The transition from a hunter-gatherer lifestyle to a farming lifestyle, i.e. the Neolithisation, is arguably the most important event in human prehistory. While the geography and dating of the Neolithisation is well known, the process is still under debate, especially if it occurred through diffusion of ideas or with migrating farmers. The process accelerated when alternative use of domesticated animals increased. Especially the use of dairy products, and the consumption of unprocessed milk, appears to be of importance. As milk consumption (lactose digestion) is dependent upon genetic components, it is debated whether the genetic disposition allowed for dairy production to evolve, or if the usages of dairy products added selection pressure that eventually lead to present day allele frequencies. Molecular genetics have the potential to solve this and similar questions, but only if the contamination problem, where authentic DNA can be distinguished from modern contaminating DNA, can be resolved. Here I investigate the nature and extent of contamination with modern human DNA in museum specimens and explore several approaches to minimise this contamination and to authenticate DNA results from ancient humans. I use real-time quantification, pyrosequencing and FLX-generated clonal sequencing assays to generate data on ancient humans and ancient dogs. I further use the techniques to study the development of lactase persistence and the nature of animal domestication. The results presented show that sample-based contamination is extensive, but can be minimised if treated with bleach. I retrieved authentic HVSI sequences from 30 Neolithic hunter-gatherers and farmers from Sweden, of which eighteen also yielded nuclear data indicating that the farmers had a higher frequency of the allele linked to lactase persistence compared to the hunter-gatherers. I conclude that genetic data from ancient humans as well as from ancient animals can be retrieved and used, but only under high stringency.

Les céréales domestiques, blé et orge, sont apparues sur plusieurs sites éloignés du Proche-Orient à partir de précurseurs sauvages originaire d'Anatolie. Cette thèse propose que la domestication de ces céréales est le résultat de quatre étapes successives et indépendantes: 1) au Natoufien ancien, une sédentarisation a augmenté la fertilité en rapprochant les naissances. Ceci a créé un nouveau besoin en aliments de sevrage qui a rendu les céréales indispensables comme ressource alimentaire. La croissance démographique a fait évoluer la structure sociale des communautés des groupes familiaux à des groupes locaux; 2) au Natoufien récent, la crise environnementale du Dryas récent a obligé certaines communautés à combler leurs besoins en céréales avec les premières mises en culture. Ces communautés ont réussi à maintenir leur vie sédentaire, leur population et leurs capacités technologiques en rigidifiant leur structure sociale en chefferies; 3) au PPNA, une expansion coloniale des communautés qui ont survécu au Dryas récent a transplanté les céréales sauvages dans l'ensemble du Proche-Orient en les adaptant à des sols et des climats nouveaux; 4) au PPNB, la recherche d'une plus grande productivité et un heureux hasard ont fait apparaître les céréales domestiques sur quelques sites. La domestication des céréales au Proche-Orient est donc le résultat d'un processus évolutif qui a modifié à la fois le contexte socio-culturel des communautés humaines et leur relation aux céréales. / Domestic cereals, wheat and barley, appeared at several distant sites in the Near East from wild progenitors from Anatolia. This thesis suggests that domestication of these cereals was the result of four successive and independant steps: 1) during early Natufian, sedentarisation raised fertility by decreasing the time inteval between consecutive births. This created a new need for weaning foods, so that cereals became a necessary part of subsistance. The increase in population led the social structure of communities to evolve from family groups into local groups; 2) during late Natufian, the Younger Dryas environmental crisis forced some communities to meet their needs for cereals by initiating their first cultivations. These communities could remain sedentary and maintain both their population and their technological potential by rigidifying their social structures into chiefdoms; 3) during PPNA, a colonial expansion of communities that survived the Younger Dryas transplanted wild cereals throughout the Near East and adapted them to new soils ans climates; 4) during PPNB, the search for an increased productivity and some chance led to the appearance of domestic cereals at some sites. Cereal domestication in the Near East thus appears as resulting from an evolutionary process which modified both the socio-cultural context of human communities and their relationship to cereals.

À partir de 12000 BC. se mettent en place au Proche-Orient de profondes mutations sociales, économiques, techniques et culturelles qui, sur près de 5 millénaires, ont conduit à l’émergence de sociétés sédentaires dont l’économie alimentaire va reposer sur l’agriculture et l’élevage. Ce processus, la Néolithisation, s’observe au Levant Nord, notamment dans le village de Dja’de, occupé durant un millénaire par des chasseurs-cueilleurs en passe de devenir agriculteurs et éleveurs. Si l’industrie en silex des niveaux PPNB ancien (9e mill.) a déjà fait l’objet d’études technologiques et typologiques, aucune analyse tracéologique n’a été menée jusqu’à ce jour sur cet assemblage. Dans ce contexte où les rapports entre les hommes et leur environnement ont été profondément bouleversés, l’étude de la fonction des outils en pierre permet d’appréhender la nature de ces changements. Au cours de ce processus, il apparaît que la gestion de l’outillage devient plus complexe : l’intensité d’utilisation des outils s’accroit, le degré de réaffutage augmente, le recyclage est plus fréquent, les modalités de stockage évoluent. Cette analyse de l’outillage en silex de Dja’de a associé une approche fonctionnelle aux aspects habituellement étudiés (technologie et typologie). Pour cette phase encore mal connue du Néolithique précéramique, l’analyse des traces d’utilisation, appuyée sur l’expérimentation, a permis d’obtenir des éléments de réflexion nouveaux sur les activités au sein du village, sur les techniques mises en oeuvre par ses habitants et sur la gestion de l’industrie lithique et ainsi de mieux comprendre le mode de vie et l’organisation des sociétés préagricoles au Levant Nord. / Starting from 12000 BC. deep social, economic, technical and cultural mutations took place that will lead to the emergence of sedentary societies in which the food economy will rely on agriculture and farming. This process –known as Neolithisation – can be observed in Northern Levant, particularly in the village of Dja’de that has been occupied during one millennium by hunters-gatherers who will eventually become farmers. Although the chipped stone industry of the early PPNB (9e millennium) has already been the object of technological and typological studies, no use-wear analysis has yet been done. In the context where relationship between humans and their environment changed, the study of the function of stone tools is primordial to understand the nature of these changes. During this process, it appears that the management of the tools becomes more complex: the use of the tools intensifies, the degree of sharpening increases, the recycling is more frequent, and the storage modalities evolve. This analysis of flint tools from Dja’de combined a functional approach with other aspects usually studied (technology and typology). For this period of the aceramic Neolithic that is still not well documented, the analysis of the traces of use, backed up by experimentation, has brought us new insights about the village activities, the techniques used by its inhabitants and the management of the lithic production, providing us a better understanding of the way of life and the organisation of pre-agricultural societies in Northern Levant.

La Syrie intérieure est composée d’une mosaïque de milieux et de micromilieux dont les caractéristiques lithologiques, édaphiques et hydrologiques permettent de compenser l’aridité climatique, ou renforcent au contraire les contraintes imposées aux modes de vie et de subsistance, de nos jours comme par le passé. Cette étude multiscalaire – supra-régionale, régionale et microrégionale – de l’environnement des sites PPNA et PPNB (9 500-6 500 av. J.-C.) a permis de comprendre comment ont pu être opérés les choix d’implantation, définies les stratégies de subsistance et l’exploitation des ressources. Au-delà des critères évidents orientant les choix des lieux d’implantation, tel que l’accès à une ressource en eau, il a été démontré que les communautés néolithiques ont très tôt sélectionné des lieux d’installation bénéficiant de milieux propices aux pratiques agricoles et de terroirs complémentaires permettant de mettre en œuvre des stratégies culturales diversifiées. Leur capacité d’adaptation à un milieu contraignant, le développement progressif des activités agro-pastorales ainsi que leur maîtrise croissante de l’eau, leur ont permis de coloniser l’ensemble de la Syrie intérieure aux PPNB récent et final. Les prémices du nomadisme pastoral seraient nées dans ce contexte, et dès lors que l’élevage fut maîtrisé, d’une recherche par les groupes mobiles du mode de vie et de subsistance le plus adapté aux contraintes de la steppe. Cette étude a par ailleurs permis de tester à grande échelle – spatiale et temporelle – une méthode d’analyse microrégionale, s’inspirant de la démarche de type Site Exploitation Territory, et d’en faire l’analyse critique avec comme objectif l’élaboration ultérieure d’un modèle d’analyse plus abouti, si possible en concertation avec les spécialistes des disciplines concernées par ces problématiques / Inland Syria is made up of an environment and microenvironment mosaic with specific lithological, edaphic and hydrological characteristics which compensate climatic aridity or, on the contrary, increase the pressure imposed on settlement and subsistence strategies, nowadays as in the past. This multiangelfish study – supra-regional, regional and microrégional – of PPNA and PPNB (9 500-6 500 BC) sites environment allowed to understand settlement choices, subsistence patters and resources exploitation. Beyond the obvious criteria that have oriented the choices of settlement places, like the access to a water resource, it was demonstrated that the Neolithic communities have early selected settlement places with environment suitable for crop processing and complementary land to conduct varied farming strategies. Their adaptability to a restrictive environment, the progressive development of agro-pastoral activities and also their increasingly water controlling, allowed them to colonize the whole inland Syria during recent and final PPNB. The beginnings of pastoral nomadism could have emerged in this context, since the husbandry is well controlled, from the research by mobile groups of the best adapted settlement and subsistence pattern to the steppe pressure. In addition, this study has allowed us to carry out a large scale test – spatial and temporal – of a microrégional analysis method, based on a Site Exploitation Territory approach, in order to elaborate in the future a complete analysis model, in collaboration with the specialists involve in those kind of study

The importance of the elk (Alces alces) in the Stone Age societies of northern Sweden constitutes the major focus of this thesis. The point of departure is a simple but crucial observation: this animal is the common denominator between the three stationary types of remains known in this region from the period 4000-1800 BC. Here, I refer to the pit falls, the rock art sites, and the mounds of burnt stone. Pit falls have been used for trapping elks, and can be found on the migration trails that have been used by these animals for thousands of years. On the rock art sites, the elk constitutes the most frequently depicted motif, and the mounds of burnt stones contain extremely large quantities of elk bones. If the elk had not held a central position in the life world of prehistoric people in the northern Swedish region of Norrland, these archaeological materials would certainly have had a different appearance. I claim that it is the significance of this animal that has led to, and shaped, the emergence of these material remains. In this study the overall importance of the elk is investigated. My main question is how the elk’s significance affected the prehistoric societies of Norrland. I found that the elk’s material remains led to a range of consequences. The pit falls, rock art sites and mounds of burnt stone tied the prehistoric people to certain areas in the landscape. However, at the same time, these remains required to be constantly in transformation to be usable. Pit falls, for example, have to be re-digged in order to at all function as traps for big game. The conceptual dichotomy between permanence and change can be traced in the ways in which the elk motif at the rock art site at Nämforsen was altered. The elk figures are depicted with either straight or angled legs. I interpret this variation as an indication of the fact that the elk motif functioned as a key symbol – a motif that is able to express a range of meanings when it becomes altered and varied. The emergence of depicting the opposition between mobility and permanence tells us that the Stone Age societies had problems uniting these two concepts. I interpret this as signifying that these hunter-gatherers became aware of the “Neolithic aspects” of their own social structure.

La Néolithisation au Proche-Orient est une période phare de l’histoire de l’humanité : c’est en effet à ce moment qu’interviennent de grands changements dans l’économie de subsistance, apportés par l’invention de l’agriculture et de l’élevage. D’autres changements dans le mode de vie sont également engendrés par la sédentarisation et, en dernier lieu, par l’invention de la céramique en tant que récipient. Ces bouleversements que connaissent les populations néolithiques s’observent aussi bien dans l’état sanitaire que dans les pratiques funéraires. Le travail entrepris a donc consisté à étudier les sépultures et les restes humains provenant de sept sites syriens répartis sur toute la période de la Néolithisation. Les pratiques funéraires se complexifient tout au long de la période, bien que les sépultures primaires et individuelles, avec un dépôt des corps en position fléchie sur le côté, soient longtemps restées la norme. Dès le PPNA, des sépultures sont directement associées à certains bâtiments, avant que des lieux d’inhumations spécifiques apparaissent à la fin du PPNB. L’étude anthropologique s’est concentrée sur les pathologies infectieuses osseuses et dentaires ainsi que sur les indicateurs de stress, selectionnés parmi les marqueurs les plus pertinents. Ainsi la tuberculose, la périostite, les caries, les abcès, la perte de dents ante-mortem, la maladie parodontale, les hypoplasies de l’émail dentaire, la Cribra orbitalia et l’hyperostose poreuse ont été systématiquement recherchés sur les squelettes. Après une étude des changements dans l’état de santé des populations site par site, les individus ont été regroupés par périodes afin de mettre en évidence l’impact de la Néolithisation dans une étude diachronique. L’avènement de l’agriculture semble avoir entrainé une augmentation des pathologies dentaires et des indicateurs de stress à la période du PPNB ancien, tandis qu’un pic de stress, enregistré au PPNB moyen, pourrait être relié à l’introduction de l’élevage, qui a pu entrainer des carences alimentaires et peut-être l’apparition de nouvelles maladies infectieuses. De même, la plupart des indicateurs laissent entrevoir une certaine dégradation de l’état sanitaire lors de la dernière période étudiée, le Néolithique céramique. Ce travail a permis de mettre en évidence que les changements intervenus dans l’état de santé sont loin d’être linéaires ; des fluctuations se produisent entre les périodes selon les différents indicateurs, et c’est au PPNB qu’apparaissent les bouleversements les plus importants. Il semblerait en outre que le degré de gravité des pathologies évolue de façon non linéaire tout au long de la Néolithisation. / The Neolithisation of the Near-East is a key period in the history of humanity, when huge changes occur in subsistence economy, triggered by agriculture and animal husbandry. Other changes in lifestyle are generated by sedentarization and eventually by the invention of pottery as container. The disruptions known by the Neolithic populations are to be found both in their health status and funerary practices. The sepultures and human remains from seven Syrian archaeological sites are studied in this work over the entire period of Neolithisation. The funerary practices become more complex over time, although the primary individual sepultures, with the corpse laid in a flexed position on one side, remain the standard for a long time. From the PPNA, some sepultures are directly associated with particular buildings, until specific burial areas appear towards the end of the PPNB. The bioanthropological study focuses on infectious diseases affecting bones and teeth and on stress indicators, with a selection of the most relevant features. The skeletons were thus systematically examined for signs of tuberculosis, periostitis, dental caries and abcesses, ante-mortem tooth loss, periodontal disease, dental hypoplasia, Cribra orbitalia and porotic hyperostosis. A site by site study of health status changes was carried out first, then the individuals were gathered by period in order to bring to light the impact of the Neolithisation processes in a diachronic study. The advent of agriculture seems to have entailed an increase in dental pathologies and stress indicators in the early PPNB, and a peak of stress registered in the middle PPNB could be related to the introduction of animal husbandry, creating dietary deficiency and new infectious diseases. Most of the markers indicate a deterioration in health status during the last studied period, the Pottery Neolithic. This work establishes that changes in health status were far from linear; the different indicators pointing to fluctuations between the periods, with the most important changes featuring in the PPNB. Furthermore, it suggests that the severity of the pathologies evolved in a non linear way throughout the Neolithisation.

Isotope analyses on human and faunal skeletal remains from different Swedish Neolithic archaeological contexts are here applied as a means to reconstruct dietary strategies and mobility patterns. The chronological emphasis is on the Middle Neolithic period, and radiocarbon dating constitutes another central focus. The results reveal a food cultural diversity throughout the period in question, where dietary differences in part correspond to, but also transcend, the traditionally defined archaeological cultures in the Swedish Early to Middle Neolithic. Further, these differences, and the apparent continued utilisation of marine resources in several regions and cultural contexts, can only in part be explained by chronology or availability of resources depending on geographic location. Thus, the sometimes suggested sharp economic shift towards an agricultural way of life at the onset of the Neolithic is refuted. Taking the potential of isotope analyses a step further, aspects of Neolithic social relations and identities are discussed, partly from a food cultural perspective embarking from the obtained results. Relations between people and places, as well as to the past, are discussed. The apparent tenacity in the dietary strategies observed is understood in terms of their rootedness in the practices and social memory of the Neolithic societies in question. Food cultural practices are further argued to have given rise to different notions of identity, some of which can be related to the different archaeological cultures, although these cultures are not to be perceived as bounded entities or the sole basis of self-conceptualisation. Some of these identities have been focused around the dietary strategies of everyday life, whereas others emanate from practices, e.g. of ritualised character, whose dietary importance has been more marginal. Isotope analyses, when combined with other archaeological indices, have the potential to elucidate both these food cultural aspects. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Submitted. Paper 5: In press. Paper 6: Accepted.

Des preuves archéopalynologiques directes appuient maintenant l’hypothèse d’une lente adaptation horticole durant la néolithisation amérindienne de la région de Montréal. Les sites archéologiques Hector-Trudel (BhFl-1a) de Pointe-du-Buisson et Séminaire de Saint-Sulpice (BjFj-18) dans le Vieux-Montréal ont été retenus pour élaborer une méthodologie archéopalynologique d’étude des sols archéologiques. Cela a permis de caractériser l’impact de la présence humaine sur l'environnement végétal des sites et d’identifier des indices de culture et de gestion de plantes allogènes et indigènes. Un complexe horticole de production à petite échelle de maïs (Zea mays), de tournesol (Helianthus annuus) et de petit tabac (Nicotiana rustica) et une forme de gestion des arbustes à petits fruits sont identifiés au site Hector-Trudel durant le Sylvicole moyen tardif (500 à 1000 A.D.). Ces cultigènes sont aussi identifiés au site du Séminaire pour la fin du Sylvicole supérieur ancien (1200 à 1300 A.D.), dans des proportions toutefois plus importantes, et une activité de gestion forestière au profit des arbres à noix et du tilleul d’Amérique (Tilia americana), reflet des pratiques d’entretien des champs cultivés, témoignent d’une évolution dans les comportements / Direct archaeopalynological proof now supports the hypothesis of a slow horticultural adaptation during the Native American neolithisation of the Montreal area. Archaeological sites Hector-Trudel (BhF1-la) of Pointe-du-Buisson and Séminaire de Saint-Sulpice (BjFj-18) in Old Montreal were retained to elaborate an archaeopalynological methodology of archaeological soil study. This has allowed to characterize the impact of human presence of a vegetal environment on the sites and to identify signs of cultivation and management of alien and indigenous plants. A horticultural complex producing corn (Zea mays), sunflower (Helianthus annuus) and native tobacco (Nicotina rustica) on a small scale and a form of fruit-bearing shrubs management are identified at the Hector-Trudel site during the Late Middle Woodland (A.D. 500 to 1000). These cultigens are also identified at the Séminaire site for the end of the Early Late Woodland (A.D. 1200 to 1300), though in bigger proportions, and a woodland management activity benefiting nut trees and the American basswood (Tilia americana), reflecting cultivated field maintenance practices, are evidence of an evolution in behaviors.

Des preuves archéopalynologiques directes appuient maintenant l’hypothèse d’une lente adaptation horticole durant la néolithisation amérindienne de la région de Montréal. Les sites archéologiques Hector-Trudel (BhFl-1a) de Pointe-du-Buisson et Séminaire de Saint-Sulpice (BjFj-18) dans le Vieux-Montréal ont été retenus pour élaborer une méthodologie archéopalynologique d’étude des sols archéologiques. Cela a permis de caractériser l’impact de la présence humaine sur l'environnement végétal des sites et d’identifier des indices de culture et de gestion de plantes allogènes et indigènes. Un complexe horticole de production à petite échelle de maïs (Zea mays), de tournesol (Helianthus annuus) et de petit tabac (Nicotiana rustica) et une forme de gestion des arbustes à petits fruits sont identifiés au site Hector-Trudel durant le Sylvicole moyen tardif (500 à 1000 A.D.). Ces cultigènes sont aussi identifiés au site du Séminaire pour la fin du Sylvicole supérieur ancien (1200 à 1300 A.D.), dans des proportions toutefois plus importantes, et une activité de gestion forestière au profit des arbres à noix et du tilleul d’Amérique (Tilia americana), reflet des pratiques d’entretien des champs cultivés, témoignent d’une évolution dans les comportements / Direct archaeopalynological proof now supports the hypothesis of a slow horticultural adaptation during the Native American neolithisation of the Montreal area. Archaeological sites Hector-Trudel (BhF1-la) of Pointe-du-Buisson and Séminaire de Saint-Sulpice (BjFj-18) in Old Montreal were retained to elaborate an archaeopalynological methodology of archaeological soil study. This has allowed to characterize the impact of human presence of a vegetal environment on the sites and to identify signs of cultivation and management of alien and indigenous plants. A horticultural complex producing corn (Zea mays), sunflower (Helianthus annuus) and native tobacco (Nicotina rustica) on a small scale and a form of fruit-bearing shrubs management are identified at the Hector-Trudel site during the Late Middle Woodland (A.D. 500 to 1000). These cultigens are also identified at the Séminaire site for the end of the Early Late Woodland (A.D. 1200 to 1300), though in bigger proportions, and a woodland management activity benefiting nut trees and the American basswood (Tilia americana), reflecting cultivated field maintenance practices, are evidence of an evolution in behaviors.