Denisova Cave is located in the Altai mountains of Russia. Excavations from this cave have yielded two large hominin molars and three hominin phalanxes from the Pleistocene. One of the phalanxes (Denisova 3) had extraordinary DNA preservation allowing the sequencing of high quality nuclear and mitochondrial DNA (mtDNA) genomes and has been shown to belong to a young girl from hereto unknown sister group of Neandertals, called Denisovans. The mtDNA of Denisova 3 surprisingly split from the mtDNA ancestor of modern humans and Neandertals twice as long ago as the split of modern humans and Neandertals. The mtDNA of one of the molars (Denisova 4) was also sequenced and differs at only two positions from the mtDNA of Denisova 3. A second phalanx (Altai 1) also yielded a high quality genome, and was a Neandertal. While Neandertals show an admixture signal of 1-4% into present-day non-Africans, Denisovans show an admixture of up to 5% in present-day Oceanians, and to a much lesser extent East Asians. This thesis encompasses two studies. In the first study, we sequenced the complete mtDNA genome of the additional molar (Denisova 8), as well as a few megabases of nuclear DNA from Denisova 4 and Denisova 8. While the mtDNA of Denisova 8 is clearly of the Denisova type, its branch to the most recent common ancestor of Denisovans is half as long as the branch leading to Denisova 3 or Denisova 4, indicating that Denisova 8 lived many millenia before the other two. Both Denisova 4 and 8 fall together with Denisova 3 based on nuclear DNA, bringing the number of known Denisovans from one to three. In the second study, we sequenced an almost complete mtDNA and a few megabases of nuclear DNA from the third hominin phalanx from Denisova Cave, Altai 2. Both the mtDNA and the nuclear DNA show Altai 2 to be a Neandertal. The mtDNA also showed the presence of substantial Pleistocene spotted hyena contamination. Low levels of spotted hyena contamination were also found in Altai 1, Denisova 3 and Denisova 4. Partial mtDNA genomes of the contaminating spotted hyenas from these four hominins were compared to mtDNA genomes of other extant and extinct spotted hyenas. We show that the spotted hyenas that contaminated the two Denisovans come from a population of spotted hyenas found in Pleistocene Europe as well as present-day Africa, while the spotted hyenas that contaminated Altai 2, and possibly Altai 1, come from a population of spotted hyenas found in Pleisticene eastern Russia and northern China. This indicates that Denisova Cave was a meeting point of eastern and western hominins as well as eastern and western spotted hyena populations.

abstract: The ability of Neandertals to cope with the oscillating climate of the late Pleistocene and the extent to which these climate changes affected local Neandertal habitats remain unanswered anthropological topics of considerable scientific interest. Understanding the impact of climatic instability on Neandertals is critical for reconstructing the behaviors of our closest fossil relatives and possibly identifying factors that contributed to their extinction. My work aimed to test the hypotheses that 1) cold climates stressed Neandertal populations, and 2) that global climate changes affected local Neandertal habitats. An analysis of Neandertal butchering on Cervus elaphus, Rangifer tarandus, and Capreolus capreolus skeletal material deposited during global warm and cold phases from two French sites - Pech de l'Az&eacute; IV and Roc de Marsal - was conducted to assess the impact of climate change on butchering strategies and resource extraction. Results from a statistical analysis of surface modification on all marrow yielding long bones, including the 1st phalanx, demonstrated that specimens excavated from the cold levels at each cave have more cut marks (Wald &chi;2= 51.33, p= <0.001) and percussion marks (Wald &chi;2= 4.92, p= 0.02) than specimens from the warm levels after controlling for fragment size. These results support the hypothesis that Neandertals were nutritionally stressed during glacial cycles. The hypothesis that global climates affected local habitats was tested through radiogenic strontium isotopic reconstruction of large herbivore mobility patterns (e.g., Bison, Equus, Cervus and Rangifer), because it is known that in the northern hemisphere, mammals migrate less in warm, well-vegetated environments, but more in cold, open environments. Identifying isotopic variation in mammalian fossils enables mobility patterns to be inferred, providing an indication of whether environments at Pech de l'Az&eacute; IV and Roc de Marsal tracked global climates. Results from this study indicate that Neandertal prey species within the Dordogne Valley of France did not undertake long distance round-trip migrations in glacial or interglacial cycles, maintaining the possibility that local habitats did not change in differing climatic cycles. However, because Neandertals were nutritionally stressed the most likely conclusion is that glacial cycles decreased herbivore populations, thus stressing Neandertals. / Dissertation/Thesis / Ph.D. Anthropology 2012

Denisova Cave is located in the Altai mountains of Russia. Excavations from this cave have yielded two large hominin molars and three hominin phalanxes from the Pleistocene. One of the phalanxes (Denisova 3) had extraordinary DNA preservation allowing the sequencing of high quality nuclear and mitochondrial DNA (mtDNA) genomes and has been shown to belong to a young girl from hereto unknown sister group of Neandertals, called Denisovans. The mtDNA of Denisova 3 surprisingly split from the mtDNA ancestor of modern humans and Neandertals twice as long ago as the split of modern humans and Neandertals. The mtDNA of one of the molars (Denisova 4) was also sequenced and differs at only two positions from the mtDNA of Denisova 3. A second phalanx (Altai 1) also yielded a high quality genome, and was a Neandertal. While Neandertals show an admixture signal of 1-4% into present-day non-Africans, Denisovans show an admixture of up to 5% in present-day Oceanians, and to a much lesser extent East Asians. This thesis encompasses two studies. In the first study, we sequenced the complete mtDNA genome of the additional molar (Denisova 8), as well as a few megabases of nuclear DNA from Denisova 4 and Denisova 8. While the mtDNA of Denisova 8 is clearly of the Denisova type, its branch to the most recent common ancestor of Denisovans is half as long as the branch leading to Denisova 3 or Denisova 4, indicating that Denisova 8 lived many millenia before the other two. Both Denisova 4 and 8 fall together with Denisova 3 based on nuclear DNA, bringing the number of known Denisovans from one to three. In the second study, we sequenced an almost complete mtDNA and a few megabases of nuclear DNA from the third hominin phalanx from Denisova Cave, Altai 2. Both the mtDNA and the nuclear DNA show Altai 2 to be a Neandertal. The mtDNA also showed the presence of substantial Pleistocene spotted hyena contamination. Low levels of spotted hyena contamination were also found in Altai 1, Denisova 3 and Denisova 4. Partial mtDNA genomes of the contaminating spotted hyenas from these four hominins were compared to mtDNA genomes of other extant and extinct spotted hyenas. We show that the spotted hyenas that contaminated the two Denisovans come from a population of spotted hyenas found in Pleistocene Europe as well as present-day Africa, while the spotted hyenas that contaminated Altai 2, and possibly Altai 1, come from a population of spotted hyenas found in Pleisticene eastern Russia and northern China. This indicates that Denisova Cave was a meeting point of eastern and western hominins as well as eastern and western spotted hyena populations.

No description available.

In this thesis we have addressed three different although related topics. First, we studied the post-mortem mutation damage rate of contaminated DNA sequences in ancient human remains focusing on the development of strategies to avoid pre-laboratory derived contaminations. We proposed a guideline to control them consisting in typing every single person involved on the manipulation of the remains, especially when they have not been excavated and washed under controlled conditions. Second, we successfully develop a non-invasive technique to sequence ancient remains but preserving it from the destruction. And third, we sequenced ancient human remains from different evolutionary times (from Paleolithic to post-Neolithic) to make inferences about the peopling of Western Europe focusing mainly in the Iberia peninsula. We found that there is a long term genetic continuity at least since the Neolithic. The only clear genetic discontinuity found is that involving two different human species, H. sapiens and H. neanderthalensis. / En la presente tesis hemos tratado tres temas diferentes aunque muy relacionados. Primero, hemos estudiado la tasa de mutación post-mortem de secuencias de ADN contaminante en restos humanos antiguos centrándonos en el desarrollo de estrategias para evitar que las muestras se contaminen antes de llegar al laboratorio. Proponemos una guía que consiste en el tipado genético de cada persona implicada en la manipulación de los restos, especialmente cuando estos han sido excavados y lavados bajo condiciones no controladas. Segundo, hemos desarrollado una técnica no invasiva para secuenciar DNA de restos humanos antiguos pero sin destruirlos. Y por ultimo, hemos secuenciado restos humanos antiguos pertenecientes a diferentes periodos evolutivos (desde el Paleolitico hasta el post-Neolitico) que nos han permitido hacer inferencias sobre el poblamiento Europeo centrándonos básicamente en la Península Ibérica. Hemos encontrado que ha habido una continuidad genética desde el Neolítico. La única clara discontinuidad genética encontrada es entre dos especies distintas: H. Sapiens y H.neanderthalensis.

Previous studies proposed that Neandertals had one third higher energetic cost of locomotion than anatomically modern humans. Greater cost of locomotion could disadvantage Neandertals in competition with anatomically modern humans and could be a factor in their extinction. Greater cost of Neandertal locomotion was ascribed to their shorter lower limb and greater body mass. However, Neandertals differed also in other morphological parameters that were not considered in estimation of their locomotor cost. In this dissertation we model locomotor cost of Neandertals and anatomically modern humans using previously described relation between muscle force production and energetic cost of movement. We estimate the key locomotor parameters using a model developed by us from osteometric data from literature (n =50) and from our measurement (n = 21), and from kinematic data of 26 individuals. Further, we analyze the effect of relative lower limb length (in relation to body mass) and crural index on energetic cost of locomotion. Our results suggest that walking of Neandertal males was 9-14% energetically more demanding than walking of anatomically modern males. Nevertheless, the walking cost of Neandertal females was similar to that of anatomically modern females. Inclusion of lower limb proportions into the...

Doctorat effectué en cotutelle Pour le département d'histoire de l'Université de Montréal, M.M. Jacques G. Ruelland et Othmar Keel, Pour le laboratoire P.A.C.E.A.– U.M.R. 5199. C.N.R.S., de l'École doctorale des sciences Terre-Mer, directeurs successifs, M. P.-Y. Demars, puis M. Michel Lenoir. Thèse soutenue à Bordeaux le 6 juin 2012. / Cette thèse a pour objectif d’étudier sur le plan historique une controverse scientifique persistante en préhistoire : le problème de la transition entre Paléolithiques moyen et supérieur, en tentant d’en expliquer la durée en termes de construction et de transformation des modèles antagoniques, ainsi que le rôle de cette controverse dans l’acquisition de connaissances, afin d’élucider comment s’est produit le déplacement des enjeux que présente son état actuel. Il s’agit de dresser un historique de la controverse entourant la transition entre Paléolithiques moyen et supérieur afin de circonscrire sur le plan chronologique les persistances et l’évolution des positions antagonistes dans leurs composantes épistémologiques. Pour clarifier cette démarche, il faut d’abord caractériser ce qui constitue cette controverse particulière pour les préhistoriens à l’aide de l’apport de l’histoire des sciences, et quelle méthode d’analyse sera utilisée dans le présent travail. Il sera ainsi possible de relier ces éléments au problème scientifique choisi comme sujet d’étude, présenté dans ses caractères généraux et spécifiques, pour modéliser la définition structurale des modèles explicatifs protagonistes au débat sur la transition entre Paléolithiques moyen et supérieur. La méthodologie proposée sera ensuite appliquée à la controverse, pour découper son déroulement chronologique en trois phases historiques distinctes par leur axe de recherche spécifique, chacune des phases étant décrite sur trois niveaux structuraux (données et méthodologie, paradigmes opératoires, paradigme métaphysique), afin d’isoler les constantes et les inflexions, et d’établir un modèle explicatif de sa dynamique historique jusqu’à son état actuel. L’ambition de cette thèse est de s’appuyer sur l’histoire des sciences pour clarifier sur le plan théorique pour les préhistoriens la dynamique historique de cette controverse centrale à l’étude du changement culturel en préhistoire, et des modèles qui s’y confrontent toujours, et tenter, à partir de l’étude de ce problème d’archéologie préhistorique, d’ébaucher en retour un modèle historique et structural d’étude de cas d’une controverse spécifique et de son apport au niveau du changement conceptuel en science qui pourrait être utile à l’histoire des sciences. / This thesis’ main object is to study on an historical level a long-lasting scientific controversy in Prehistoric archaeology, the Middle to Upper Palaeolithic transition, by attempting to explain the persistence of that debate in terms of construction and transformation of antagonistic models of explanation, and by showing how that controversy had play a role on the acquisition of knowledge, to elucidate how the debate itself had change since its origin. On a chronological scale, the evolution of some epistemological elements inside the confrontation of opposed hypothesis could be contrasted with conservative notions. To make that process clear, it is necessary to characterize what constitute that specific controversy for prehistorians with the tool given by the history of sciences, and what kind of analytical methodology can be call upon for doing so. Then, it will be possible to link those elements with the scientific problem itself to establish a structural model of this debate’s theoretical positions of the protagonists. This methodology could then be use to separate the history of that debate in three sections, each with its specific research axis, each phase in three structural level (data and methods, paradigms, meta-paradigm) to create a general model of the evolution of that controversy. The ambition of that thesis is to use history of science’s contribution as a way to clarify on a theoretical level the goals of that debate, and its implication on the study of cultural change for prehistorical archaeologists community, and to initiate for science’s historians a historical and structural model of scientific controversies, and their weight on conceptual change base on a specific case study.