Genetic mapping contributes to the understanding of functional mechanisms that underlie the constitution of living organisms and their physiology. For example, genetic mapping can be used in conceiving new treatments of congenital or infectious diseases and in selecting plants and animals that have a higher and better production. The most common approaches of genetic mapping exploit the allelic segregation in a pedigree during only a few number of generations and, consequently, they do not have a sufficient resolution to allow an effective gene isolation and cloning. An alternative to these approaches is to study allelic associations along the history of a population. This requires accurate models of population demography, genetic inheritance and allelic associations. This thesis contributes to the modelling of allelic associations (linkage disequilibrium, LD) and to the assessment of the effects of selection and inbreeding. In a simulation framework, we fitted the multimarker-multiallelic LD with an exponential function characterised by two parameters: the distance (R) at which LD is independent of the genetic distance and the LD reached at this distance (residual LD, rs). As an application of this approach, the LD was estimated in five populations of pigs. We observed a long range LD (>10cM) that was explained by the random drift. Moreover, significantly increased LD was found in regions harbouring selected QTL (quantitative trait loci), suggesting an effect of selection. Fitting LD with the exponential model proposed in simulations indicated that mapping methods using LD (LDM) can achieve a resolution of ~3cM in the populations of pigs we have studied and can be powerful with a marker spacing of 5-10cM. As illustrated with these data from pigs, the model that we used to fit LD offers opportunities to characterise allelic association in populations, estimate the required marker density for genome-wide LD studies and determine the expected resolution of LDM. It is also shown that the proposed model can help overcoming the assumptions of asymptotic linkage equilibrium and independence between markers that are commonly made in LDM but are not always fulfilled.

Light entering the eye is transformed by the retina into electrical signals. Extensive processing takes place in the retina before these signals are transmitted to the brain. Beginning in the outer retina, light-evoked electrical signals are distributed into parallel pathways specialized for different visual tasks, such as the detection of dark vs. bright ambient light, the onset or offset of light, and the direction of stimulus motion. Pathway diversity is a consequence of cell type diversity, differential cell connectivity, synapse organization, receptor expression, or any combination thereof. Cell connectivity itself can be accomplished through excitatory or inhibitory chemical synapses, or electrical coupling via gap junctions. Gap junctions are further specialized based on the expression of different connexin subunit isoforms. In aggregate, this diversity gives rise to ganglion cells with highly specialized functions, including ON and/or OFF responses, contrast-tuning and direction-selectivity (DS). The directionally-selective circuit, a circuit specialized for the encoding of stimulus motion, makes use of many of these circuit specializations. Bipolar cells, in response to glutamate release from cone photoreceptors, provide highly-sensitive glutamatergic input to amacrine cells and DS ganglion cells (DSGCs) in this circuit, while amacrine cells provide cholinergic and directionally-tuned GABAergic input to DSGCs. One population of DSGCs also transmit signals laterally to one another via gap junctions. Thus numerous specializations in bipolar cells, amacrine cells and ganglion cells endow DSGCs with their unique encoding abilities. In Chapters 2 and 3 of this dissertation I focus on synchronized firing between gap junction-coupled DSGCs. sDSGCs exhibit fine-scale correlations, with action potentials in an sDSGC more likely within ~2ms of action potential firing in a coupled neighbour. I first characterize electrical coupling of DSGCs through the identification of the molecular composition of DSGC gap junctions (Chapter 2). Physiological and immunohistochemical methods allowed me to demonstrate an important role for connexin 36 subunits in DSGC electrical coupling. Next (Chapter 3) I investigate the sub-cellular mechanisms underlying neuronal correlations between electrically coupled DSGCs. Using paired recordings, I show that chemical input (from bipolar cells and amacrine cells), electrical input (from gap junctions), and Na+ channel activity in DSGC dendrites underlie the generation of correlated spiking activity. While a common feature of electrically coupled networks, the mechanisms underlying correlations were previously unclear. In Chapter 4 I focus on the mechanisms within the DS circuit that endow these neurons with impressive sensitivity to stimulus contrast. Using physiological and pharmacological methods I first assess the relative contrast sensitivity of ganglion cells and starburst amacrine cells (SACs) in the DS circuit. The sensitivity of DSGC and SAC excitatory currents to antagonists of Na+ channels suggests an important role for these channels in amplifying low contrast responses and other weak inputs to the circuit. This role is later attributed to the differential expression of voltage-gated Na+ channels in specific bipolar cell populations. In aggregate, this dissertation describes several novel circuit mechanisms within the well-studied DS circuit. I also provide specific roles for such specializations in visual coding. / Graduate

The field of conservation genetics, in combination with non-invasive sampling, provides a powerful set of tools for investigating the conservation status and natural history of rare species that are otherwise difficult to study. A systematic literature review demonstrated that this is certainly the case for many forest associated antelope species, which are poorly studied and yet constitute some of the most heavily hunted wildlife in Africa. The aim of the present study was to use non-invasive sampling to investigate genetic patterns in forest antelope populations in the high-biodiversity Udzungwa Mountains, Tanzania, within the context of the conservation of these species and the wider ecosystem. Genetic information was derived from faecal samples collected across the Udzungwa landscape and assigned to five antelope species (N = 618, collected 2006-09). Faecal pellet length was measured for a subset of samples but statistical assignment to species by this method proved unreliable. Phylogenetic analysis using mitochondrial control region sequences unexpectedly revealed that Harvey’s duiker within the Udzungwas are paraphyletic with respect to sequences from a putative sister species from southern Africa. However, there was no corresponding pattern in the microsatellite dataset suggesting that these mitochondrial lineages do not represent contemporary genetic isolation. Instead, Harvey’s duiker nuclear variation is shaped both by isolation by distance, due to positive spatial autocorrelation at short distances, and clustering of distinct genotypes from western outlying forests. These forests also harbour the endangered Abbott’s duiker and therefore require effective conservation management. Despite being detected throughout the Udzungwas, genetic diversity in Abbott’s duiker was very low in comparison to other species. These results suggest several promising research directions but also have significant conservation implications that will be disseminated to the Tanzanian wildlife authorities and the wider conservation community.

In addition to habitat loss and fragmentation, habitat degradation can have important consequences for biodiversity and population persistence, including effects on ecological and genetic processes beyond decreased demographic viability and the loss of genetic variation. Particularly interesting is the potential for evolutionary changes and adaptation to degraded habitats, that can affect population viability even in the short-term. Here, I explore how environmental changes after habitat degradation affect the evolutionary dynamics of populations of the rainforest cycad Zamia fairchildiana, specifically how habitat degradation affects gene dispersal, inbreeding, directional selection, and genotype-by-environment interactions, and the potential for genetic differentiation between populations. Colonies of Z. fairchildiana showed little genetic differentiation in neutral molecular markers across study sites, thus can be considered as subpopulations. Subpopulations in the disturbed habitat are experiencing different environmental conditions when compared to subpopulation in their native habitat. Disturbed-habitat subpopulations showed a faster life-history. This faster life history is associated with a weaker spatial genetic structure and higher levels of inbreeding in the disturbed-habitat subpopulations. In addition, higher light availability in the disturbed habitat seems to be a major agent of selection on traits like leaf production that have the potential to respond to selection in these subpopulations. Different traits were under selection in the native-habitat subpopulations, suggesting the potential for genetic differentiation between native and disturbed-habitat subpopulations. Genotype by environment interactions in seed germination and seedling survival, in response to light and water availability, further suggested that subpopulations can adaptively diverge between habitats, but the relative role of genetic and environmental factors, particularly maternal effects, on the magnitude and rate of genetic differentiation between subpopulations remains to be evaluated. These results suggest that habitat degradation can have important consequences for the evolutionary dynamics of populations of this cycad, not necessarily typical of habitat loss and fragmentation. This study identified factors and processes important for population persistence in degraded habitats, but population responses to habitat degradation are complex. Thus further studies and long-term experiments are required for better understanding the effects of habitat degradation on population viability.

Today biodiversity is rapidly decreasing and an increasing number of threatened species live in modified and human dominated landscapes. Therefore it is essential to learn more about how species cope with the changes of their habitat. The focus of this study lies on a primate species, the critically endangered Javan slow loris (Nycticebus javanicus), endemic to the densely populated island of Java, Indonesia.  In cooperation with the Little fire face project in West Java, I used a step selection function (SSF) framework, to understand how landscape structure affects the movement of Javan slow lorises within a fragmented mountain-agroforest landscape of Cipaganti, West Java. To investigate the movement and fine scale habitat selection of slow lorises I used one hour locations of 6 radio-collared slow lorises. The habitat and vegetation of observed and random steps was investigated in multiple variables such as presence of food trees and signs of human disturbance. For the analysis I paired observed steps (1h relocations) with 3 random habitat locations and used a conditional logistic regression to parameterize the SSF, which represents the probability of a focal slow loris to select a given step as a function of the habitat and vegetation factors surveyed. In average the slow lorises travelled about 450 m each night and most frequently they used a step length of about 0 – 50 m. My result reveals that slow lorises fine scale habitat selection is positively influenced by the presence of trees and tree trunk cover (indirect increasing the canopy cover and connectivity). They are also to a high extent positively affected by the presence of a feeding tree species, Calliandra calothyrsus. Surprisingly slow lorises selected steps associated with a higher number of fields (fields may indicate an increased biodiversity within the location). The results also indicate that slow lorises are limited in their movement by the presence of fields or rivers, which indicates that slow lorises are negatively influenced in their movement by a declining ability to move and forage within Cipaganti. I found no significant differences between sexes in their distance travelled. The recommendation for future conservation of slow lorises in Cipaganti is to prevent further habitat loss and fragmentation through activities that protect or maintain the present suitable slow loris habitat. Further research is needed to increase the knowledge of these primates’ abilities to live in this modified landscape.

No description available.

Background Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other "fast" evolving plastid markers. Results Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae). Conclusions While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.

L’animation faciale est l’un des points clés dans le réalisme des scènes 3D qui mettent en scène des personnages virtuels. Ceci s’explique principalement par les raisons suivantes : le visage et les nombreux muscles qui le composent permettent de générer une multitude d’expressions ; ensuite, notre faculté de perception nous permet de détecter et d’analyser ses mouvements les plus fins. La complexité de ce domaine se retrouve dans les approches existantes par le fait qu’il est très difficile de créer une animation de qualité sans un travail manuel long et fastidieux. Partant de ce constat, cette thèse a pour but de développer des techniques qui contribuent au processus de création d’animations faciales. Trois thèmes sont principalement abordés. Le premier concerne la paramétrisation du visage pour l’animation. La paramétrisation a pour but de définir des moyens de contrôle pour pouvoir déformer et animer le visage. Le second s’oriente sur l’animation, et plus particulièrement sur le transfert d’animation. Le but est de proposer une méthode qui permette d’animer le visage d’un personnage à partir de données variées. Ces données peuvent être issues d’un système de capture de mouvement, ou bien elles peuvent être obtenues à partir de l’animation d’un personnage virtuel qui existe déjà. Enfin, nous nous sommes concentrés sur les détails fins liés à l’animation comme les rides. Bien que ces rides soient fines et discrètes, ces déformations jouent un rôle important dans la perception et l’analyse des émotions. C’est pourquoi nous proposons une technique d’acquisition mono-caméra et une méthode à base de poses références pour synthétiser dynamiquement les détails fins d’animation sur le visage. L’objectif principal des méthodes proposées est d’offrir des solutions afin de faciliter et d’améliorer le processus de création d’animations faciales réalistes utilisées dans le cadre d’applications en temps réel. Nous nous sommes particulièrement concentrés sur la facilité d’utilisation et sur la contrainte du temps réel. De plus, nous offrons la possibilité à l’utilisateur ou au graphiste d’interagir afin de personnaliser sa création et/ou d’améliorer les résultats obtenus / Facial animation is one of the key points of the realism of 3D scenes featuring virtual humans. This is due to several reasons : face and the many muscles that compose it can generate a multitude of expressions ; then, our faculty of perception provides us a great ability to detect and analyze its smallest variations. This complexity is reflected in existing approaches by the fact that it is very difficult to create an animation without a long and a tedious manual work. Based on these observations, this thesis aims to develop techniques that contribute to the process of creating facial animation. Three main themes have been addressed. The first concerns the rigging issue of a virtual 3D face for animation. Rigging aims at defining control parameters in order to deform and animate the face. The second deals with the animation, especially on the animation retargeting issue. The goal is to propose a method to animate a character’s face from various data. These data can be obtained from a motion capture system or from an existing 3D facial animation. Finally, we focus on animation finescale details like wrinkles. Although these are thin and discreet, their deformations play an important part in the perception and analysis of emotions. Therefore we propose a monocular acquisition technique and a reference pose based method to synthetise dynamically animation fine details over the face. The purpose is to propose methods to facilitate and improve the process of creating realistic facial animations for interactive applications. We focused on ease to use in addition to the real-time aspect. Moreover, we offer the possibility to the user or graphist to interact in order to personalize its creation and/or improve the results

Du fait de l’isolement géographique de l’océan austral et des conditions météorologiques qui y règnent, la collecte de données océanographiques par les moyens conventionnels est particulièrement couteuse dans cette région du globe. Pour pallier à ces difficultés, l’utilisation d’enregistreurs électroniques embarqués sur des prédateurs marins, et notamment sur les éléphants de mer austraux, s’est révélée être une approche intéressante. Les femelles éléphants de mer s’alimentent en grande partie de petits poissons méso-pélagiques bioluminescents, les myctophidés. Leur forte abondance et leur comportement de migration nycthémérale confèrent à ces organismes un rôle écologique de première importance dans l’océan austral. Cependant, la distribution spatiale des proies de l’éléphant de mer, et les processus physiques et biologiques qui influent sur la dynamique de cette distribution sont encore mal connus. Cette thèse se propose d’enquêter sur ces sujets à partir des données à haute fréquence d’échantillonnage collectées par des femelles éléphants de mer. L’analyse du comportement de plongée des femelles éléphants de mer, en relation avec les variations du taux de rencontre de proie dont les données d’accélération permettent d'avoir une estimation, est au cœur des différents travaux développés dans cette thèse. Les résultats obtenus suggèrent notamment, (1) une diminution de l’abondance des proies avec la profondeur ainsi qu’une homogénéisation de leur distribution, (2) une distribution en couches de cette ressource, (3) l’intervention de contraintes verticales délimitant l’étendue verticale de ces couches et ainsi capable de moduler leur densité, (4) au sein des couches, une dispersion relativement importante des proies en comparaison de la portée des capacités de perception du prédateur, et enfin (5) un rôle significatif des tourbillons méso-échelle et de leur bordure sur la structuration de la distribution des ressources alimentaires de l’éléphant de mer durant l’été austral. / Because of the remoteness and harsh meteorological conditions of the southern ocean, data sampling is more costly in this area. Use of electronic devices attached to marine predators (Bio-logging), such as southern elephant seals, has emerged as an interesting approach to cope with this problem. Female southern elephant seals primarily feed on small bioluminescent meso-pelagic fishes called myctophids. Because of their large abundance and of their diel vertical migration behaviour, these organisms have a major ecological importance in the southern ocean. However, the spatial distribution of the elephant seals prey, as well as the bio-physical processes affecting the dynamics of this distribution, are still poorly known. This thesis intends to investigate this issue using high sampling frequency bio-logging data collected by female southern elephant seals. This work is based on the analysis of elephant seals diving behaviour in relation to changes in the occurrence of prey encounter events detected from acceleration data. Our results suggest that (1) prey abundance decreases with depth and that their distribution tend to standardize, (2) prey are distributed into layers, (3) vertical constraints could modulate the prey density by acting on the vertical spread of these layers, (4) prey items are well dispersed in comparison to the perception range of elephant seals, and finally (5) that meso-scale eddies, notably their edges, play a structuring role in the prey distribution during the austral summer.

Background Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other 'fast' evolving plastid markers. Results Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae). Conclusions While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.