In the wild, a variety of inter-group behavioural differences have been reported for chimpanzees (Pan troglodytes) and it has been suggested that these may have resulted from social learning. To determine whether chimpanzees show the necessary propensity for social learning, groups of captive chimpanzees were tested in a series of experiments involving the use of two-action and bidirectional apparatuses. For comparison, and to shed light on any contrasts between our own and chimpanzee learning strategies, similar tests were also conducted with children (Homo sapiens) to ascertain the nature of their observational learning when watching conspecifics. Through the use of open diffusion and diffusion chain techniques, it was shown that both species learnt how to operate different foraging devices from observing an expert conspecific and this learning was strong enough for the generation of behavioural traditions which passed along multiple test ‘generations’. Additionally, ghost conditions were used to distinguish imitative and emulative learning by both species. With one of the two test devices used (the Slide-box) the first evidence for emulation learning by chimpanzees, through the use of a ghost condition, was shown. Children in this condition also showed apparent emulation; a contrast to previous research which has concluded that children tend to rely on imitation. Additionally, to test its potential for use in future social learning experiments, the ability of chimpanzees to learn from video-footage of an unknown conspecific was tested. It was found that the chimpanzees not only learnt how to operate two devices from observing this footage but also used the same alternative method used by the model chimpanzee.

L'examen des asymétries oro-faciales fournit un indice indirect et fiable pour déterminer la spécialisation hémisphérique des processus liés à la communication socio-émotionnelle chez les primates non humains. Cependant, à ce jour, peu d'études ont été réalisées et les théories formulées chez l'homme sont peu consensuelles. Afin de contribuer à la question de la latéralisation cérébrale des processus cognitivo-émotionnels chez le primate, quatre études expérimentales ont été réalisées au cours de cette thèse. Tout d'abord, deux méthodes ont été utilisées pour mesurer les asymétries oro-faciales dans une population de babouins adultes (une méthode morphométrique et une méthode dite des « chimères »). Une spécialisation hémisphérique droite dominante pour le traitement des émotions négatives a été notée. Une troisième étude a démontré, pour la première fois, une asymétrie oro-faciale au niveau populationnel chez des jeunes macaques et babouins. Enfin, une dernière étude a été réalisée chez des chimpanzés afin de tester la robustesse d'une recherche qui avait mis en évidence une différence d'asymétrie selon la fonction communicative intentionnelle (hémisphère gauche) vs. émotionnelle (hémisphère droit) des vocalisations. Les résultats ont confirmé ceux de la première étude et permettent de discuter des hypothèses concernant l'origine de l'évolution du langage. Ces travaux sont discutés à la lumière des recherches récentes concernant de nombreuses espèces animales. Ils apportent des connaissances nouvelles pour appréhender la phylogénèse de la spécialisation hémisphérique des processus associés à la communication verbale et non verbale chez l'homme. / The study of oro-facial asymmetries offers an indirect and suitable index to determine the hemispheric specialization of the processes associated to socio-emotional communication in non-human primates. However, few studies have been made in this domain and the available theories in humans are in part contradictory. In order to contribute to this field, i.e., hemispheric specialization of cognitive and emotional processing in primates, four experimental studies have been carried out during this doctorate. Firstly, two methods have been used to assess oro-facial asymmetries in adult baboons (a morphometric one and a free viewing of chimeric faces). A right hemispheric specialization for negative emotions was noticed. A third study demonstrated for the first time a population-level hemispheric specialization for the production of emotions in infant macaques and baboons. A last study tested the robustness of previous findings in chimpanzees concerning differences of hemispheric lateralization patterns depending on the communicative function of the vocalizations: intentional (left hemisphere) vs emotional (right hemisphere). Results confirmed the previous conclusions and allowed to discuss hypotheses about the origin of the evolution of language (speech). These collective findings are discussed within the context of the phylogeny of hemispheric specialization mechanisms underlying verbal and nonverbal communication in humans.

I tested two pairs of captive chimpanzees (Pan troglodytes) in the informed forager paradigm: a subordinate saw the location of hidden bait, and then searched with a naïve dominant. This paradigm has tested what subjects know about others' states of knowledge, but my focus was to determine how subjects used different movement types and different gaze types to modify their competitive tactics. In particular, I investigated whether chimpanzees follow opponents' gaze to gain information. Learning more about how primates use visual information to predict others' behaviour can shed light on the continuing debate over to what degree apes possess theory of mind capacities. Previous published studies in this paradigm included narratives of ignorant competitors exploiting informed subjects by following their movement and gaze, and informed subjects avoided this exploitation by walking away from hidden food. The subordinate's behaviour can be considered tactical deception, which is a good place to seek strong evidence of second-order intentionality. Analyses with descriptive statistics, however, fail to capture the complexity of these interactions, which range from single decision-making points to larger patterns of following and misleading. I introduced a novel method of statistical analysis, cross correlations, that enabled me to examine behavioural patterns quantitatively that previous authors have only been able to describe in narrative form. Though previous studies on chimpanzees' understanding of gaze found that they were unable to use (human-given) gaze cues to locate hidden food, the subjects I tested followed their conspecific opponent's gaze, and used information gained from the gaze interaction to modify their own movement towards the hidden bait. Dominants adjusted their physical following of the subordinates as the interaction progressed, which reflected their changed states of knowledge. Subordinates used their movement and gaze differentially to manipulate dominants' behaviour, by withholding information and by recruiting towards a less-preferred bait.

With more than ¾ of the forest surface of Cameroon allocated to logging, the survival of many rainforest species will depend on the way in which timber production forests will be managed in this country for the next decades. Management decisions to be applied should be directed systematically towards a minimization of the negative impacts on the ecosystem as a whole, including on the animal populations living in these forests. This requires a detailed understanding of the response of wildlife to selective logging as it is currently practised in Central Africa. This thesis reports results of a longitudinal monitoring of abundances of nine mammal species in a forest concession over a four years period. From 2003 to 2006, four wildlife censuses have been conducted in the active core of FMU 10.030 allocated to the logging company PALLISCO. Our study area covers 176 sq-km and include several logging compartments and unlogged areas. The diversity of specific responses to the introduction of human activities into the habitat is at the scale of the biological diversity of the habitat itself. A particular attention was paid to two emblematic species of the Cameroonian forests, western lowland gorillas G.g. gorilla and the common chimpanzees Pan troglodytes. During this work, we studied 1) how logging at industrial scale affects the spatial distribution of nine mammal species, including great apes, in timber production forests of South-eastern Cameroon, and 2) the nature of pressures exerted on animal populations within an active forest concession (anthropic, ecological, ethologic, etc). Our first results indicate that the extraction of valuable timber species generates a spatial reorganization of gorillas and chimpanzees, inducing local modifications of population densities. This spatial reorganization seems to be mainly due to human activities per se rather than to modifications of the habitat structure or changes in the availability of fruits for these species. Compared with other mammals, great apes are at the two extreme opposites of a gradient of sensitivity to the habitat disturbances created by logging. Gorillas, as well as other "generalist" species like duikers, seem to thrive in logged forests, probably attracted in these areas by the secondarisation of the vegetation. Their densities decrease temporarily in logging compartments during logging operations but these species recover quickly, suggesting a repulsive effect of the human presence in the forest rather than a major alteration of the habitat quality for them. Rather "specialist" species seem to react by increasing the size of their foraging area. These are the sitatungas Tragelpahus spekei and bushpigs Potamochoerus porcus, two typical species of swamp forest with Raffia spp. and semi-inundated forests. These particular biotopes in the heart of the production forests seem to be playing the role of refuge zone for these species. Finally, two species were identified as being explicitly vulnerable to logging activities: the chimpanzees and forest elephants Loxodonta africana cyclotis. Their abundances did not recover to original values during the period of study indicating that they still undergo some kind of ecological and/or anthropic pressures after the end of logging operations that is strongly adverse to them. In order to contrast the ecological and/or anthropic factors ruling gorillas' and chimpanzees' spatial distribution in the habitat, we have used a spatial modelling technique called “Ecological Niche Factor Analysis - ENFA". ENFA-generated models for these two species mainly retained anthropic variables to explain great apes local repartition in the study area. For gorillas, it was mainly explained by the local pattern of logging compartments and the time that passed since the end of logging operations. Globally, this species avoids the areas of forests showing a high rate of human frequentation and is attracted to old logged areas. As for the chimpanzees, their spatial distribution is influenced mainly by the presence of roads which are largely avoided. The periphery of logged compartment seems to be a zone of convergence for chimpanzee communities that have probably been driven out from logging compartments during operations, but these movements of populations would be limited to short distances. The vulnerability of the chimpanzees is consequently explained by the absence of demographic mechanisms enabling them to avoid the disturbed zones while reducing the territorial conflicts. The general trend in great ape abundances in an active logging concession confirms that even closely related species can show divergent capacities of survival when confronted to human disturbances. Our work highlights that chimpanzee communities demonstrate some spatial inertia, contrarily to gorillas which easily manage to avoid human activities. This inertia would be probably at the origin of its sensitivity to current forestry practices. Our results confirm White & Tutin (2001)'s socio-ecological explanation for the vulnerability of chimpanzees to logging in forests of Central Africa. Knowing this, it is imperative to set up concrete conservation actions aiming at maintaining the chimpanzee populations of in Cameroonian timber production forests. Practically, selective logging would easily be compatible with the preservation of the majority of rainforests mammals if concrete measures aiming at decreasing the negative impacts of logging were effectively applied. As a general rule, the proximity between logged areas and some zones that can serve as refuge seems to be a determining factor of the persistence of rainforests mammals in logged forests. A line of thought would be thus to ensure safe shifts of populations towards these zones in order to guarantee the avoidance of disturbances and, later, the recovery of densities in logged forests. In this sense, our main recommendation consists in promoting a delimitation of logging compartments into narrow strips so as to reduce the distance to be walked by an animal to geographically avoid human disturbances. Additionally, it is necessary to set up well-designed biomonitoring programmes to follow up trends in wildlife abundances and promote a flexible management that can be adapted according to the evidence of detrimental events to wildlife. / Avec plus de ¾ de la surface forestière du Cameroun allouée à l'exploitation forestière, la survie de nombreuses espèces de mammifères dépendra de la façon dont seront gérés les massifs de forêt de production de ce pays dans les décennies à venir. Les mesures de gestion à appliquer devraient être orientées systématiquement vers une minimisation des impacts négatifs sur l'écosystème dans son ensemble, y compris sur les populations animales résidant dans ces forêts. Ceci nécessite une compréhension détaillée de la réponse de la grande et moyenne faune à l'exploitation forestière sélective telle qu'elle est effectivement pratiquée en Afrique Centrale. Cette thèse de doctorat rapporte les résultats d'un suivi longitudinal, sur une période de quatre ans, des abondances de neuf espèces de mammifères au sein d'une concession forestière du Sud-est Cameroun. Au total, quatre recensements de la faune ont été réalisés entre 2003 et 2006 dans la partie active de l'UFA 10.030 allouée à la société PALLISCO. La zone étudiée couvre 176 km2 et englobe plusieurs parcelles annuelles d'abattage ainsi que des compartiments non exploités. La diversité des réponses spécifiques vis-à-vis de l'introduction d'activités humaines dans l'habitat est à l'échelle de la diversité biologique de l'habitat lui-même. Une attention particulière a été portée sur deux espèces emblématiques des forêts camerounaises, les gorilles des plaines occidentales G.g. gorilla et les chimpanzés communs Pan t. troglodytes. Durant ce travail, nous avons étudié 1) comment l'exploitation forestière à l'échelle industrielle affecte la distribution spatiale de neuf espèces de mammifères, dont les grands singes, dans les massifs de forêt de production du Sud-est Cameroun, et 2) de quelle nature sont les pressions exercées sur les populations animales au sein d'une concession forestière active (anthropique, écologique, éthologique, etc.). Nos premiers résultats indiquent que l'extraction d'essences précieuses dans les forêts camerounaises génère notamment une réorganisation de la distribution spatiale des gorilles et des chimpanzés, induisant des modifications locales de densité de population. Cette réorganisation spatiale semble être due aux activités humaines elles-mêmes plutôt qu'aux modifications de la structure de l'habitat ou à une diminution de la disponibilité de certaines ressources alimentaires importantes pour ces espèces. Comparés à d'autres mammifères, les grands singes se placent aux deux extrêmes d'un gradient de sensibilité aux perturbations de l'habitat causés par l'exploitation forestière. Les gorilles, ainsi que d'autres espèces "généralistes" comme les céphalophes, semblent prospérer dans les forêts exploitées, probablement attirés dans ces zones par la secondarisation de la végétation. Leurs densités diminuent ponctuellement dans les parcelles d'abattage pendant les opérations d'extraction, mais retrouvent très vite leur niveau initial. Ceci suggère un effet répulsif de la présence humaine sur ces espèces plutôt qu'une altération majeure de la qualité de l'habitat pour ces dernières. D'autres espèces plus "spécialistes" semblent réagir en augmentant la taille de leurs aires de fourragement. Il s'agit des sitatungas Tragelpahus spekei et des potamochères Potamochoerus porcus, deux espèces appréciant les biotopes humides (marécages à Raphia spp., des zones de forêt inondées, etc.). Ces biotopes particuliers, non-affectés par l'exploitation forestière, au coeur des forêts de production semblent servir de refuge pour ces espèces. Enfin, deux espèces ont été identifiées comme étant explicitement très vulnérables aux activités d'exploitation: les chimpanzés et les éléphants des forêts Loxodonta africana cyclotis. Leurs abondances n'ont pas recouvré les valeurs originelles durant la période d'étude, indiquant que ces espèces subissent encore des pressions écologiques et/ou anthropiques jusqu'à quatre ans après la fin des activités d'exploitation forestière. Afin de contraster les facteurs écologiques et/ou anthropiques régissant la distribution spatiale des gorilles et des chimpanzés, nous avons fait usage d'une technique de modélisation spatiale appelée "Ecological Niche Factor Analysis – ENFA". Les modèles ENFA pour ces deux espèces ont principalement retenu les variables anthropiques pour expliquer la distribution spatiale des grands singes dans l'aire d'étude. Il a ainsi été démontré que la répartition des gorilles était en grande partie expliquée par l'agencement local des AACs et le temps qui s'est écoulé depuis la fin des opérations d'extraction dans celles-ci. De manière générale, cette espèce évite les zones présentant un haut taux de fréquentation humaine et préfère les forêts exploitées quelques années auparavant. Quant aux chimpanzés, leur distribution spatiale est principalement expliquée par la présence de routes et pistes forestières qui sont amplement évitées. La périphérie des zones exploitées semble être une zone de convergence pour les chimpanzés qui y seraient vraisemblablement refoulés lors des perturbations, mais ces mouvements seraient limités à de courtes distances. La vulnérabilité des chimpanzés s'expliquerait dès lors par l'absence de mécanismes démographiques leur permettant d'éviter les zones affectées tout en réduisant les conflits territoriaux résultant d'une réorganisation spatiale. La tendance globale des variations d'abondance des grands singes au sein d'une concession forestière en cours d'exploitation confirme que même des espèces très proches phylogénétiquement peuvent faire preuve de capacités différentes de survie face aux perturbations anthropiques. Il ressort de nos observations que les communautés de chimpanzés font preuve d'une certaine inertie spatiale, contrairement aux gorilles qui parviennent à éviter les activités humaines. Cette inertie serait probablement à l'origine de sa vulnérabilité face aux pratiques forestières actuelles. Nos résultats viennent confirmer l'hypothèse socio-écologique émise par White & Tutin (2001). Face à ce malheureux constat, il est impératif de mettre en place des mesures concrètes de gestion visant à maintenir les populations de chimpanzés dans les forêts de production camerounaises. Pratiquement, l'exploitation sélective serait compatible avec la conservation de la plupart des mammifères si certaines mesures de gestion visant à diminuer les impacts négatifs étaient rapidement mises en application. La proximité entre les zones exploitées et les zones pouvant servir de refuge semble être un facteur déterminant de la survie de nombreuses espèces de mammifères dans les forêts de production du Cameroun. Une ligne de réflexion serait donc d'assurer les mouvements de populations vers ces zones-refuge sans heurts afin de garantir l'émigration des populations animales en dehors des zones affectées et la recolonisation ultérieure des forêts exploitées. En ce sens, notre principale recommandation consiste à promouvoir un découpage en assiettes de coupe en bandes relativement étroites (<2,5 km) de façon à réduire la distance à parcourir pour éviter géographiquement les perturbations anthropiques. De même, il serait nécessaire de mettre en place des programmes de suivi régulier des abondances faunistiques afin de permettre une gestion adaptative qui s'ajusterait au vu d'événements critiques pour la faune.

The chimpanzee is humankind’s closest living relative and the two species diverged ~6 million years ago. Comparative studies of the human and chimpanzee genomes and transcriptomes are of great interest to understand the molecular mechanisms of speciation and the development of species-specific traits. The aim of this thesis is to characterize differences between the two species with regard to their genome sequences and the resulting transcript profiles. The first two papers focus on indel divergence and in particular, indels causing premature termination codons (PTCs) in 8% of the chimpanzee genes. The density of PTC genes is correlated with both the distance to the telomere and the indel divergence. Many PTC genes have several associated transcripts and since not all are affected by the PTC we propose that PTCs may affect the pattern of expressed isoforms. In the third paper, we investigate the transcriptome divergence in cerebellum, heart and liver, using high-density exon arrays. The results show that gene expression differs more between tissues than between species. Approximately 15% of the genes are differentially expressed between species, and half of the genes show different splicing patterns. We identify 28 cassette exons which are only included in one of the species, often in a tissue-specific manner. In the fourth paper, we use massive parallel sequencing to study the chimpanzee transcriptome in frontal cortex and liver. We estimate gene expression and search for novel transcribed regions (TRs). The majority of TRs are located close to genes and possibly extend the annotations. A subset of TRs are not found in the human genome. The brain transcriptome differs substantially from that of the liver and we identify a subset of genes enriched with TRs in frontal cortex. In conclusion, this thesis provides evidence of extensive genomic and transcriptomic variability between human and chimpanzee. The findings provide a basis for further studies of the underlying differences affecting phenotypic divergence between human and chimpanzee.

Zoological institutions emphasise the importance of excelling in the areas of animal welfare, conservation, education, and research, not only to better the lives of the animals under their care, but to also influence the general population in the pursuit to conserve the natural world. As a result, zoo life is anything but simple. This research project monitored the lives of a captive group of chimpanzees over a two-and-a-half-year period, during which time we explored four research topics while assessing the development of a cognitive research programme and chimpanzee (Pan troglodytes) introductions in a zoo: welfare, cognition, public engagement with science, and animal management. The project’s use of touchscreen technology and on-exhibit research was the first of its kind for the Royal Zoological Society of Scotland’s Edinburgh Zoo. As a result, the researchers placed a great deal of importance not only on assessing the welfare of the chimpanzees throughout training and testing phases, but also assessing the public’s perception of cognitive research being conducted through an internationally broadcast documentary about the project. In the short duration of the project, these research naïve chimpanzees did not fully grasp the concept of video selection in our free-choice activity, but overall, the introduction of a cognitive research programme did not compromise welfare, and the chimpanzees’ repeated interest suggests that chimpanzees found the research to be reinforcing. Partly funded by the BBC, the Chimpcam Project was shown in the UK (broadcast January 2010) and in a variety of other countries, including the United States and Canada (on Animal Planet in 2011). The broadcast allowed us to gather information over the internet on the wider public’s perception of conducting research with great apes in zoos, to complement data collected on visitors to the exhibit itself. Our assessment of the documentary’s impact on public perception showed that it had a positive influence on perceptions of zoo research, scientists, welfare, and the importance of choice for animals. During this research project, a new group of chimpanzees arrived in Edinburgh as part of the international breeding programme for western chimpanzees (Pan troglodytes verus). As the zoo’s focus switched to helping the two chimpanzee groups merge into one, we took the opportunity to apply psychological research to this context, namely the use of video as a research tool and the recognition of the importance of individual differences in response to challenge. The project maintained the cognition and welfare focus by using video introductions (allowing the chimpanzees to watch video footage of the individuals they were about to meet and track the formation of other sub-groups). In addition, personality ratings and chimpanzee behaviour during the visual access period (an animal management technique used prior to physical introductions where the groups could see each other without physical contact) were collected to examine the efficacy of these measures in guiding introductions in order to reduce risk. Personality ratings and behaviours observed during the video introductions could predict the chimpanzees’ behaviour during the physical introductions, however, the visual access period had no predictive power. The welfare implications of the introduction process were also assessed and suggested that: the choice of location (i.e. options of where to be) was more important than the total amount of available space; having individuals removed from your group was more stressful than having individuals added; self-directed behaviour (SDB) performance was context-specific where rubbing significantly increased during periods of uncertainty that were not necessarily negatively valenced; regurgitation and reingestion (R/R) decreased over time; and both in-group members and those of high ranks spent more time grooming others. Overall our data indicate that the chimpanzees coped well with both cognitive challenges and social upheaval during introductions. Despite being regularly studied in captivity and in the wild, chimpanzees have a great deal more to teach us about their world. In order to provide the best welfare for the chimpanzees in our care, we need to understand how research and management practices affect their lives and how the public interpret what we do as researchers. By understanding these aspects of their world, we can better serve those in captivity and influence public opinion on the importance of conserving those in the wild.

Les variations entre les nourrissons quant à la vitesse à laquelle ils atteignent l'indépendance nutritionnelle affectent les trajectoires de développement des nourrissons et entraînent des différences entre les femelles au niveau de la performance reproductive. Le moment des transitions alimentaires, notamment l'âge auquel les nourrissons commencent à consommer des aliments solides et l'âge du sevrage (c'est-à-dire le dernier allaitement avec transfert de lait), est difficile à déterminer par l'observation chez les primates sauvages. Il est difficile de distinguer le moment où les nourrissons se livrent à une mise en bouche exploratoire de celui où ils ingèrent réellement des aliments solides, et de déterminer si les contacts observés avec les mamelons reflètent une lactation continue, car les petits sevrés peuvent s'allaiter de confort (sans transfert de lait). Les isotopes stables de carbone et d'azote (δ13C, δ15N, %N) dans les fèces ou les poils peuvent être utilisés pour déterminer les transitions alimentaires. Alors que les isotopes stables fécaux sont sensibles à l'échantillonnage occasionnel d'aliments solides et montrent une forte variation quotidienne, les isotopes stables des poils montrent un amalgame de l'apport alimentaire sur quelques mois. Pour atténuer les limites des isotopes stables fécaux et de l'observation, j'ai appliqué des analyses δ13C, δ15N, %N à la kératine des fils de poils (0-7 ans, N = 169 échantillons de poils) collectés auprès de mères et de nourrissons chimpanzés sauvages (Pan troglodytes) à Ngogo, en Ouganda. En 2013-2014 et 2018, les poils ont été collectés de manière non invasive lorsqu'ils se collaient aux excréments, ou sur le sol après que les mères et les nourrissons se soient toilettés ou reposés. Premièrement, mon objectif était d'utiliser une combinaison de techniques visuelles (longueur et diamètre des fils de poils), associées à des isotopes stables des poils pour distinguer les fils de poils maternels des fils de poils infantiles. Deuxièmement, mon objectif était de déterminer l'âge précis auquel la contribution relative de la nourriture solide l'emporte sur la contribution relative du lait dans le régime alimentaire des bébés chimpanzés sauvages afin de suivre les processus d'alimentation transitoire et de sevrage. Les mèches de cheveux du nourrisson n'ont pas pu être distinguées des mèches de cheveux de la mère en utilisant uniquement des techniques visuelles. Les longueurs (cm) et les diamètres (μm) des poils de la mère et du nourrisson ne présentaient pas de différences suffisamment importantes et cohérentes pour pouvoir être utilisées seules pour distinguer les poils. Cependant, les poils des mères et des nourrissons se sont avérés plus fins et plus courts que ceux des mâles adultes (~20 μm de moins pour les nourrissons). Pour évaluer les limites des isotopes stables fécaux et de l'observation, des analyses δ13C, δ15N, %N ont été appliquées à la kératine de mèches de cheveux (0-7 ans, N = 169 échantillons de cheveux) collectées auprès de mères et de nourrissons chimpanzés sauvages (Pan troglodytes) à Ngogo, en Ouganda. Les nourrissons ≤ 2 ans présentaient le plus grand rapport d'isotopes stables de carbone et d'azote (δ13C et δ15N). Les nourrissons âgés de 1.5 à 2 ans présentaient des ratios moyens de δ13C (-22,2 permil, ‰) et de δ15N (9,2‰) supérieurs à ceux des nourrissons ≤ 1.5 ans (valeur moyenne de δ13C de -23,2‰, valeur moyenne de δ15N de 8,6‰). Cela indique que les nourrissons ≤ 2 ans avaient un régime alimentaire global dominé par le lait maternel et consommaient moins d'aliments végétaux solides par rapport aux nourrissons plus âgés (δ13C de -23.8 ‰, δ15N de 7.4 ‰). Le changement dans les rapports δ13C une fois que les nourrissons ont dépassé 2 ans a suggéré que les nourrissons ont incorporé une plus grande quantité d'aliments solides dans leur régime alimentaire vers cet âge, ce qui pourrait être le moment où le processus de sevrage a commencé. Nous n'avons pas pu évaluer l'âge de la fin du sevrage, et nous aurons besoin à l'avenir de plus d'échantillons de poils de nourrissons plus âgés pour établir quand le sevrage se termine chez les chimpanzés. Cette étude peut être utilisée dans les évaluations futures des régimes alimentaires des primates, et pour déterminer les âges précis des transitions alimentaires chez les chimpanzés, ce qui fournira des données de base pour reconstruire le chemin évolutif qui a conduit à l'histoire de vie unique (sevrage précoce, fécondité élevée) des humains. / Variation between infants in the speed in which they reach nutritional independence affects infant developmental trajectories and leads to differences between females in reproductive output. Timings of feeding transitions, including the age infants begin consuming solid food, and age at the weaned event (i.e. last nursing bout with milk transfer), are difficult to determine both obervsationally and behaviourally in wild primates. It is difficult to distinguish when infants engage in exploratory mouthing versus actual ingestion of solid food, and to identify if observed nipple contacts reflect continued lactation, as weanlings can comfort nurse (without milk transfer). Stable carbon and nitrogen isotopes (δ13C, δ15N, %N) in feces or hair can be used to determine feeding transitions. While fecal stable isotopes are sensitive to occasional sampling of solid food and show high day-to-day variation, hair stable isotopes show an overall average of dietary intake over a few months. To assess fecal stable isotope and observational limitations, δ13C, δ15N, %N analyses were applied to keratin of hair strands (0-7 years, N = 169 hair samples) collected from wild chimpanzee (Pan troglodytes) mothers and infants at Ngogo, Uganda. In 2013-2014 and 2018, hairs were collected non-invasively when they stuck to feces, or from the ground after mothers and infants groomed or rested. First, my goal was to use a combination of visual techniques (hair strand length and diameter), combined with hair stable isotopes to distinguish maternal hair strands from infant ones. Second, my goal was to determine the precise age when the relative contribution of solid food outweighs the relative contribution of milk in the infant diet of wild chimpanzees to track the processes of transitional feeding and weaning. Infant hair strands could not be distinguished from maternal hair strands using only visual techniques. The lengths (cm) and diameters (μm) of maternal versus infant hair strands did not show great enough and consistent differences that could alone be used to distinguish the hairs. However, maternal and infant hair strands proved to be thinner and shorter to that of adult male hair (~20 μm lower for infants). I therefore relied on the stable isotope values themselves to distinguish the hairs, as infant hairs were enriched in the heavy carbon and nitrogen isotopes compared to their mothers. Infants ≤ 2.0 years old had the greatest ratio of stable carbon and nitrogen isotopes (δ13C and δ15N). Infants between 1.5 and 2.0 years old had greater average ratios of δ13C (-22.2 permil, ‰) and δ15N (9.2 ‰) than infants ≤ 1.5 years old (δ13C mean value of -23.2 ‰, δ15N mean value of 8.6 ‰). This indicated that infants ≤ 2.0 years old had an overall diet dominated by maternal milk and consumed less solid plant foods compared to older infants (δ13C mean value of -23.8 ‰, δ15N mean value of 7.4 ‰). The change in δ13C ratios once infants surpassed two years old suggested that infants incorporated a greater amount of solid food into their diet near this age. This indicated that the weaning process begins at approximately two years old. As the age of the weaned event remained unassessed, more hair samples are required from older infants to establish when weaning ends in chimpanzees. This study can be used in future assessments of primate diets, and to determine precise ages at feeding transitions in chimpanzees, which will provide basic data to reconstruct the evolutionary path that led to the unique life history (early weaning, high fecundity) of humans.

Despite having being discovered nearly 80 years ago, bonobos (Pan paniscus) are still one of the least well understood of the great apes, largely remaining in the shadow of their better known cousins, the chimpanzees (Pan troglodytes). This is especially evident in the domain of communication, with bonobo vocal behaviour still a neglected field of study, especially compared to that of chimpanzees. In this thesis, I address this issue by exploring the natural vocal communication of bonobos and its underlying cognition, focusing on the role that vocalisations play during two key contexts, food discovery and sex. In the context of food-discovery, I combine observational and experimental techniques to examine whether bonobos produce and understand vocalisations that convey meaningful information about the quality of food encountered by the caller. Results indicate that bonobos produce an array of vocalisations when finding food, and combine different food-associated calls together into sequences in a way that relates to perceived food quality. In a subsequent playback study, it was demonstrated that receivers are able to extract meaning about perceived food quality by attending to these calls and integrating information across call sequences. In the context of sexual interactions, I examine the acoustic structure of female copulation calls, as well as patterns in call usage, to explore how these signals are used by individuals. My results show that females emit copulation calls in similar ways with both male and female partners, suggesting that these signals have become partly divorced from a function in reproduction, to assume a greater social role. Overall, my results highlight the relevance of studying primate vocalisations to investigate the underlying cognition and suggest that vocalisations are important behavioural tools for bonobos to navigate their social and physical worlds.

Comment humains et chimpanzés définissent et brouillent les frontières entre leurs espèces lors de leurs interactions ? Tel sera le leitmotiv de notre étho-ethnographie, à l’intersection de l’anthropologie sociale, des études des sciences, et de la primatologie. Au fondement de cette recherche se trouve un travail de terrain de longue durée mené dans un laboratoire de sciences cognitives situé au Japon, au sein duquel sont enseignées aux chimpanzés des compétences langagières dans le but de caractériser leur monde perceptuel. Cependant, au cœur même du contexte ce laboratoire, la nature des relations entre humains et chimpanzés est un aspect crucial de ce programme de recherche ; les deux espèces y forment une communauté hybride faite d’affects, de relations sociales et de collaboration scientifique. Afin de fournir une étude comparative, nous avons également mené une série d’ethnographies plus brèves – sur le modèle de la méthodologie multi-site – en observant cette même problématique à l’œuvre au sein de diverses institutions au Japon - zoo, sanctuaires et réserves - ainsi qu’au sein de la station japonaise pour l’étude de la culture des chimpanzés qui se trouve à Bossou, en République de Guinée. En outre, ce travail narre l’expérience que nous avons faite de devenir expérimentatrice au sein du laboratoire étudié. Le résultat en est multiple. Nous commencerons par explorer l’histoire des études sur les chimpanzés menées à l’Institut de Recherche sur les Primates de l’Université de Kyoto (KUPRI) ainsi que les pratiques de soin et de recherche qui s’y sont mises en place. Ensuite, nous étudierons les dynamiques qui caractérisent (1) les frontières physiques, lors d’interactions sociales entre deux espèces qui peuvent s’avérer dangereuses, (2) les frontières expérimentales, lorsque le chimpanzé n’est pas seulement celui qui fait l’objet d’une expérience mais qui met également à l’épreuve son expérimentateur, (3) et les frontières symboliques, lorsqu’est interrogée la définition de la « personne » humaine et non humaine. Ainsi, quatre points principaux sont examinés à nouveaux frais, en particulier (a) la socialisation interspécifique (b) l’incarnation des relations inter-espèces dans un espace donné (c) les relations inter-espèces dans un contexte scientifique (d) l’examen de perspectives zoocentrées sur la « personne ». Nous conclurons avec l’évocation de nos espoirs et de nos attentes quant à un dialogue fructueux entre les différentes disciplines en jeu. L’apport de ce travail consistera en effet à mobiliser des concepts et des outils de la primatologie et des sciences sociales afin de proposer une analyse plus symétrique des relations entre humains et animaux. / How do humans and chimpanzees set and blur boundaries between species when interacting with each other? This is the leitmotif of this etho-ethnography at the intersection of social anthropology, social studies of science and primatology. This endeavor is based on long-term fieldwork conducted in a cognitive sciences laboratory in Japan, which teaches chimpanzees language-like skills as means to understand their perceptual world. However, in this laboratory setting, the human-chimpanzee relationship is a vital part of the research philosophy and both species constitute a hybrid community of affections, social relationships, and scientific partnering. As a comparative effort, a short-term multi-sited ethnography was conducted following the theme across institutions in Japan of zoo, sanctuary and field-site type, in addition to the Japanese field station for the study of chimpanzee culture, in Bossou, Africa. Moreover, this work draws on the experience of becoming, at the same time, an experimenter in the targeted laboratory. The result is multifold. We shall explore first, the history as well as the caretaking and research practices in chimpanzee studies at the Primate Research Institute of Kyoto University (KUPRI). Then, we shall investigate the dynamics of physical boundaries in dangerous interspecies social interactions; the experimental boundaries of testing and being tested by chimpanzees; and the symbolic boundaries concerning human and nonhuman personhood. As a result, four major points are brought to light in a renewed perspective, namely (a) interspecies socialization (b) the embodiment of interspecies social relations in space (c) interspecies social relations in scientific settings (d) animalcentric perspectives on personhood. We conclude with the hopes and prospects for a fruitful dialogue across disciplines. Overall, the differential endeavor of this work consists in mobilizing concepts and tools from both primatology and social sciences to propose a more symmetric analysis of the human-animal relationship.

A signal transduction process refers to chain of highly regulated biochemical steps which results in the transfer of signal in response to a stimulus in the extracellular environment to the intracellular compartments such as nucleus. Variety of biomolecules such as proteins and lipids participate in such processes. One of the superfamilies of proteins which actively participate in signaling processes is protein kinase which transfers γ-phosphate from Adenosine Triphosphate (ATP) to the specific hydroxyl group(s) in the protein substrates. Phosphorylation and dephosphorylation events are critical in many signal transduction pathways affecting biological system as a whole. Protein phosphorylation carried out by protein kinases has emerged as pre-eminent mechanism for the regulation of variety of cellular processes such as cell growth, development, differentiation, homeostasis, apoptosis, metabolism, transcription and translation. The current thesis encompasses the investigations carried out by the author, using various bioinformatics tools and methods, to comprehend the structural and functional roles of diverse set of protein kinase subfamilies in various eukaryotic and prokaryotic organisms. The present thesis has been divided into various chapters. Chapter 1 of the thesis provides introduction to the superfamily of protein kinases and covers the relevant literature. The database of Kinases in Genomes (KinG) set-up in the author’s group a few years ago (Krupa et al, 2004a), comprises of a collection of Serine/Threonine/Tyrosine protein kinases recognized using bioinformatics approaches, from the genomic data of various eukaryotes, prokaryotes and viruses (Krupa et al, 2004a). KinG database also provides classification of protein kinases into various groups and subfamilies (Hanks et al, 1988). Information on non-kinase domains which are tethered to the catalytic kinase domains is also available for every kinase in the KinG database. KinG is periodically (annually) updated with rise in the number of genome sequence datasets of various organisms, increase in the number of known protein domain families and refinement or reannotation of genomic datasets (Anamika et al, 2008c). Author describes the work on annual update of KinG database in Chapter 2 of the thesis. Availability of an improved version of the human genomic data has provided an opportunity to re-investigate protein kinase complement of the human genome and enabled an analysis of the splice variants. This analysis is also described in Chapter 2. Chapter 3, Chapter 4 and Chapter 5 report recognition and analysis of repertoire of protein kinases in Chimpanzee, two Plasmodium species (Plasmodium falciparum and Plasmodium yoelii yoelli) and Entamoeba histolytica respectively. A detailed analysis of the non-kinase domains which are tethered to catalytic protein kinase domains in eukaryotic organisms is presented in Chapter 6. Chapter 7 discusses a systematic classification framework developed by the author to classify Serine/Threonine protein kinases in prokaryotic organisms. Investigation carried out on 3-D structural aspects of protein kinase-substrate interactions is described in Chapter 8. While identifying protein kinases from genomic data occurrence of protein kinase-like non-kinases (PKLNK), which lack aspartate in a specific position in the amino acid sequence (and hence are unlikely to function as a kinase), has also been observed. Chapter 9 presents an analysis of PKLNKs with an objective of obtaining clues to their functions. Chapter 10 summarizes the main conclusions of the thesis and provides an outlook of the current study. Chapter 1: Chapter 1 provides an introduction to cell signaling and the involvement of protein kinases in various signaling pathways compiled from author’s literature survey. This chapter provides a description of molecular events in cell signaling in prokaryotic and eukaryotic organisms. The diversity, specificity and cellular roles of protein kinases are discussed in detail. Chapter 2: Chapter 2 describes KinG (Kinases in Genomes) database which was first established by Krupa et al (2004a). The KinG database is an on-line compilation of the putative Serine/Threonine/Tyrosine protein kinases encoded in the completely sequenced genomes of archaea, eubacteria, viruses and eukaryotes. Surge in the datasets of genomes, improvements in the quality of the genomic data for various organisms and growing number of protein domain families necessitates periodic update of KinG database. The updated version of KinG holds information on protein kinases for 483 organisms (Anamika et al, 2008c). Availability of draft version of the human genome data in 2001 enabled recognition of repertoire of human protein kinases (Krupa and Srinivasan, 2002a; Manning et al, 2002; Kostich et al, 2002). Over the last 7 years human genomic data is being refined and at present the quality of the human genomic data available is much superior to the one available in 2001. By gleaning the latest version of human genome data, 46 new human protein kinase splice variants have been identified which were not recognized in the earlier studies on human kinome. Improper regulation or mutant forms of many of these newly identified protein kinase splice variants are directly involved in various diseases such as different kinds of cancer, Severe Combined Immunodeficiency Disease (SCID) and Huntington disease. In addition, abnormal forms of mouse orthologues of some of the newly identified human kinase splice variants are known to cause various diseases in mice. This raises the possibility of the human orthologues playing similar roles in the disease processes. Such observations and detailed analysis of these protein kinase splice variants would have a profound influence on drug design and development against various diseases. Chapter 3: Investigations on the identification and analysis of protein kinases encoded in the genome of chimpanzee (chimp) has been discussed in Chapter 3. Further, the kinome complement has been compared between chimp and its evolutionary close relative, human (Anamika et al, 2008b). The shared core biology between chimp and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains present in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain (PKLNK). Remarkably, for 160 out of 587 chimpanzee kinases no human orthologue with sequence identity greater than 95% could be identified. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin / Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Though chimpanzee and human have close evolutionary relationship, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This chapter provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles. Chapter 4: Chapter 4 describes genome-wide comparative analysis for protein kinases encoded in the two apicomplexa namely Plasmodium falciparum (P. falciparum) (3D7 strain) and Plasmodium yoelii yoelii (P. yoelii yoelii) (17XNL strain) genomes which are causative agents of malaria in human and rodent respectively (Anamika and Srinivasan, 2007). Sensitive bioinformatics techniques enable identification of 82 and 60 putative protein kinases in P. falciparum and P. yoelii yoelii respectively. These protein kinases have been classified further into subfamilies based on the extent of sequence similarity of their catalytic domains (Hanks et al, 1988). The most populated kinase subfamilies in both the Plasmodium species correspond to CAMK and CMGC groups. Analysis of domain architectures enables detection of uncommon domain organisation in kinases of both the organisms such as kinase domain tethered to EF hands as well as pleckstrin homology domain. Components of MAPK signaling pathway are not well conserved in Plasmodium species. Such observations suggest that Plasmodium protein kinases are highly divergent from other eukaryotes. A trans-membrane kinase with 6 membrane spanning segments in P. falciparum seems to have no orthologue in P. yoelii yoelii. 19 P. falciparum kinases (Anamika et al, 2005; Anamika and Srinivasan, 2007) have been found to cluster separately from P. yoelii yoelii kinases and hence these kinases are unique to P. falciparum genome. Only 28 orthologous pairs of kinases could be identified between these two Plasmodium species. Comparative kinome analysis of the two Plasmodium species has thus provided clues to the function of many protein kinases based upon their classification and domain organisation and also implicate marked differences even between two Plasmodium species. Chapter 5: Identification and analysis of the repertoire of protein kinases in the intracellular parasite Entamoeba histolytica (E. histolytica) using sensitive sequence and profile search methods forms the basis of Chapter 5. A systematic analysis of a set of 307 protein kinases in E. histolytica genome has been carried out by classifying them into different subfamilies originally defined by Hanks and Hunter (Hanks et al, 1988) and by examining the functional domains which are tethered to the catalytic kinase domains (Anamika et al, 2008a). Compared to other eukaryotic organisms, protein kinases from E. histolytica vary in terms of their domain organisation and displays features that may have a bearing in the unusual biology of this organism. Some of the parasitic kinases show high sequence similarity in the catalytic domain region with calmodulin/calcium dependent protein kinase subfamily. However, they are unlikely to act like calcium/calmodulin dependent kinases as they lack non-catalytic domains characteristic of such kinases in other organisms. Such kinases form the largest subfamily of protein kinases in E. histolytica. Interestingly a Protein Kinase A/Protein Kinase G-like hybrid kinase subfamily member is tethered to pleckstrin homology domain. Although potential cyclins and cyclin-dependent kinases could be identified in the genome the likely absence of other cell cycle proteins suggests unusual nature of cell cycle in E. histolytica. Some of the unusual kinases recognized in the analysis include the absence of Mitogen activated protein kinase kinase (MEK) as a part of the Mitogen Activated Kinase signaling pathway and identification of trans-membraneous kinases with catalytic kinase region showing a good sequence similarity to Src kinases which are usually cytosolic. Sequences which could not be classified into known subfamilies of protein kinases have unusual domain architectures. Many such unclassified protein kinases are tethered to domains which are cysteine-rich and to domains known to be involved in protein-protein interactions. The current chapter on kinome analysis of E. histolytica suggests that the organism possesses a complex protein phosphorylation network that involves many unusual protein kinases. Chapter 6: Protein kinases phosphorylating Serine/Threonine/Tyrosine residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Classification based on sequence similarity of their catalytic domains, results in clustering of protein kinases sharing gross functional properties into various subfamilies. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules, aiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their molecular interaction which has been discussed in Chapter 6. Recent studies on repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation in model organisms across various subfamilies. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by the protein kinase in order to regulate variety of biological processes. In addition, domain architectures of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. The repertoire of non-kinase domains tethered to multi-domain kinases in the higher eukaryotes is discussed in Chapter 6. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. Chapter 7: Chapter 7 describes systematic classification of Serine/Threonine protein kinases encoded in archaeal and eubacterial genomes. Majority of the Serine/Threonine protein kinases which have been identified in archaeal and eubacterial genomes could not be classified into any of the well known subfamilies (Hanks et al, 1988) of protein kinases suggesting their diversity from kinases in eukaryotes. The extensive prokaryotic Serine/Threonine protein kinase dataset obtained from KinG (Krupa et al, 2004a, Anamika et al, 2008c) has given an opportunity to classify these prokaryotic Serine/Threonine protein kinases mainly into three categories based upon sequence identity based clustering: 1) Species/Genus-specific clusters: Species/Genus-specific Serine/Threonine protein kinases contain members from a particular species or genus of the eubacteria or archaea suggesting requirement of these Serine/Threonine protein kinases for certain lineage specific function. 2) Organism-specific clusters: Organism specific clusters has members from certain specific types of organisms which suggests role of these Serine/Threonine protein kinases in some specific function being carried out by limited sets of prokaryotes. 3) Organism-diverse clusters: Organism diverse clusters suggest common function performed by such kinases in wide variety of organisms. Interestingly, occurrence of several species/genus or organism specific subfamilies of prokaryotic kinases contrasts with classification of eukaryotic protein kinases in which most of the popular subfamilies of eukaryotic protein kinases occur diversely in several eukaryotes. Function-based classification has also been proposed which shows that members of each cluster has specific function to perform. In this analysis, almost 50% of the “clusters” obtained have only one member suggesting their sequence and probably functional divergence. Many prokaryotic Serine/Threonine protein kinases exhibit a wide variety of modular organisation which indicates a degree of complexity and protein-protein interactions in the signaling pathways in these microbes. Chapter 8: A wide spectrum of protein kinases belonging to different Hanks and Hunter groups of kinases and subfamilies has been identified in various eukaryotes. However, specific biological targets (substrates) of many protein kinase subfamilies are still unknown and this is one of the active areas of research. In the current analysis reported in Chapter 8, an attempt has been made to understand protein kinase-substrate interaction and substrate consensus prediction by analyzing known 3-D structures of complexes of kinases and peptide substrates/pseudosubstrates. Considering protein kinase ternary complex structures in their active states, it has been observed that protein kinase residues which are interacting with the substrate residues having constraint are at topologically equivalent positions despite belonging to different Hanks and Hunter protein kinase subfamilies. In this analysis, it has also been observed that the residues in a given kinase subfamily interacting with consensus substrate residues are usually conserved across homologues. Interestingly, in Protein Kinase B and Phosphorylase Kinase subfamily homologues, residues interacting with substrate residue/s having no constraint are not well conserved even within the kinase subfamily suggesting different evolutionary rate of substrate interacting residues. This result is anticipated to be helpful in furthering our understanding of protein kinase-substrate relationship which is likely to be helpful in drug design. Chapter 9: Protein Kinase-Like Non-kinases (PKLNKs) are closely related to protein kinases but they lack the crucial catalytic aspartate in the catalytic loop and hence cannot function as a protein kinase. PKLNKs have been analyzed (Chapter 9) with an objective of obtaining clues about their functions. Using various sensitive sequence analysis methods, 82 PKLNKs from four higher eukaryotic organisms namely, Homo sapiens, Mus Musculus, Rattus norvegicus and Drosophila melanogaster have been recognized. On the basis of their domain combinations and functions of tethered domains, PKLNKs have been classified mainly into four categories: 1) Ligand binding PKLNKs 2) PKLNKs having extracellular protein-protein interaction domain 3) PKLNKs involved in dimerization 4) PKLNKs with cytoplasmic protein-protein interaction module. While members of the first two classes of PKLNKs have transmembrane domain tethered to the PKLNK domain, members of the other two classes of PKLNKs are entirely cytoplasmic in nature. The current classification scheme hopes to provide a convenient framework to classify the PKLNKs from other eukaryotes and it should be helpful in deciphering their roles in cellular processes. Chapter 10: This is a chapter on conclusions of the entire thesis work. Summary of the major outcomes of this thesis work is provided and implications of the work in the area of signal transduction are discussed. In addition to above mentioned work, studies on repertoire of protein kinases from two plant organisms have been carried out and the kinomes have been comparatively analyzed (Krupa et al, 2006) (Appendix 1). Comparison of plant protein kinases with other eukaryotes revealed remarkable differences. Trans-genomic comparison of the protein kinase repertoires of Arabidopsis thaliana and Oryza sativa has enabled identification of members that are uniquely conserved within the two species. Analysis on the domain organisation of plant protein kinases has also been carried out. Appendix 2 presents the work done on Entamoeba histolytica (E. histolytica) ornithine decarboxylase (ODC)-like protein which regulates the polyamine biosynthesis. DFMO (Difluoromethylornithine) is unable to inhibit the E. histolytica ODC-like protein while it inhibits the homologues of ODC in other organisms. Modelling study has suggested substitution of three amino acids in the E. histolytica ODC-like protein because of which DFMO is unable to inhibit the activity of ODC-like protein (Jhingran et al, 2008). All the computational modeling work reported in Appendix 2 was performed by the author while all the laboratory experiments were performed in the laboratory of the collaborator Prof. Madhubala of JNU, New Delhi. The supplementary data pertaining to this thesis is presented in an accompanying CD. The supplementary data in this CD is organized into different folders corresponding to various chapters.