aligns with the Hypothesis. Additionally, pet dogs with floppier ears were more sociable with people and less prone to aggression and dogs with more white fur were more sociable with people, such also supports the Hypothesis. However, some of the results did not support the Hypothesis. For example, heifers with more white fur vocalized more during palpation and pigmentation did not predict stress hormone levels in shelter dogs. Also, pet dogs with more white fur were less playful and obedient and dogs with more floppy ears were less obedient. Recent research on the Domestication Syndrome Hypothesis in dogs did not find a connection between how dogs behave and look. This might have been due to recent changes to why dogs are bred, which also could have influenced my results. Both the supportive and conflicting results help us to better understand the Domestication Syndrome Hypothesis. Additional research studying more animals, using more consistent evaluations, and asking why these traits seem to be linked can further deepen our understanding of the Domestication Syndrome Hypothesis and its relevance to animal domestication.

Doctor of Philosophy / Genetics Interdepartmental Program / Bikram S. Gill / Threshability is an important agronomic trait in wheat as free-threshing forms facilitate mechanical threshing of grain. All wild relatives of wheat have tough glumes and are non-free-threshing, whereas most cultivated wheats have soft glumes and are free-threshing. Two genetic loci are known to govern the threshability trait in bread wheat. The Q gene located on chromosome 5AL and glume tenacity genes located on homoeologous group-2 chromosomes seem to interact to produce a free-threshing phenotype. Although, the Q gene was found to be a member of APETALLA 2 (AP2) class of transcription factors, the molecular nature of the tough glume genes remains unknown. In the present study, genetic and molecular characterization of two of the threshability genes in wheat was undertaken. The soft glume (sog) gene of diploid wheat and tenacious glume (Tg) gene of hexaploid wheat were characterized and mapped on short arm of chromosome 2Am and 2D respectively. Comparative mapping of sog and Tg genes suggested their independent origins. The sog gene was mapped in a low-recombination region near the centromere on 2AmS. Genomic targeting using deletion bin mapped ESTs assigned the Tg gene to a 4.9 cM interval in the distal 16% of short arm of chromosome 2D. In order to find additional markers for fine-mapping the Tg gene, macrocolinearity between rice and wheat was explored in the Tg region. Although synteny between rice and wheat was found to be conserved in the distal region of chromosome 2DS, the genomic region encompassing the Tg gene in wheat showed some rearrangements relative to rice. Molecular characterization of ethyl methanesulfonate-induced free-threshing mutants in two different non-free-threshing backgrounds revealed point mutations as well as variable sized deletions at Tg locus. Targeting of Tg to the high-recombination gene-rich region in wheat and availability of several genomic resources from the present study will aid in the cloning and further characterization of this important agronomic gene.

This study combines perspectives from domestication theory, feminist technology studies and sociological research on ageing in order to understand older people’s internet use. The suggested approach enables us to examine the complexity of social inequalities in domestication processes. Firstly, I argue that domestication theory benefits from the integration of gender-technology relations, a perspective developed from within feminist technology studies. This allows a better understanding of different dimensions of gender (structure, symbolism, identity) as well as mutual shaping processes between gender and technology. Secondly, this analysis of gender-technology relations can also be utilised to enhance our understanding of age-technology relations. Gender and age are examined in relation to (i) different phases of domestication, (ii) the use of the internet for different activities and (iii) forms of social connectedness in everyday life. The research draws upon 33 semi-structured interviews with women and men between the ages of 55 and 80 about their internet and web 2.0 use experiences. My study demonstrates the diversity of intersections between age, gender and technology within older women’s and men’s internet use experiences, and highlights the significance of traditional age-gender-technology relations (which marginalise older women) for internet use. Furthermore, it identifies specific mechanisms found within domestication processes which serve to maintain these traditional relations. This thesis proposes a research perspective for studying age-gender-technology relations, and examines mutual shaping processes in the domestication of the internet.

The mechanisms behind early domestication of animals are still unknown and an important question is how the changes leading to what is called the domesticated phenotype have developed. It has been suggested that the domestication process has been based on tameness of animals, and that tameness is genetically correlated to other traits. This study aimed to assess whether selection based on tameness induces changes in undisturbed behaviours related to general activity in the red junglefowl (Gallus gallus) housed in semi-natural environments. Two strains of red junglefowl, selected for high and low fear of humans respectively, were studied and compared in terms of general activity. It was found that there was a selection effect on exploratory behaviour and activity, with low fear-birds being more explorative and more active, an interaction effect of selection and sex on feather preening, with high fear-males preening more, and no selection effect on comfort behaviour. Results from this study indicate that tameness is genetically correlated to exploratory behaviour, activity and feather preening in the red junglefowl. These results support the suggestion that the early domestication process was based on tameness and that genetic correlations between tameness and other traits led to the phenotypic variation that is today seen in domestic animals.

Deciphering the genetic basis of phenotypic diversity is one of the central aims of biological research. Domestic animals provide a unique opportunity for making substantial progress towards this goal. Intense positive selection has lead to a rich reservoir of phenotypes and underlying genotypes that can be interrogated using genetic tools to gain insight into the genetic basis of phenotypic diversity. The dog is the most phenotypically diverse mammal. It was domesticated from the grey wolf 11-30,000 years ago. After domestication, a period of intense breeding has lead to the massive phenotypic diversity seen amongst dog breeds today. These two phases of strong positive selection at domestication and at breed creation are likely to have left their signature on the genome. In this thesis, we have analysed genome-wide patterns to detect genomic regions involved in selection in both of these phases. We used whole genome sequences from 60 dogs and 12 wolves, to detect dog domestication selective sweeps. We find evidence for genes involved in memory formation, neurotransmission and starch digestion. To decipher the genetic signals underlying breed diversity, we used genome-wide genotype data from >170,000 SNPs in 509 dogs from 46 different breeds. We find evidence for genes under selection in many breeds, and only a few breeds. In addition, we identify novel sweeps underlying morphology and behavior. Recombination can influence the configuration of alleles present on a haplotype, and can thus increase or decrease the efficiency of selection. The PRDM9 protein has been shown to be important for determining recombination hotspot locations in humans and other mammals, but of all the mammals studied so far the dog is the only one to have a non-functional PRDM9. We used the genome-wide genotype data described above to characterise the fine scale recombination map in dogs. We find that recombination hotspots exist in dogs despite the absence of PRDM9. Moreover, we show that these hotspots are enriched for GC rich peaks and that these peaks are getting stronger over time. Our results show that the absence of PRDM9 has lead to the stabilisation of the recombination landscape in dogs.

La systématique du genre Ovis est restée confuse jusqu'à aujourd'hui, et plusieurs classifications ont été proposées. Sept principaux groupes de moutons sauvages sont distingués sur la base de différences caryotypiques, morphologiques et géographiques. Le présent travail fournit de nouvelles données sur la systématique et l'évolution du genre Ovis, à partir de phylogénies de Cytochrome b. Ces phylogénies sont basées sur l'analyse de 267 échantillons représentatifs de la plupart des sous-espèces d'Ovis et de l'ensemble de leur aire de répartition. L'Urial et le Mouflon, qui sont considérés soit comme une seule espèce (Ovis orientalis) soit comme deux espèces séparées (O. orientalis and O. vignei), forment un groupe monophylétique fortement soutenu. Les hybrides entre O. vignei et O. orientalis apparaissent dans l'un ou l'autre des groupes, indépendamment de leur origine géographique au sein de la zone hybride. Le mouflon européen (O. musimon) appartient clairement au clade d'O. orientalis. Les autres espèces, O. dalli, O. Canadensis, O. nivicola et O. ammon sont monophylétiques. Trois des espèces sauvages, O. orientalis, O. vignei et O. ammon, ont été considérées comme pouvant être à l'origine du mouton domestique. Les relations phylogénétiques entre ces espèces et le mouton montrent maintenant que le seul véritable ancêtre est le mouflon asiatique (O. orientalis). La comparaison de la diversité mitochondriale de 130 moutons avec celle de 140 mouflons asiatiques représentatifs de l'ensemble de l'aire de répartition, permet de localiser l'aire de domestication. Elle s'étend de l'est de l'Anatolie aux monts Zagros, et exclue la basse vallée de l'Indus et l'Asie de l'Est. Une grande partie de la diversité génétique sauvage a été capturée, indiquant des tailles efficaces de population importantes au moment de la domestication. Ceci remet en question l'existence couramment admise de goulots d'étranglement au début de la domestication.

<p>The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock.</p><p>In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones.</p><p>Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.</p>

<p>Osteoporosis is a disease that leads to decreased bone mineral density (BMD), an altered bone micro-architecture and fragile bones. The disease is highly heritable and numerous genes are thought to be involved, making it difficult to identify the causative genetic elements.</p><p>Animal models, mainly intercrosses between laboratory strains of mice, have been succesfully used to map genes affecting these traits, but may not mirror the multifactorial genetic etiology of highly complex traits such as osteoporosis.</p><p>Over the course of tens of thousand years humans have kept domestic animals whose phenotypic repertoires have been tailored to meet our needs. Wild-type red junglefowl (RJ) and domestic White Leghorn (WL) chicken differ for several bone traits. </p><p>In this thesis Quantitative Trait Loci (QTL) mapping was used to trace the inheritance of bone traits in two separate intercrosses between RJ and WL. In these studies we identified several QTL that contributed to differences in BMD, bone size and biomechanical strength of bone. In a comparison of QTL identified in the two intercrosses it was observed that nine QTL had overlapping genomic positions, implicating these loci as important to bone phenotypic variation in chicken.</p><p>In two separate studies, microarray technology was used to compare global gene expression in bone tissue from RJ and WL. In these studies, differential expression was observed for 779 and 560 genes, respectively. Many differentially expressed genes were co-localized with QTL, which implicates them as QTL-candidates. </p><p>Results presented in this thesis link several genomic regions and genes to variation in bone traits. Increased knowledge about these identified genes and regions will contribute to a better understanding of the mechanisms underlying inter-individual differences in bone metabolism, both in chicken and man.</p>