L’étude des interactions entre système fourrager, santé et croissance des lapins contribuera à proposer de nouvelles pratiques pour des systèmes d’élevage cunicole alternatifs, tels que ceux en agriculture biologique (AB) incluant une gestion intégrée de la santé. Mais cette stratégie est limitée par le manque de références sur la cuniculture AB, i) sur l'alimentation au pâturage (ingestion de fourrages verts, qualités nutritionnelles pour les lapins, etc) ; et ii) sur les risques sanitaires notamment le parasitisme, identifié comme un frein important au développement de la cuniculture AB. L’emploi de plantes riches en tannins condensés (TCs) comme le sainfoin, permettrait de diminuer l’utilisation d’antiparasitaires comme cela a été montré chez les petits ruminants, tant pour la gestion des nématodes que celle des coccidies. Mais le potentiel d’activité des TCs chez le lapin, tout comme le niveau d’ingestion et les performances de croissance, restent à explorer, et pourra servir la cuniculture AB et conventionnelle. Ce travail de thèse a pour objectif i) d’étudier l’intérêt du sainfoin comme ressource pour l’alimentation du lapin, et pour ses propriétés antiparasitaires, ii) définir le niveau d’ingestion au pâturage des lapins et les conséquences sur la production et iii) d’évaluer, le risque parasitaire au pâturage pour des lapins en production. Nous avons montré qu’un aliment enrichi en sainfoin distribué à partir du sevrage, avec une teneur en tannins de 1,8% d’équivalent d’acide tannique, n’a pas réduit l’installation de L3s de Trichostrongylus colubriformis, ni la fertilité des vers adultes, mais a réduit le potentiel d’éclosion des oeufs (-27 points), contribuant à réduire l’infestation de l’environnement. Un aliment enrichi en sainfoin contenant 1,2% d’équivalent d’acide tannique, distribué aux mères et aux lapins en croissance a eu un effet coccidiostatique : l’excrétion oocystale fécale de lapins nourris avec un aliment enrichi en sainfoin a été réduite de 60% par rapport à ceux ayant reçus l’aliment témoin. Si la réduction de l’excrétion oocystale de l’espèce Eimeria magna n’a pas pu être démontrée, en revanche, la réduction d’oocystes toutes espèces confondues dans l’environnement pourrait contribuer à diminuer le risque de coccidiose en élevage. Comparé à la luzerne, le sainfoin, plus riche en lignines, a une forte concentration en énergie (11,2 MJ/kg) et en protéines digestibles (110 g/kg). Au pâturage, lorsque la quantité d’herbe offerte dépasse 85 g MS/kg0,75, il semble que l’ingestion d’herbe soit régulée d’une part lorsque la teneur en énergie digestible de l’herbe dépasse 9 MJ/kg (régulation chémostatique), ou d’autre part si la teneur en lignocellulose (ADF) dépasse 350 g d’ADF/kg (régulation physique : encombrement digestif). Mais la quantité d'herbe disponible dépasse rarement 85 g MS/kg0,75. C’est-à-dire que dans la majorité des cas, une surface pâturable de 0,4 m² (minimum réglementaire) n’a pas permis de combler la capacité d’ingestion et les besoins énergétiques de lapin en croissance. De plus, si l’offre d’herbe est limitante, le lapin ne peut pas exprimer une préférence alimentaire vers des plantes plus jeunes et riches en protéines. La limitation de l’ingestion de protéines a aussi pour conséquence de réduire les potentialités de croissance des lapins et d’allonger la période d’engraissement. Au cours de trois saisons successives de pâturage (université de Perpignan), la pression parasitaire (nématodes et coccidies) a augmenté, avec des infestations par Trichostrongylus sp. et de Graphidium strigosum. Si le délai d'attente entre deux pâturages n’a pas eu d’effet visible sur l’infestation par des nématodes, cela influerait le niveau d’infection par les coccidies. Nos travaux établissent l’intérêt de l’incorporation du sainfoin dans l’alimentation du lapin et ouvrent des perspectives pour établir des pratiques innovantes et bénéfiques à la production cunicole biologique et conventionnelle. / The study of the interactions between grazing systems, health and growth in organic rabbit farming (ORF) will contribute to propose new practices including integrated management of health. However, this strategy is limited by the lack of references on ORF and in particular on rabbit intake of green fodder when grazing, nutritional qualities of forages for rabbits, the supply of grass in relation with animal’s density (stocking rate), the related parasitic challenge, etc. The acquisition of such references is a key issue for the development of ORF. The use of plants rich in condensed tannins (CTs), such as sainfoin, could reduce the use of antiparasitic agents, as shown in small ruminants, both for the management of nematodes and for coccidia. However, the potential for CTs containing resources in rabbits, as well as the intake levels and the effects on growth performances, remain to be explored in both OF and conventional rabbit breeding. The aim of this thesis was (i) to investigate the interest of sainfoin as a resource for rabbit feeding and its antiparasitic properties, (ii) to define the intake level in grazing rabbit and the consequences on production and (iii) to evaluate the parasitic risk associated with pasture for rabbits’ production. We have shown that a sainfoin-enriched diet distributed from weaning, with a feed containing 1.8% of tannic acid equivalent, did not reduce neither the establishment of Trichostrongylus colubriformis L3s, nor the fertility of adult worms. In contrast, the development of nematode’s egg to infective larvae was compromised and may reduce the risk of environmental contamination. Besides, a sainfoin-enriched diet containing 1.2% tannic acid equivalent, distributed to does and growing rabbits, had a coccidiostatic effect. With an overall fecal oocyst excretion in rabbits fed with sainfoin reduced by 60% compared to control diet. Although, the pathogenic species Eimeria magna was not concerned by these decrease, such a general reduction in oocyst excretion in the environment could help to reduce on long term the risk of coccidiosis in the rearing units. Sainfoin could constitute a real alternative to dehydrated alfalfa, since it has high digestible energy (DE, 11.12 MJ DE/kg), and protein (110 g/kg), and provide a high supply of lignins. At grazing, when the herbage allowance exceeded 85 g DM/kg0,75, it appeared that the herbage intake was limited by an increase in the DE content when it exceeds 9 MJ / kg, or else by a lignocellulose content higher than 350 g of ADF/kg. However, herbage allowance, rarely exceeds 85 g DM/kg0,75. In other words, in the majority of cases access to a 0.4 m² grazing area did not allow sufficient supply to reach the intake capacity and energy requirements of the rabbits. In addition, rabbits with limited supply cannot express their dietary preference to young and high protein plants. Limiting the intake of proteins also reduced the growth potential of rabbits and extended the fattening period. During the first three grazing seasons (University of Perpignan), the parasitic pressure (nematodes and coccidia) increased, particularly with cases of Trichostrongylus sp. and Graphidium strigosum. While rotation rhythms had no visible effects on nematode infestation, it had an influence on coccidian infection. This work enabled us to establish the advantage of sainfoin enriched diet for the rabbit. It gives prospects to further research projects regarding the establishment of beneficial and innovative practices for organic and conventional rabbit breeding.

Les systèmes d'élevage des petits ruminants au pâturage sont les plus répandus en zone tropicale humide mais l'exposition aux strongles gastro-intestinaux entraîne des pertes importantes de production. L'objectif de ce travail est d'évaluer un système de gestion mixte du pâturage associant diverses espèces animales permettant à priori d'accroître les performances via la réduction du parasitisme et!ou une meilleure alimentation. L'étude de la littérature a conduit à une méta-analyse confirmant de meilleures performances individuelles ou à l'hectare pour les ovins en mixte. Préalablement un dispositif visant à vérifier la non-transmission des larves d'Haemonchus contortus des caprinsaux génisses Créoles a été validé. Un second dispositif avec des chevrettes conduites en mixte, infestées ou pas par Haemonchus comortus (Ml et MnI) ont été comparées à des chevrettes contrôles infestées ou non (CI et CnI). Ce dispositif a été conduit pendant 2 ans avec des mesures du couvert pâturé, des mesures individuelles des quantités ingérées, de la digestibilité, du parasitisme et de la croissance. De plus fortes croissances ont étéobservées en pâturage mixte que les chevrettes soient infestées ou pas (43.25 et 31.68 glj pour MDI et MI vs. 32.44 et 17.91 glj) avec une moindre biomasse. Les mesures d'ingestion et d'ingéré digéré ont été corrélées aux croissances des chevrettes contrairement aux variables parasitaires et met en évidence le rôle de l'alimentation et de la résilience dans le bénéfice du pâturage mixte. Une autre gestion intégrée du pâturage a été étudiée basée sur l'utilisation du vermicompost et s' ant sur les mêmes leviers d'action: l'alimentation et le itisme / Systems of small ruminant grazing are most prevalent in the humid tropics but this environment exposes animals to gastro-intestinal with production losses. The objective ofthis thesis is to evaluate a system ofmixed management ofthe pasture combining various animal species, which allows a priori to increase animal performance by reducing the parasitism and/or better nutrition. The study of literature bas led to a meta-analysis confirming the better individual performances or calculated per ha for sheep reared mixed. The first experiment validated the non-transmission of Iarvae ofHaemonchus contortus from goats to heifers. In a second experiment, goats mixed with heifers, infested or not with Haemonchus contortus (Ml vs MnI) were compared with controls goats, reared alone, infested or not (CI and CNI). This deviee with a continuous driving was studied for two years with measurements on the sward, individual measures of intake, digestibility, parasitism and growth ofthe goats. The highest growth rates were measured with the mixed pasture as goats are infested or not (43.25 and 31.68 g / d for MN! and MI vs. 32.44 and 17,91 g / d) with lower biomass. The herbage intake and the digested herbage intake were well correlated to the growth rate, unIike parasitic variables, and highlight the role of diet in the benefit of mixed driving for goats. Therefore, the infested goats with Haemonchus, expressed greater resilience with improved growth performance compared with controls. Parallel to the study ofmixed pasture, another integrated management of grazing was studied, based on the use of vermicompost and relying on the same levers. namelv throuzh feedinz and parasitism

Members of the group Archamoebae are free-living or endobiotic amoeboid flagellates and amoebae. They live in anoxic or microoxic habitats, and their mitochondria have been reduced. They were originally thought to lack mitochondria and represent one of the earliest eukaryotes. However, this hypothesis has been refuted, and now it is evident that the Archamoebae belongs to the lineage Conosa within the supergroup Amoebozoa, together with aerobic slime molds (Macromycetozoa) and variosean amoebae and flagellates. Relatively simple microtubular cytoskeleton is a characteristic feature of Archamoebae. It consists of a single basal body from which a flagellum arises, lateral root, and microtubular cone. Cytoskeleton of aflagellated genera has been completely reduced. About 350 species names of Archamoebae have been created so far. However, most descriptions were based on inadequate morphological features. The identity of numerous species is uncertain, and many of them are likely synonymous. Another problem is a small amount of available molecular data. During our project, we have substantially improved the dataset of DNA sequences of archamoebae. On the basis of molecular and morphological data, we described 13 new species. We showed that genus Rhizomastix belongs to Archamoebae and displays a new type...

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Master of Science / Department of Biology / Brett K. Sandercock / Grassland birds are declining throughout their native range. The Flint Hills of eastern Kansas and Oklahoma contain large tracts of tallgrass prairie, but intensification of agricultural practices may be contributing to ongoing population declines. Common rangeland management practices include annual burning coupled with heavy grazing by cattle. This system, known as intensive early stocking and burning, promotes homogeneous utilization of forage by cattle but may not provide habitat for some grassland bird species. Patch-burn grazing is an alternative management system that aims to restore heterogeneity on rangelands by recreating the fire-grazing interaction that would have historically occurred throughout the Great Plains. From 2011-2013, we examined responses of grassland birds to traditional rangeland management and patch-burn grazing by conducting vegetation surveys, line transect surveys, and nest monitoring on privately-owned pastures in Chase County and Greenwood County, Kansas. Vegetative heterogeneity was higher on patch-burned pastures, with unburned patches having higher visual obstruction and less bare ground. Densities of grassland birds differed by species and among habitat strata. Unburned patches on patch-burned pastures were associated with increased densities of Dickcissels (Spiza americana), Eastern Meadowlarks (Sturnella magna) and Grasshopper Sparrows (Ammodramus savannarum). Henslow’s Sparrows (A. henslowii) were only detected on patch-burned pastures. Nest survival of grassland songbirds was similar among management systems but varied by year. Probability of nest parasitism by Brown-headed Cowbirds (Molothrus ater) varied among years and between treatments for Dickcissels and Grasshopper Sparrows, with overall lower rates on burned areas and during drought years. For Dickcissels and Grasshopper Sparrows, there was a significant reduction in host clutch size between parasitized versus unparasitized nests. Overall, nest survival of grassland songbirds in managed rangelands was low. Patch-burn grazing improved rangeland conditions and provided habitat for more species of birds, but did not increase nest survival. Drought conditions in 2012 and 2013 may have influenced the results of this study, as many landowners were unable to burn as planned. Further study is needed to determine underlying factors driving variation in nest success and parasitism rates for grassland birds, particularly on private lands which make up the vast majority of remnant tallgrass prairies.

De l’éclosion à l’abattage, le saumon Atlantique et la truite arc-en-ciel d’élevage sont soumis à divers événements inducteurs de stress. Le stress influe directement sur la physiologie, le comportement et les performances zootechniques des animaux. Ainsi, l’intérêt grandissant du public pour le bien-être des animaux nous a amené à améliorer les connaissances sur le stress des salmonidés d’élevage pour en proposer des méthodes d’évaluation et de contrôle. Partant de ce constat, nous avons étudié les conséquences de deux situations inductrices de stress et proposé une méthode d’évaluation du bien-être de la truite arc-en-ciel d’eau douce. Nous avons ensuite étudié l’interaction entre stress et pathologie à travers l’exemple du parasite du saumon Lepeophtheirus salmonis. Après avoir mis au point un test d’attractivité du saumon pour ce parasite, nous avons étudié les conséquences du stress aigu puis chronique sur l’attractivité des saumons. Le stress de manipulation augmente l’attractivité des saumons pour le parasite, alors qu’il n’y a pas de différence entre les saumons stressés chroniquement et les témoins. Nous avons ensuite proposé une méthode de contrôle de ce parasite en isolant un sémiochimique issu du mucus de saumon et inhibant l’attachement du parasite. L’ensemble de nos travaux ouvre des perspectives intéressantes quant à l’amélioration des méthodes d’évaluation et de contrôle du stress en élevage des salmonidés. L’étude des conséquences du stress est importante pour mesurer l’impact, à la fois sur le bien-être de l’animal, mais aussi sur les coûts de production. Le sémiochimique inhibiteur de l’attachement du parasite sur le saumon promet de nombreuses études pour comprendre ses mécanismes d’action et son éventuelle utilisation en élevage. / From hatching to slaughter, Atlantic salmon and Rainbow trout are subjected to several stressful events. Stress impairs physiological, behavioral and zootechnical performances of animals. The public interest in animal welfare brings us to study the assessment and control methods of stress in farmed salmonids. To do that, we studied the consequences of two different stressful events and proposed a method for assessing welfare of freshwater Rainbow trout. We also studied the interaction between stress and pathology with the salmon louse Lepeophtheirus salmonis. After developing an attractiveness test of salmon for the parasite, we investigated the influence of shortand long-term stress on salmon attractiveness for the parasite. Handling stress increased attractiveness of salmon for the parasite, while there was no difference between chronically stressed and control salmon. We proposed then a method to control this parasite by isolating a semiochemical which inhibit the hooking behavior of the parasite on the host. These results open interesting prospects for improving the assessment and control methods of stress in farmed salmonids. The investigation of stress consequences on animal welfare and on production performances is crucial. The semiochemical inhibiting the hooking behavior of the parasite on the salmon needs more studies to identify its mechanisms of action for use in farms.

M.Sc. (Zoology) / Please refer to full text to view abstract

Under the Dobzhansky-Muller model, postzygotic isolation results from incompatibility between interacting genes. Evidence points to regulatory networks as a rich source of incompatibilities that impact hybrid fitness. Pleiotropy is a natural feature of regulatory networks because regulatory elements generally have multiple targets. Both pleiotropy and hybrid incompatibility arise due to genetic interactions; therefore we can expect an intimate association between them. In the following chapters, I investigate the relationship between pleiotropy and hybrid incompatibility in the context of regulatory networks. In chapter one, I extend a general network-based study of hybrid incompatibility by incorporating a sequence-based thermodynamic model of transcriptional regulation. In the absence of pleiotropy, hybrid misregulation of a positively selected trait evolves quickly as a consequence of non-recognition or spurious binding in regulatory interactions across species boundaries. In a conserved trait, hybrid incompatibility evolves much slower as a product of compensatory drift. In chapter two, I show that pleiotropy can promote or constrain the evolution of hybrid incompatibility in a regulatory network depending on its fitness landscape, which emerges from the thermodynamic properties of molecular binding. Pleiotropy may promote hybrid incompatibility in accordance with the "selection, pleiotropy, and compensation model" of evolution, in which compensation for the pleiotropic side-effects of adaptation accelerates incompatibility in conserved traits. Pleiotropy can limit the evolution of hybrid incompatibility by constraining change in trans-acting regulatory elements in favor of adaptation at less pleiotropic downstream cis-regulatory targets. Without change in both interactors, incompatibility does not occur under the Dobzhansky-Muller model. In chapter three, I evaluate the hypothesis that pleiotropy facilitates the onset of hybrid incompatibility under antagonistic coevolution, an ubiquitous and persistent source of natural selection. When infectivity and resistance in a host-parasite system are determined epistatically by network interactions, reciprocal selective pressure results in a genotypic chase. This causes pleiotropic mutations to accumulate and be compensated over time, producing intrinsic hybrid incompatibility in both species independent of local adaptation. Thus, cyclical antagonistic coevolution eventually overcomes constraint on pleiotropic loci, facilitating the evolution of regulatory incompatibilities commonly observed in hybrids.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24875号 / 理博第4985号 / 新制||理||1712(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 MacIntosh Andrew, 教授 岡本 宗裕, 教授 明里 宏文 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

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