Stable isotope analyses are powerful tools for reconstructing ancient ecologies and ecosystems, as they are independent of morphology and directly reflect dietary ecology. The application of stable isotope analyses, however, is not without limitations, as determination of food web dynamics using these methods often relies on poorly tested assumptions. The guiding thread of this thesis is the testing of foundational cornerstones on which these methods rely, in order to validate the suitability of applying these techniques to different mammalian clades, and to more reliably and confidently interpret the isotopic signals preserved in extinct organisms. The first chapter of this thesis tests the validity of an important assumption behind the interpretation of stable carbon isotope analyses for understanding diet in terrestrial mammalian herbivores: if, as assumed for almost two decades, mammalian bioapatite δ¹³C is enriched by 14‰ relative to dietary δ¹³C. By analyzing new isotopic data from a never before assessed herbivorous group spanning a broad range of body masses—sloths (Xenarthra, Mammalia)— and other mammals with experimentally controlled or observationally known diets, I discovered considerable variation in diet–bioapatite δ¹³C enrichment among mammals. Statistical tests (ordinary least squares, quantile, robust regressions, Akaike information criterion model tests) documented independence from phylogeny, and a previously unrecognized strong and significant correlation of δ¹³C enrichment with body mass for all mammalian herbivores. A single-factor body mass model outperformed all other single-factor or more complex combinatorial models evaluated, including for physiological variables (metabolic rate and body temperature proxies), and indicated that body mass alone predicts δ¹³C enrichment. These analyses, spanning more than 5 orders of magnitude of body sizes, yield a size-dependent prediction of isotopic enrichment across Mammalia and for distinct digestive physiologies, permitting reconstruction of foregut versus hindgut fermentation physiologies for fossils and refined mean annual paleoprecipitation estimates based on δ¹³C of mammalian bioapatite. Second, I sought to evaluate the existing paradigm governing identification of closed canopy rainforests in the fossil record using mammalian δ¹³C data: the presence of mammals with dietary δ¹³C <-31‰, which has only been observed in closed canopy rainforests in Equatorial Africa, the only other tropical ecosystem sampled extensively. This chapter provides a characterization of δ¹³Cbioapatite, δ¹³Chair and δ¹⁵Nhair of a modern mammalian community in western Amazonia, in Peru, to test if the isotopic structure of mammals in this Neotropical ecosystem is similar to those in African tropical rainforests. The results indicate that despite their marked geographical and taxonomic differences, median δ¹³Cdiet values from closed canopy rainforests in Amazonia (-27.4‰) and equatorial Africa (-26.9‰) are not significantly different. Amazonian mammals, however, seem to exploit a narrower spectrum of dietary resources than equatorial African mammals, as depicted by the absence of highly negative δ¹³Cdiet values previously proposed as indicative of rainforests (<-31‰). I hypothesize that differential effects of late Pleistocene extinction may be responsible for the ecological disparities among the two rainforests, by significantly reducing evolutionary time and dietary breadth reflected in the modern Amazonian mammalian community. Finally, the third chapter of this dissertation evaluates assumptions behind δ¹⁵N amino acid compound specific analyses in order to test the controversial hypothesis of carnivory and consumption of proteins of animal origin in fossil sloths. This analytical technique relies on three main assumptions. First, that the offset between the δ¹⁵N of glutamic acid (δ¹⁵NGlx) and phenylalanine (d15NPhe) in the organism under study will increase with increasing trophic level. Second, that the offset between δ¹⁵NGlx and δ¹⁵NPhe at the base of the food chain is relatively constant and has a value of -8.4‰ for C3 ecosystems. Third, that the trophic discrimination factor in all ecosystems (the difference in δ¹⁵NGlx relative to δ¹⁵NPhe with increasing trophic level) is 7.6‰. The results of my experiments conducted on extant xenarthrans (sloths and anteaters) with controlled diets document that only the first assumption holds true. Rather than relying on an equation with constants introducing uncertainties and that are not applicable to organisms feeding on a combination of items of different origin (e.g., C3 + C4 plants), δ¹⁵NGlx and δ¹⁵NPhe values by themselves can accurately reconstruct the trophic position of organisms. Indeed, the results on δ¹⁵NGlx and δ¹⁵NPhe herein obtained for five xenarthran species in controlled feeding experiments, combined with mammalian data available from the literature, show strong and significant correlations between these two AAs and with trophic positions. Both the TP equation and the regression analyses of δ¹⁵NGlx and δ¹⁵NPhe suggest that the Pleistocene fossil ground sloths 𝘔𝘺𝘭𝘰𝘥𝘰𝘯 𝘥𝘢𝘳𝘸𝘪𝘯𝘪𝘪 and 𝘕𝘰𝘵𝘩𝘳𝘰𝘵𝘩𝘦𝘳𝘪𝘰𝘱𝘴 𝘴𝘩𝘢𝘴𝘵𝘦𝘯𝘴𝘪𝘴 were not pure herbivores as commonly presumed, but rather that they were both mixed feeders/omnivores, incorporating items of animal origin in their diets.

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La chasse – comme la prédation naturelle - induit des réponses comportementales par les individus chassés qui cherchent ainsi à éviter ou à reduire le risque. Il est en particulier fréquent d'observer un changement dans leur utilisation de l'espace, mais l'articulation et les déterminants des réponses aux différentes échelles spatiales restent mal compris. De même, s'il a été suggéré que ces modifications comportementales pouvaient affecter en cascade la végétation, cela reste à tester. Pour combler ces lacunes, j'ai, (1) étudié, dans un paysage agricole du sud de la France, une population chassée de chevreuils et leur utilisation des milieux ouverts risqués et des couverts boisés, au cours de périodes de risque contrasté ; (2) testé, sur une population canadienne de cerfs à queue noire dépourvue de prédateurs et exempte de chasse, l'influence d'une chasse expérimentale sur le comportement des animaux et sur la végétation. J'ai montré que les chevreuils répondaient à une augmentation du risque à plusieurs échelles spatiales. Ils réduisaient leur utilisation des habitats risqués, et dans certains cas se rapprochaient des couverts, de jour ces deux réponses étant couplées au niveau individuel. Le gradient paysager d'ouverture du milieu contraignait cependant les niveaux de réponses observées et les stratégies individuelles. Au Canada, j'ai observé un évitement de la zone chassée par les cerfs les plus sensibles à la présence humaine, corrélé à une diminution de l'abroutissement pour deux des quatre espèces de plantes étudiées. J'ai intégré ces résultats dans une discussion sur l'utilisation de la chasse pour gérer les populations d'herbivores et leurs impacts sur la végétation. / Hunting – similarly to natural predation – induces behavioural responses of hunted individuals which aims at avoiding or reducing risk. Particularly, changes in space use are frequently observed, but the articulation and determinants of these changes at multiple spatial scales are still poorly understood. Also, although it has been suggested that these changes might cascade on the vegetation, this remains to be tested. To fill these gaps, I (1) studied a hunted roe deer population living in an agricultural landscape in southern France where roe deer can find open risky habitats and woody covers; and (2) tested black-tailed deer behavioural response to an experimental hunt in a predator- and hunting-free population in the Haïda-Gwaii archipelago (BC, Canada). I also investigated the possible cascading effects on the vegetation. I showed that roe deer responded to increased hunting pressure at multiple scales, reducing their use of the risky habitats and, in specific situations, their distance to the nearest cover. At day-time those two responses were coupled at the individual level. Generally, landscape openness constrained individual responses and strategies. In the hunting-for-fear experiment conducted on Haida Gwaii, I found that only the deer less-tolerant to human disturbance avoided the hunting area. A simultaneous reduction in browsing pressure on two out of the four plant species monitored was found however. I integrated these results in a general discussion on the possible role of hunting as a tool to manage abundant deer populations and their impacts on the vegetation.

Dans l’hémisphère Nord, les populations de grands herbivores ont connu ces dernières décennies des modifications environnementales majeures, liées d’une part à l’augmentation importante de leur densité, et d’autre part aux changements globaux qui affectent leur habitat (notamment réchauffement climatique, modification des activités humaines, et fragmentation de l’habitat). Mieux comprendre comment ces espèces vont adapter leurs stratégies d’histoire de vie pour répondre à ces modifications est une question majeure de l’écologie des populations, et une étape nécessaire pour pouvoir adapter leur gestion aux enjeux environnementaux et sociétaux actuels. C’est dans ce contexte que nous avons étudié quelles étaient les sources de variation des tactiques de survie et de reproduction chez trois espèces de grands herbivores de montagne (l’isard Rupicapra pyreneica, le chamois Rupicapra rupicapra, et le mouflon méditerranéen Ovis gmelini musimon × Ovis sp.). A partir de suivis longitudinaux par capture-marquage-recapture (CMR) nous nous sommes plus particulièrement focalisés sur le rôle de l’hétérogénéité individuelle latente, de la variabilité climatique et de la structuration spatiale sur les paramètres démographiques.Ce travail s’est appuyé sur l’utilisation de modèles de mélange et d’une combinaison innovante du robust-design et des modèles multi-événements pour analyser des données démographiques collectées à différentes échelles spatio-temporelles. L’hétérogénéité individuelle s’est avérée être une composante majeure de la démographie des 3 espèces étudiées, avec l’identification chez le mouflon et l’isard de femelles aux performances reproductives contrastées, et l’existence chez le chamois de différences de survie entre individus liées à la qualité de l‘habitat occupé. Ces modèles ont aussi permis de révéler une augmentation de l’investissement reproducteur en fin de vie chez les femelles de mouflon au détriment de leur survie et d’étudier chez les femelles d’isard les différentes phases de l’effort reproducteur, de la gestation au sevrage, pour mettre en évidence que seule la lactation a un coût sur la reproduction suivante. Nos résultats ont également mis en exergue le rôle prépondérant du climat hivernal et printanier sur les paramètres démographiques des 3 espèces, tout en confirmant que ces effets sont souvent spécifiques à la population et au site étudiés. Cette étude montre également que l’isard et le mouflon, bien que relativement comparables en termes de taille, de traits écologiques, et de position phylogénétique, adoptent des stratégies d’histoire de vie contrastées.Au final, nos résultats soulignent donc l’importance des études démographiques comparatives à plusieurs niveaux d’organisation (inter-espèces, inter-population, intra-population), pour mieux comprendre le devenir des espèces de grands herbivores face aux perturbations environnementales. / In Northern hemisphere, populations of large herbivores have to cope with major environmental modifications linked to the increase of their density and to global change which strongly impacts their habitat (climate change, modification of human activities and habitat fragmentation). Understanding how these species adjust their life history strategies in response to such modifications is central for population ecology and for management issues. In this context, this work aimed to identify the sources of variation of survival and reproductive tactics in 3 species of mountain ungulate (Pyrenean chamois Rupicapra pyreneica, Alpine chamois Rupicapra rupicapra, and Mediterranean mouflon Ovis gmelini musimon × Ovis sp.). Using capture-mark-recapture monitoring we specifically investigated the role of individual heterogeneity, climate change, and spatial heterogeneity in shaping vital rates.This work relied on mixture models and an innovative combination of robust-design into a multi-events framework to explore demographic data collected at different spatio-temporal scales. Fixed heterogeneity appeared as a major demographic component in the 3 studied species by highlighting in mouflon and Pyrenean chamois two groups of females with contrasted reproductive performance, and by providing evidence in chamois of among-females differences in survival rates linked to the quality of their habitat. These models allowed us to provide evidence for the terminal investment hypothesis in female mouflon and to decompose reproductive effort in females of Pyrenean chamois from gestation to weaning, to unveil that lactation only led to cost on subsequent reproduction. Our results also highlighted the major influence of winter and spring climatic conditions on demographic parameters in the 3 studied species, and confirmed the general trend that climate effects are often species- and site-specific. Our findings provided evidence that Pyrenean chamois and mouflon evolved contrasted life history strategies, although both species share strong similarities in terms of body mass, ecological traits and phylogenetic position.Finally, our work stresses the importance of conducting comparative demographic studies, based on longitudinal monitoring of marked individuals, at inter-specific, inter-population and within population levels, to better understand and predict the future of large herbivores populations in the current context of global changes.

Fire plays an important role in structuring and maintaining savanna grassland ecosystems. Although regular fires are a characteristic feature of savannas, the effects of fire frequency on these systems are less well known, particularly with respect to how frequency of fire influences large herbivore distribution and behaviour. The expectation is that large herbivores should be attracted to frequently burned sites as a consequence of changes in forage quality and quantity, and/or vegetation structure and composition. The former could be driven by alterations in soil nutrients, such as N and P. Alterations in vegetation also could be important in determining risk of predation. For example, an increase in woody vegetation could decrease predator visibility making large herbivores more vulnerable to predation. The objectives of this study were to investigate the effects of long-term alterations in fire frequency on herbivore distribution and behaviour, as well as the mechanisms (soil nutrients, vegetation structure and composition, and forage quality and quantity) potentially driving the distribution of large herbivores. To address these objectives, I conducted large herbivore surveys on a bi-weekly basis from 2009-2010 in a series of plots in the Experimental Burn Plots (EBPs) burnt at different frequencies (annual, triennial and unburnt) over the last five decades at three study sites in the Kruger National Park, South Africa. Surveys also were conducted on new plots that were established adjacent to the long-term plots. These new plots have a fire return interval of 4 years which is similar to the triennially burned plots of the EBPs. They were established in the landscape adjacent to the EBPs to assess whether the responses of herbivores to fire observed in the EBPs reflected was at landscape level. The distribution of all large herbivore species combined and of grazers (e.g. zebra) or browsers (e.g. kudu) only were not affected by fire frequency. In contrast, the abundance of mixed-feeders, such as impala, was significantly higher in the unburnt (control) and annually burned plots than the triennially burned plots. Although season did not have a significant impact on the distribution of browsers and mixed-feeders, overall more grazers were recorded across all burn treatments in the dry season compared to the wet season. Similar patterns of herbivore distribution were observed between the new plots and the triennially burned EBP plots, suggesting that responses observed to the long-term fire frequency treatments reflects herbivore responses at the landscape level. The long-term fire frequency treatments significantly affected soil nutrients (N, organic C, P, and K were significantly lower with annual burning), vegetation structure (abundance of woody plants were greater in unburned plots), and forage quantity (unburned plots had higher biomass) but not quality. More frequent fires improved visibility by reducing tree height and density and herbaceous biomass, thereby potentially reducing predation risk, when compared to less frequent burning. As a result, herbivores selected sites with more frequent fires. The behaviour of the herbivore species investigated was predominantly influenced by seasonal-induced changes to their environment rather than fire frequency. In the wet season irrespective of the burning treatment visibility was low due to high rainfall that increases plant biomass, whereas in the dry season visibility was improved because there is little to no rainfall. This potential alteration in predation risk likely resulted in herbivores being more vigilant in the wet season than the dry season. Overall, results from this study suggest that the combination of fire frequency and season drive herbivore distribution and behaviour by altering mainly the vegetation structure which can influence predation risk. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

L'augmentation de populations de cerfs pose d'importants problèmes écologiques et socio-économiques à l'échelle locale et mondiale. Des signes de densité-dépendance sont souvent observés, mais les cerfs restent abondants malgré l'importante dégradation du milieu qu'ils provoquent. Ceci soulève la question de l'ajustement des cerfs aux changements de milieu qu'ils créent ? Nous avons abordé cette question en recherchant comment les cerfs gèrent leur ressource alimentaire en fonction du risque de prédation. La prédation, en plus de son effet consommateur (élimination de proie), peut moduler le comportement et la physiologie des proies (effet non consommateur) qui doivent balancer le fait de se nourrir et le risque de prédation. Cette étude contribue à mieux comprendre comment les cerfs maintiennent d'abondantes populations dans des milieux qu'ils ont eux-mêmes appauvris.Notre projet s'est intéressé au cerf-à-queue-noire Sitka (Odocoileus hemionus sitkensis) sur trois îles de l'archipel d'Haïda Gwaii (B.C., Canada). Ces îles sont dépourvues des principaux prédateurs naturels du cerf (loup et puma) et ont été colonisées par les cerfs il y a plus de 60 ans. Lors de notre étude, ces îles présentaient des niveaux contrastés de nourriture et de risque de prédation : sur deux îles, les cerfs vivaient sans prédateur mais avaient fortement appauvri leur milieu (îles sans risque/pauvre). Sur la troisième île, les cerfs étaient chassés et bénéficiaient d'un sous-bois forestier partiellement restauré comme nourriture (île risquée/riche).Dans ce cadre, nous avons étudié : 1) sur quelles ressources les cerfs pouvaient maintenir de denses populations dans des milieux très abroutis ?; 2) comment le stress alimentaire ou le risque de prédation influençaient la réponse physiologique au stress des cerfs?; 3) les cerfs naïfs à la prédation ont-ils maintenu des niveaux de vigilance dans des milieux très abroutis et comment répondaient-ils à des stimuli olfactifs de prédateurs ?; et 4) comment, dans des milieux très abroutis, les cerfs naïfs à la prédation répondaient-ils à une chasse expérimentale pour faire peur et comment cela affectait la végétation ?Notre étude a montré que : 1) les chutes de feuilles de la canopée et la pousse annuelle de plantes rhizomateuses offraient une grande quantité d'énergie pour les cerfs et contribuaient au maintien de denses populations de cerfs dans des milieux appauvris ; 2) La présence de stress alimentaire ou de risque de prédation n'affectaient pas la réponse physiologique au stress des cerfs, suggérant l'existence d' ajustements comportementaux et/ou physiologiques permettant de réduire l'exposition des cerfs à ces deux stresseurs ; 3) sur les îles sans risque/pauvre, les cerfs ont maintenu la vigilance malgré 60 ans d'isolation à la prédation. En outre, les cerfs naïfs à la prédation évitaient de manger en présence d'urine de loup (dangereux) mais pas en présence d'urine d'ours (moins dangereux), suggérant que les cerfs présentaient une stratégie innée de nourrissage sensible au risque. Les cerfs restaient aussi moins longtemps aux stations d'appâtage en présence d'urine de loup mais n'augmentaient pas leur niveau de vigilance, suggérant qu'ils géraient le risque spatialement plutôt que par la vigilance ; 4) En réponse à une chasse expérimentale pour faire peur réalisée sur une des îles sans risque/pauvre, seuls les cerfs les moins tolérant à la perturbation humaines évitaient la zone chassée. Ceci souligna l'importance de la sélection des traits comportementaux induis par l'homme dans la gestion de la faune et de la flore. Nous avons aussi suivi la croissance de quatre espèces de plantes côtières à croissance rapide et avons montré que notre chasse expérimentale favorisait la croissance de la moitié d'entre elles, soulignant l'interaction complexe entre le comportement de nourrissage et les caractéristiques des plantes, ainsi que l'importance des objectifs dans le choix des outils de gestion. / In many temperate environments deer populations have been increasing, raising serious ecological and socio-economic concerns both locally and globally. Signs of density dependence are often observed in such populations, but deer abundance often remains high with regard to the dramatic degradation of the environment they have induced. This raises the question: How do deer do to adjust to the environmental changes they created? The present study addressed aspects of this question focusing on how deer manage their food resource in relation to predation risk. In addition to its consumptive effect (prey removal), predation is increasingly recognized for its non-consumptive effect on prey behavior and physiology, the importance of which is linked to the strength of the trade-off between foraging and predation risk. A better understanding on how deer manage food resource and predation risk in heavily browsed environment may thus help to better understand how deer maintain abundant populations in self-induced depleted environment.We tackled this question by studying Sitka black tailed deer (Odocoileus hemionus sitkensis) on three islands of the Haida Gwaii archipelago (B.C., Canada). These islands are devoid of the main natural predators of deer (wolves and cougars) and were colonized by deer over 60 years ago. At the time of the study, these islands presented contrasted levels of food and predation risk: on two islands, deer were predator-free but had strongly depleted their environment (safe/poor islands). On the third island, deer were culled by means of regular hunts and had access to a partially recovered forest understory in terms of food supply (risky/rich island).We considered four questions: 1) on what resources do abundant deer populations rely in heavily browsed environment?; 2) how do deer physiological stress response vary with either food stress or predation risk?; 3) do predator-naïve deer maintain anti-predator behaviors, like vigilance, in heavily browsed environments and how do they respond to predator olfactory cues?; and 4) how do predator-naïve deer respond to an experimental hunting for fear in a heavily browsed environment and how does it affect the vegetation? We showed that: 1) the subsidies from canopy litterfall and the annual growth from rhizomatous plants offered a large energy supply for deer and contributed to maintain abundant deer population in forests with depleted understory; 2) deer did not mount a physiological stress response in presence of either starvation or predation risks, and we suggested that behavioral and/or physiological adjustments allowed deer to mitigate their exposure to either stressor; 3) on safe/poor islands, deer maintained vigilance despite 60 years of isolation from predation. Predator-naïve deer avoided eating bait in presence of urine of wolf (dangerous) but not of bear (less dangerous). This suggested an innate threat-sensitive foraging strategy in deer. Deer also remained less time at the bait stations in presence of wolf urine but did not increase their vigilance levels. This suggested that deer were likely to manage risk more by space use than by vigilance; 4) In response to an experimental hunting for fear conducted on one of the safe/poor island, we showed that the deer less-tolerant to humans avoided the hunting area; The deer more-tolerant to human disturbance did not. This stressed the importance to consider the human-induced selection of behavioral traits during wildlife management. We also monitored the growth of four fast-growing coastal plant species and showed that the hunting for fear promoted the growth of half of them. This highlighted the intricate interaction among deer foraging behavior and plant characteristics and emphasized the importance of management targets in the choice of management tools. We discussed the long-terms effect of hunting as management tool for deer.

The aim of this study was to determine firstly if there exist variations in fibrolysis among herbivore microbial ecosystems and secondly, the effect on fibre hydrolysis of compositing the most active systems with ruminal microbial ecosystem harvested from a Jersey cow. A literature review pointed to the complexity of carbohydrate (fibre) and how the physical and chemical nature of the forage carbohydrate can present barriers that hinder digestion in the rumen, especially its association with hemicelluloses, pectin, lignin and tannins. Fresh rumen fluid was collected from fistulated herbivores (Jersey cow and sheep) and faecal samples from non-fistulated herbivores (buffalo, horse, impala, camel, elephant, llama, sheep, wildebeest and elephant). Crude protein samples were precipitated with 60% ammonium sulfate. Sample activities were monitored and optimised by incubating with carboxymethyl cellulose (CMC) for 2 h at 39°C. The crude protein samples precipitated from the 11 herbivore microbial ecosystems were active. This was confirmed by an increase in enzyme specific activity with a decrease in total crude protein concentration. In vitro pH optimisation showed a broad range of activity for all ecosystems (4.5-8.0) but for the zebra, horse and elephant which peaked at pH 5. In experiment two (Chapter 4), seasonal variation of the enzymes (exocellulase, endocellulase, cellobiase and xylanase) were monitored through winter and summer. Enzyme specific activity of exocellulase, endocellulase, cellobiase and xylanase were determined by incubation with the specific substrates, crystalline cellulose, CMC, pNPG and xylan, respectively. The amount of reducing sugar released was used to determine the enzyme specific activity. Exocellulase analysis was suitable in winter while summer was preferred for carboxymethyl cellulase and xylanase due to their relative abundance. Cellobiase analysis did not depend on any particular season. Eleven herbivore microbial ecosystems were characterised according to their fibrolytic enzyme specific activities. Enzyme catalytic activities were calculated from kinetic parameters (Km and Vmax) obtained from Eisenthal and Cornish-Bowded plots (Chapter 5). Fibrolytic enzyme expression as well as their activities differed among the 11 ecosystems (P<O.OOOI). They were classified into three groups based on fibrolytic enzyme concentrations; group A with high enzyme concentrations (horse, impala, zebra, wildebeest and the elephant), group B with intermediate (cow, llama, camel, buffalo and giraffe) and group C with low enzyme concentrations (sheep). Exocellulase activity was reasonably correlated with endocellulase activity (r = 0.8978). Xylanase activity was also correlated with carboxymethyl cellulase actvity (r = 0.7104). Enzyme kinetic studies revealed that crude protein samples from the horse, zebra, wildebeest and elephant had the highest enzyme catalytic activities. Microbial or enzyme composite systems were created from the most active ecosystems (horse, wildebeest and zebra) in an attempt to improve the Jersey cow system. These systems were B (cow and horse), C (cow and wildebeest), D (cow and zebra) and E (cow, horse, zebra and wildebeest). The specific activities and enzyme efficiencies of these new systems were determined and compared with system A (cow). Microbial synergism of these systems was also investigated by measuring the amount of gas produced and true degradability (TD) after 72 h of incubation. The composite systems Band E were the most active fibrolytic enzyme systems while C and D were intermediate when compared to that of A. In vitro microbial synergism assays showed that systems B, D, and E had the highest potential of improving milky maize stover (MM) and nutral detergent fibre (NDF) fermentation and degradability in Jersey cows. It was concluded that: (i) fibrolytic and hemicellulolytic enzyme concentrations vary from one season to another with the changing forages; (ii) microbial fibrolytic activities vary among animals grazing on the same field or different geographical regions; and (iii) lastly microbial synergisms of active ecosystems have the potential of improving fibre hydrolysis. However, there is a need to conduct in vivo experimentation to determine the real potential of these in vitro observations. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

La variabilité environnementale à laquelle les individus sont constamment exposés est forte. Dans ce contexte, les conditions environnementales en début de vie sont particulièrement importantes puisqu’elles peuvent avoir des conséquences à long terme sur la performance des individus. L’objectif de cette thèse est d’améliorer notre compréhension des effets à long-terme des évènements vécus tôt dans la vie, incluant aussi bien les conditions environnementales que la croissance, sur les traits d’histoire de vie des grands mammifères herbivores. Afin de répondre à cet objectif, nous avons utilisé les suivis à long-terme de cinq populations appartenant à quatre espèces d’ongulés. Dans une première partie, nous avons montré que les conditions environnementales en début de vie peuvent influencer la trajectoire entière de croissance corporelle d’un individu. Ensuite, nous avons cherché à savoir si les effets des conditions environnementales en début de vie sur les traits d’histoire de vie à l’âge adulte représentaient des réponses adaptatives à différents environnements ou résultaient seulement de contraintes développementales dues à une restriction alimentaire. Nous avons répondu à cette question en testant notamment des hypothèses issues du domaine médical en populations sauvages / The environment to which individuals are permanently exposed varies greatly over time. The environmental conditions during early life are particularly important in this context because they can have extraordinary long-term consequences on individual performance. The main goal of this PhD thesis was to improve our understanding of the long-term effects of early-life events, including environmental conditions and growth, on life-history traits of large herbivores. In order to meet this objective, we used detailed long-term data from five populations of four species of ungulates. We highlighted that environmental conditions experienced during early life can influence the entire body growth trajectory of an individual. Then, we investigated whether the long-term effects of early environmental conditions on life-history traits represent adaptive responses to differing environments, or are only a consequence of energetic constraints on development. We aimed to address this issue by testing hypotheses issued from human medicine in wild populations

Pendant les transitions glaciaire-interglaciaires,on observe une augmentation en partie abrupte de près de 100 ppm du CO2atmosphérique, indiquant une redistribution majeure entre les réservoirs de carbone des continents, de l'océan et de l'atmosphère.Expliquer les flux de carbone associés à ces transitions est un défi scientifique, qui nécessite une meilleure compréhension du stock de carbone ‘initial’ dans la biosphère terrestre au cours de la période glaciaire. L’objectif de cette thèse est d’améliorer la compréhension du fonctionnement des écosystèmes terrestres et des stocks de carbone au cours du dernier maximum glaciaire (LGM, il y a environ21.000 ans), à travers plusieurs nouveaux développements dans le modèle global de végétation ORCHIDEE-MICT, pour améliorer la représentation de la dynamique de la végétation, la dynamique du carbone dans le sol du pergélisol et les interactions entre les grands herbivores et la végétation dans le modèle de la surface terrestre.Pour la première partie, la représentation de la dynamique de la végétation dans ORCHIDEEMICT pour les régions des moyennes et hautes latitudes, a été calibrée et évaluée avec un ensemble de données spatiales de classes de végétation, production primaire brute, et de biomasse forestière pour la période actuelle.Des améliorations sont obtenues avec la nouvelle version du modèle dans la distribution des groupes fonctionnels de végétation. Ce modèle a ensuite été appliqué pour simuler la distribution de la végétation au cours de laLGM, montrant un accord général avec les reconstructions ponctuelles basées sur des données de pollen et de macro-fossiles de plantes.Une partie du pergélisol (sols gelés en permanence) contient des sédiments épais,riches en glace et en matières organiques appelés Yedoma, qui contiennent de grandes quantités de carbone organique, et sont des reliques des stocks de carbone du Pléistocène.Ces sédiments ont été accumulés sous des climats glaciaires. Afin de simuler l'accumulation du carbone dans les dépôts de Yedoma, j’ai proposé une nouvelle paramétrisation de la sédimentation verticale dans le module de carbone dans le sol de ORCHIDEE-MICT. L'inclusion de ce processus a permis de reproduire la distribution verticale de carbone observée sur des sites de Yedoma. Une première estimation du stock de carbone dans le pergélisol au cours du LGM est obtenue, de l’ordre de ~ 1550 PgC, dont 390 ~446 PgC sous forme de Yedoma encore intacts aujourd’hui (1,3 millions de km2).Potentiellement, une plus grande surface de Yedoma pourrait être présente pendant leLGM, qui a disparue lors de la déglaciation.Pour la troisième partie, à la lumière des impacts écologiques des grands animaux, et le rôle potentiel des méga-herbivores comme une force qui a maintenu les écosystèmes steppiques pendant les périodes glaciaires, j'ai incorporé un modèle de d’herbivores dans ORCHIDEE-MICT, basé sur des équations physiologiques pour l'apport énergétique et les dépenses, le taux de natalité, et le taux de mortalité pour les grands herbivores sauvages.Le modèle a montré des résultats raisonnables de biomasse des grands herbivores en comparaison avec des observations disponibles aujourd’hui sur des réserves naturelles. Nous avons simulé un biome de prairies très étendu pendant le LGM avec une densité importante de grands herbivores. Les effets des grands herbivores sur la végétation et le cycle du carbone du LGM ont été discutés, y compris la réduction de la couverture forestière, et la plus grande productivité des prairies.Enfin, j’ai réalisé une estimation préliminaire du stock total de carbone dans le permafrost pendant le LGM, après avoir tenu compte des effets des grands herbivores et en faisant une extrapolation de l'étendue spatiale des sédiments de type Yedoma basée sur des analogues climatiques et topographiques qui sont similaires à la région de Yedoma actuelle. / During the repeated glacialinterglacialtransitions, there has been aconsistent and partly abrupt increase of nearly100 ppm in atmospheric CO2, indicating majorredistributions among the carbon reservoirs ofland, ocean and atmosphere. A comprehensiveexplanation of the carbon fluxes associatedwith the transitions is still missing, requiring abetter understanding of the potential carbonstock in terrestrial biosphere during the glacialperiod. In this thesis, I aimed to improve theunderstanding of terrestrial carbon stocks andcarbon cycle during the Last Glacial Maximum(LGM, about 21,000 years ago), through aseries of model developments to improve therepresentation of vegetation dynamics,permafrost soil carbon dynamics, andinteractions between large herbivores andvegetation in the ORCHIDEE-MICT landsurface model.For the first part, I improved theparameterization of vegetation dynamics inORCHIDEE-MICT for the northern mid- tohigh-latitude regions, which was evaluatedagainst present-day observation-based datasetsof land cover, gross primary production, andforest biomass. Significant improvements wereshown for the new model version in thedistribution of plant functional types (PFTs),including a more realistic simulation of thenorthern tree limit and of the distribution ofevergreen and deciduous conifers in the borealzone. The revised model was then applied tosimulate vegetation distribution during theLGM, showing a general agreement with thepoint-scale reconstructions based on pollen andplant macrofossil data.Among permafrost (perennially frozen) soils,the thick, ice-rich and organic-rich siltysediments called yedoma deposits hold largequantities of organic carbon, which areremnants of late-Pleistocene carbonaccumulated under glacial climates. In order tosimulate the buildup of the thick frozen carbonin yedoma deposits, I implemented asedimentation parameterization in the soilcarbon module of ORCHIDEE-MICT. Theinclusion of sedimentation allowed the modelto reproduce the vertical distribution of carbonobserved at the yedoma sites, leading toseveral-fold increase in total carbon. Simulatedpermafrost soil carbon stock during the LGMwas ~1550 PgC, among which 390~446 PgCwithin today’s known yedoma region (1.3million km2). This result was still anunderestimation since the potentially largerarea of yedoma during the LGM than todaywas not yet taken into account.For the third part, in light of the growingevidence on the ecological impacts of largeanimals, and the potential role of megaherbivoresas a driving force that maintainedthe steppe ecosystems during the glacialperiods, I incorporated a dynamic grazingmodel in ORCHIDEE-MICT, based onphysiological equations for energy intake andexpenditure, reproduction rate, and mortalityrate for wild large grazers. The model showedreasonable results of today’s grazer biomasscompared to empirical data in protected areas,and was able to produce an extensive biomewith a dominant vegetation of grass and asubstantial distribution of large grazers duringthe LGM. The effects of large grazers onvegetation and carbon cycle were discussed,including reducing tree cover, enhancinggrassland productivity, and increasing theturnover rate of vegetation living biomass.Lastly, I presented a preliminary estimation ofpotential LGM permafrost carbon stock, afteraccounting for the effects of large grazers, aswell as extrapolations for the spatial extent ofyedoma-like thick sediments based on climaticand topographic features that are similar to theknown yedoma region. Since these results werederived under LGM climate and constantsedimentation rate, a more realistic simulationwould need to consider transient climate duringthe last glacial period and sedimentation ratevariations in the next step.

Marine seaweeds constitute one of the most productive plant systems known on Earth and a rich fauna including juvenile fish and crustaceans is dependent on the habitats they form. Human influence on marine costal ecosystems has resulted in large scale changes to the abundance and distribution of species, where species introductions constitute an obvious part. The aims of this thesis were to 1) explore how non-native seaweeds impact on ecosystem functions (primary production and decomposition), and 2) study how interactions between non-native seaweeds and native communities affect invasion success. I used a combination of laboratory assays, outdoor mesocosms and field experiments. Paper I and II revealed that the impact on ecosystem functions were substantially different depending on the identity of the invader. The highly successful non-native red alga Heterosiphonia japonica had a large effect on community productivity. Due to the rapid growth of the invader, the primary production increased by more than four times in mixed species communities with the invader compared to  communities with only native species. In contrast, the morphologically similar and equally successful non-native red alga Bonnemaisonia hamifera grew slowly and had no effect on community production. But B. hamifera produces a potent defense compound that deters native herbivores and reduces the growth of micro-organisms. As a direct or indirect effect of this chemical defense, the litter from B. hamifera decomposed considerably slower compared to native seaweed litter. Rapid growth and defense against predation are likely important in explaining how the two invaders have become successful in the invaded range. These results show that traits related to invasion success may determine impacts on native communities. Paper III shows that the rapidly growing invader H. japonica is avoided as food by native herbivores, which likely enables the invader to survive during colder seasons with sub-optimal growth conditions.  In paper IV I found that competition from the native brown alga Fucus vesiculosus decreased growth of the non-native congener Fucus evanescens. Native herbivores caused more damage to the native competitor but it did not relieve F. evanescens from competitive pressure. Several native brown algae grow in the niche of F. evanescens, which may explain why the species only is growing sparingly in the invaded range. The results indicate that competition with native seaweeds have potential to reduce the success of non-native seaweeds in the new range. In summary, this thesis shows that non-native seaweeds differ strongly in their effect on ecosystem functions. Knowledge of which traits are present among abundant non-native species and how these traits relates to different effects may enable us to gain a better understanding of invasion impacts on native communities. The thesis also highlights that competitive interactions can be of importance for invasion success in seaweed communities. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p> / Alien-native trophic interactions: consequences for invasion success and ecosystem effects of invasions