En raison des changements climatiques actuels, il est primordial de comprendre comment les écosystèmes vont réagir et tout particulièrement comment les chaînes trophiques vont être impactées. Pour cela, le comportement des oiseaux marins peut être utilisé comme des indicateurs des changements se déroulant au sein de l’écosystème. Cependant, un des défis actuels dans l’étude du comportement animal est d’identifier comment la structure temporelle du comportement est dépendante des conditions intrinsèques et extrinsèques et comment la complexité de cette organisation comportementale évolue sur un gradient allant de la stochasticité au déterminisme en fonction des changements environnementaux. Ma thèse a donc pour objectif d’étudier si un comportement complexe est adapté pour faire face à une perturbation du système chez les oiseaux marins et plus particulièrement chez deux espèces de manchots étant exposées à des changements environnementaux. / Due to ongoing climate change, it is necessary to understand how ecosystems will react and more particularly, how species may cope with the challenges of living in unstable systems. Seabirds’ behavior provides a way to monitor changes occurring in the marine environment, but identifying how the temporal structure and complexity of behavior depend on intrinsic and extrinsic parameters are underexplored topics in the field of animal behavior. My thesis aims to investigate if behavioral organization, through a gradient of stochasticity-determinism complexity, allows little and adélie penguins to buffer changes in the environment under a fractal analysis approach.

La forte hétérogénéité de l'écosystème marin se traduit par une production inégale des ressources sur un large éventail d'échelles spatio-temporelles, qui conditionne par conséquent les déplacements des tortues marines. Considéré comme l’un des plus dynamiques au monde, le plateau des Guyanes est une région très complexe d'un point de vue océanographique et qui héberge trois des sept espèces de tortues marines présentes dans le monde (la tortue olivâtre, la tortue verte et la tortue luth). L'objectif de cette thèse était de comprendre comment les contraintes océanographiques peuvent-elles influencer les déplacements en mer de ces trois espèces. Le déploiement de 55 balises satellites sur des femelles reproductrices en Guyane française a permis de fournir des informations sur leurs trajectoires, sur leur comportement de plongée et sur les caractéristiques de leur environnement. Notre étude a mis en évidence une forte plasticité comportementale interspécifique qui semble être principalement dictée par les traits reproducteurs, les stratégies de reproduction, les conditions locales de l'habitat ou encore les adaptations physiologiques. / The strong heterogeneity of the marine ecosystem leads to a patchy distribution of the resources in time and space, shaping therefore the movements of sea turtles. Considered as the most dynamic ecosystem in the world, the Guiana shield is a highly dynamic system which hosts three of the seven sea turtle species in the world (the olive ridley, the green turtle and the leatherback turtle). The aim of this thesis was to understand how the oceanographic constraints can influence the at-sea movements of these three species during the reproduction and the migration phases. The deployment of 55 satellite tags on adult females in French Guiana provided information on their trajectories, their diving behavior and on the environment encountered. Our study shows a strong behavioral plasticity between species, which seems to be mainly dictated by the reproductive traits and strategies, the local conditions of the habitat and the physiological adaptations.

I extended an artificial life platform called GReaNs (the name stands for Gene Regulatory evolving artificial Networks) to explore the evolutionary abilities of biologically inspired Spiking Neural Network (SNN) model. The encoding of SNNs in GReaNs was inspired by the encoding of gene regulatory networks. As proof-of-principle, I used GReaNs to evolve SNNs to obtain a network with an output neuron which generates a predefined spike train in response to a specific input. Temporal pattern recognition was one of the main tasks during my studies. It is widely believed that nervous systems of biological organisms use temporal patterns of inputs to encode information. The learning technique used for temporal pattern recognition is not clear yet. I studied the ability to evolve spiking networks with different numbers of interneurons in the absence and the presence of noise to recognize predefined temporal patterns of inputs. Results showed, that in the presence of noise, it was possible to evolve successful networks. However, the networks with only one interneuron were not robust to noise. The foraging behaviour of many small animals depends mainly on their olfactory system. I explored whether it was possible to evolve SNNs able to control an agent to find food particles on 2-dimensional maps. Using ring rate encoding to encode the sensory information in the olfactory input neurons, I managed to obtain SNNs able to control an agent that could detect the position of the food particles and move toward it. Furthermore, I did unsuccessful attempts to use GReaNs to evolve an SNN able to control an agent able to collect sound sources from one type out of several sound types. Each sound type is represented as a pattern of different frequencies. In order to use the computational power of neuromorphic hardware, I integrated GReaNs with the SpiNNaker hardware system. Only the simulation part was carried out using SpiNNaker, but the rest steps of the genetic algorithm were done with GReaNs.

Climate change threatens to disrupt biological systems around the globe, sparking debate over natural capacity for adaptation in a fragmented landscape. Marine turtles are evolutionarily ancient and have survived millions of years of prehistoric climate change, but are threatened by the rapidity of modern warming and a history of severe overexploitation that has left most populations depleted. This thesis explores a nesting aggregation of the green turtle (Chelonia mydas) in northern Cyprus, where a longitudinal programme of both intensive and extensive monitoring enables insight into individual and population level parameters and processes. Nesting on the two coastlines covered by this project is in the early stages of recovery, possibly in response to exhaustive nest protection efforts over the last twenty years. Saturation tagging at one key site allows us to confirm that recruitment of new breeders is an important driver of this trend, and that average clutch frequency has remained stable around three nests per female per year, validating nest-count derived abundance estimates at a regional scale. Concern has been raised, however, regarding recent changes in fishing practices which are impacting the local juvenile neritic phase, which may have a lagged effect on the recovery of this nesting population. A collaborative tracking effort including all other countries with major nesting in the Mediterranean allows us to identify major foraging grounds for this species, with two hotspots accounting for >50% of tracked individuals, as well as coastal and pelagic seasonal corridors of high use. Bycatch levels and mortality rates for turtles in these key areas are largely unknown and should be prioritised for investigation. Hatchling sex ratios from the main study beach are extremely female-biased (estimated 97% female for the twenty year period 1993-2012). A 1oC rise in average incubation temperatures threatens near complete hatchling feminisation on this beach, whilst a 2oC rise could reduce hatch success to less than 50%. Thermal effects on hatchling morphometrics are evident, with a 1oC rise in temperature reducing average length, width and weight by 1%, 2% and 3% respectively. More favourable incubation conditions were found early in the season, in deeper nests laid by larger females, and on beaches of lighter sand. In contrast, adult sex ratios at the main site are male-biased, posing questions regarding sex-specific survival rates and optimal hatchling sex ratios. A phenological shift towards earlier nesting is demonstrated for the first time in this species, and could potentially ameliorate warming effects. Carry-over climate forcing effects from the foraging ground influence the breeding frequency of individuals, driving population level responses in annual magnitude of nesting. This work emphasises the utility and necessity of long-term individual-based monitoring programmes in elucidating population trends and climate responses in iteroparous species with non-annual breeding.

Magister Scientiae (Medical Bioscience) - MSc(MBS) / Some African mole-rats of the family Bathyergidea have dramatically different ecological niches which may cause selective anatomical adaptations. Bathyergus suillus lives in sandy soil and eats a wide range of food whereas Georychus capensis is restricted to the mountainous hard soil and eats mainly geophytes. Georychus capensis is considered a chisel-tooth digger in that it uses its incisors to dislodge soil while Bathyergus suillus is a scratch-digger that uses both its incisors and large front paws to dislodge soil. The purpose of this study was to compare certain aspects of the masticatory anatomy of Bathyergus suillus and Georychus capensis. In particular the question that drives this study is: Do the differences in ecology of the two species reflect in the anatomical adaptation of their masticatory apparatus? Nine whole body specimens of each species were obtained for this study. The masticatory apparatus of each specimen was dissected, examined and analysed.Selected bones of their skulls were investigated to determine their gross morphology. Digitalized images were captured by a high-resolution Olympus digital camera and were analysed by DOCU analysis software, in order to determine the morphometric parameters. In addition, the cleaned skulls of each species were weighed with a chemical balance. In order to make the comparison of the four muscles of mastication more effective than when using only their linear measurements, the mass (in grams) of each skull was divided by the length of each metric traits squared in order to yield their respective indices. Various statistical tests were used.This study has thus revealed some dissimilarities between the two species.Comparison of the two species reveals that one of the more distinguishing differences between the two is their upper incisors. There are also significant differences in the morphology and dimensions of their angular plates. And the external pterygoid muscle is significantly larger in Georychus capensis than in Bathyergus suillus, there are no significant differences between the others of the masticatory muscles of the two species.The feeding and foraging activities of Bathyergus suillus as well as Georychus capensis have close relationship with their lifestyles (digging abilities and adaptations). Bathyergus suillus is predisposed to dig with its incisors as well as its large front paws, and the range of food is large, whereas Georychus capensis uses its incisors only to dig, and the range of food is limited. Subsequently the skull of Bathyergus suillus is bigger than Georychus capensis. But, due to the environment of the latter, strong incisors are needed to perform its feeding and digging activities. The investigation thus reveals that the two selected species have successfully adapted their anatomical masticatory elements to their environments.

Depuis le début du XXème siècle, l’évolution de l’agriculture et l'intensification des pratiques agricoles ont conduit à des modifications profondes du paysage induisant des pertes importantes d’habitats naturels et semi-naturels. Ces changements, entraînant notamment la diminution des ressources végétales et impliquant l'utilisation systématique de pesticides, ont des répercussions sur les colonies d’abeilles. C’est dans ce contexte que, durant deux saisons apicoles, des inventaires botaniques ont été réalisés au sein de l’aire de butinage de deux ruchers situés en paysage de grande culture du nord-ouest de la France et que des échantillons de pelotes de pollen et de miels prélevés dans ces ruchers ont été analysés. L’objectif était de comparer les ressources floristiques disponibles et celles réellement exploitées par les abeilles et d’entrevoir les stratégies de butinage mises en place dans ce cadre paysager. Les relevés floristiques ont permis de distinguer d’une part, de larges surfaces d’espèces cultivées, à floraison ponctuelle et d’autre part, des surfaces non cultivées, de plus petite taille, occupées par de nombreuses espèces sauvages dont la floraison s’étale sur la totalité de la saison apicole. Les analyses palynologiques montrent que ces espèces floristiques sauvages sont exploitées en continu y compris pendant la période de floraison des espèces cultivées. Bien que cette étude ne soit pas en mesure de le démontrer, il est possible que les espèces sauvages procurent aux colonies un apport nutritionnel que la floraison ponctuelle des plantes cultivées ne peut totalement compenser. Une meilleure connaissance de la valeur nutritionnelle des différents pollens d’essences végétales, ainsi que des besoins alimentaires basiques nécessaires au développement et à la pérennisation des colonies devraient aider à éprouver cette hypothèse. / Since the beginning of the XXth century, the evolution of agriculture and the intensification of farming practices have led to landscape changes with the loss of natural and semi-natural habitats. These changes, involving a decrease of plant resources and a use of pesticides, may have noticeable impact on honey bee colonies. In this framework of weakened biodiversity, the initiative was taken of recording botanical species growing in the foraging area of two apiaries in cultivated landscapes of Western France and sampling pollen pellets and honey for pollen species determination during two successive beekeeping seasons. The aim of this study was to compare the available flora resources with those really exploited by the honey bees, to get a glimpse of the foraging strategies developed by the colonies in this landscape context. The floristic readings enabled to distinguish wide areas of cultivated plant species characterized by temporary blossoms from areas of wild species characterized by much smaller superficies and by flowerings spread over the year. Palynological analyses indicate that wild floristic species are exploited throughout the beekeeping season including during blooms of cultivated plant species. Even though not conclusively stated by the present study, it is possible that wild species provide colonies with nutritional intakes that cannot be totally compensated by temporary blooms of cultivated plants. A more extended knowledge of the nutritional values of pollens produced by plant species together with a better understanding of basic food needs for development and perennisation of colonies should help to test this hypothesis.

La nutrition minérale des plantes dépend à la fois du développement et du fonctionnement de leur appareil racinaire, incluant l'absorption mais aussi la capacité des plantes à influencer les cycles des nutriments, notamment par l'exsudation. Le but de cette thèse est de lier les rétroactions plantes-sol impliquant les cycles des nutriments aux stratégies d'exploration racinaire. Dans la revue bibliographique, je recense des mécanismes d'interaction plantes-sol et leurs échelles spatiales et temporelles. En considérant, à l'échelle de la rhizosphère, les interactions directes entre racines et sol, je propose que la combinaison entre exsudation et absorption des nutriments mène à des synergies entre racines d'une même plante. Ma seconde hypothèse est celle de l'existence d'un compromis entre l'exploration du sol et son occupation (défini comme la capacité des plantes à influencer efficacement le cycle des nutriments). Dans un premier chapitre, je développe un modèle général de recyclage des nutriments afin de déterminer sous quelles conditions les plantes auraient intérêt à limiter leur exploration du sol. Je montre qu'une exploration limitée est une stratégie de nutrition efficace sous certaines conditions, dont l'existence de synergies entre racines et le fait d'être dans un sol pauvre en nutriment. Dans un deuxième chapitre, je mesure le patron d'exploration racinaire et évalue le recyclage de l'azote à l'aide des outils isotopiques, chez trois espèces de Poacées pérennes de la savane de Hwange (Zimbabwe). Cette étude de terrain montre un gradient d'hétérogénéité racinaire entre ces trois espèces. Les Poacées exprimant le patron d'exploration le plus hétérogène ont un cycle de l'azote plus lent, mais potentiellement plus efficace. Dans un dernier chapitre, je développe un modèle mécaniste à l'échelle de la rhizosphère, pour une plante absorbant le phosphore et contrôlant sa disponibilité par l'exsudation de citrate. Je montre que, selon l'échelle d'influence des racines en terme d'exsudation et d'abaissement de la concentration en phosphore, la combinaison de l'exsudation et de l'absorption mène soit à une compétition, soit à une facilitation entre les racines d'une même plante. En me plaçant à l'échelle du système racinaire, je montre que les pertes en phosphore sont limitées par une exploration limitée du sol. Ce dernier résultat va dans le sens du compromis exploration/occupation. Au cours de cette thèse, j'ai donc développé des approches complémentaires, mettant en jeu différents mécanismes et échelles d'interactions plantes-sol. Le fait que les racines ne se limitent pas à un rôle d'absorption, mais agissent activement sur les cycles de nutriments a mené à deux résultats originaux : la facilitation inter-racinaire et intra-plante, et le fait qu'une exploration limitée puisse être considérée comme une stratégie efficace de nutrition. Enfin, ce travail souligne l'importance d'intégrer les divers mécanismes d'interaction plantes-sol pour comprendre les stratégies de nutrition des plantes et mieux prédire leur impact sur les cycles de nutriments à l'échelle des écosystèmes. / Plant nutrition depends on complementary mechanisms : the development of root systems, root uptake and plant ability to control nutrient cycling, e.g. through exudation. The aim of this thesis is to link plant-soil feedbacks involving the cycling of nutrients and root foraging strategies. I first review the different mechanisms of plant influence on nutrient cycling within the soil and assess their respective scales. Considering the direct effect of roots on the soil at the scale of the rhizosphere, I hypothesize that the combination of absorption and exudation may lead to synergies between the roots of a plant. At the scale of the whole root system, I propose a second, heuristic hypothesis: the existence of a trade-off between soil exploration and soil occupation (defined as the ability of plants to influence efficiently nutrient cycling). In a first chapter, I develop a general model of nutrient cycling, to determine under which condition plants should limit the exploration of soil by their roots. I show that limited exploration is an efficient strategy under specific conditions, especially nutrient-poor soils and the existence of synergies between roots. In a second chapter, I characterize soil occupation and nitrogen cycling, by the use of isotopes ratios, in the plant-soil system of three perennial grasses of the savanna of Hwange (Zimbabwe). This field study shows a gradient of root heterogeneity among these grass species. Those showing the more heterogeneous root pattern have a slower but potentially more efficient nitrogen cycling. In a last chapter, I develop a numerical mechanistic model at the rhizosphere scale for a plant taking up phosphorus and increasing its availability through exudation of citrate. I show that, depending on the extent of root influence on soil by exudation and nutrient depletion, competition between roots as well as facilitation arise from the combination of root uptake and exudation. By upscaling rhizosphere processes to the root system, I show that phosphorus losses are minimized by a restricted soil exploration, which backs the hypothesis of a trade-off between soil exploration and occupation. Overall, I developed complementary approaches that took into account several mechanisms and scales of plant-soil interactions. Considering that root functions are not limited to nutrient uptake, but also involve their influence on nutrient cycling, lead to two novel results: the potential existence of intra-plant and inter-root facilitation, and limited soil exploration as an efficient foraging strategy. This work underlines the importance of accurately integrating the mechanisms of plant-soil interaction to assess their nutrient strategies and to predict their impact on nutrient cycling within ecosystems.

Piscivorous birds are an integrated part of lake and coastline ecosystems. Despite decades of research it is yet unclear what influence fish eating birds have on the fish community. The aim of this literature study was to focus on how two fish eating birds, Great Cormorant and Great Crested Grebe, influence the fish community in shallow and eutrophic lakes. Different types of analysis methods have been used when doing research on the subject, including pellet analysis, stomach content analysis, tagging of fishes by “PIT”-techniques and analysis by observation. Results show that conclusions by studies tend to vary, but generally higher bird density, lower water temperature and a relatively high turbidity contribute to a higher influence on the fish community. Both bird species are opportunistic in their choice of food and catch prey of the species that occur locally. Both species also limit themselves in the prey size, but the choice vary over seasons because of water temperature and the birds requirements in association with breeding and migration. The significant level of influence seems to be when predation is conducted on younger and smaller fishes. The influence on the fish size can also be indirect, where predation on smaller individuals prevent fishes from becoming older and bigger. As studies tend to deviate in conclusion, no general answer to this issue can be given at present. Comprehensive research with several years of full control over both fish-and bird population is needed to find the proper conclusion.

Dyer Island is thought to host one of the most abundant populations of white sharks on the planet; this is often credited to the large (55 – 60,000) Cape fur seal colony at Geyser Rock. Yet relatively little work has ever been produced from the area. This may be attributed to the harshness in its location as a study site, exposed to wind and swell from west to east which limits research periods. This study accounts for over 220 hrs of manual tracking at Dyer Island with a further 68 added from the inshore shallow areas of the bay. Sharks focused their movements and habitat use to reefs or channels that allowed access to Cape fur seals. Movement- Based Kernel Estimates (MKDE) were used to compute home range estimates for shark movements through and around the heterogeneous structures of Dyer Island and Geyser Rock. Inshore two core areas were revealed, one being the major reef system at Joubertsdam and the other at a kelp reef where the tracked shark had fed on a Cape fur seal. At Dyer Island one core area was identified in a narrow channel, ‘Shark Alley’, here a second tracked shark foraged for entire days within meters of rafting Cape fur seals. Rate of Movement (ROM) and Linearity (LI) of tracks were low during daytime and movements were focused around areas such as Shark Alley or other areas close to the seal colony before moving into deeper water or distant reefs with higher rates of ROM and LI at night. If moonlight was strong foraging would take place to the south of Geyser Rock but with higher ROM and LI than observed during the day. Foraging patterns in this study contrast studies from other sites in South Africa and home range and activity areas were comparatively much smaller than observed in Mossel Bay. It has been established that several known white sharks forage at Dyer Island and the other studied aggregation sites, such differences in foraging would suggest that they are able to adapt their foraging behaviour to suit the environment they are in; making them site specific in their foraging ecology. Both satellite and acoustic telemetry are revealing aggregation hotspots of white sharks in South Africa. It is important that such information is used to assist the recovery of the species which has been protected since 1991, yet is rarely considered in planning of coastal developments. / Dissertation (MSc)--University of Pretoria, 2012. / Zoology and Entomology / MSc / Unrestricted

The biology and the patterns of wild environments and their organisms have solutions to the many environmental, social and economical challenges that we are facing globally. As an emerging designer, I believe that the tendencies of the ecological environments can be analyzed, mimicked and implemented by designers into different socio-cultural systems. In my design process I have been exploring practices that promote food sovereignty as a right that every living being should have. The results of my exploration is a guide to help to learn about and from wild edibles to deepen our connection with nature. My design includes my own process and iteration as well as one designed for those who are interested in exploring foraging practices.This project recognizes the different spheres and complexities of sustainability. It analyzes how our cultural and social practices impact the ecological environment, while, at the same time, it brings practical examples to understand the effects that our economy has on the overall well-being of the ecology, and suggests that we all can be beneficial participants as and in nature.The title “We grow wild” refers to the plants, which grow wildly in parks, hedgerows, paths and forests, as well as it encourages to rediscover the wild nature that re-emerges in us through active participation in the ecological environment we inhabit.