L’étude de la composition isotopique de l’oxygène de l’émail des dents de vertébrésconstitue une méthode fiable de reconstitution des paléotempératures, grâce àl’interdépendance entre le δ18O de l’apatite des dents, le δ18O des fluides corporels, del’eau ingérée et la température du milieu. L’amélioration et la miniaturisation des techniquesanalytiques a permis d’augmenter la résolution du signal reconstitué, depuis les variations detempérature sur de grandes échelles de temps jusqu’aux variations saisonnières durant laformation de la dent. Cependant, ces variations du δ18O de la dent ne sont pas uniquementdépendantes des variations de température du milieu, mais peuvent également êtreaffectées par d’autres paramètres climatiques, comme la répartition des précipitations aucours de l’année, ou biologique, comme le mode de minéralisation de la dent, l’alimentation,la physiologie de l’animal ou des migrations.Les paramètres biologiques peuvent être estimés dans le cas de taxons possédantdes parents proches dans la faune actuelle. Par exemple, la connaissance des processus deformation et de minéralisation des dents de bovinés actuels permet d’interpréter le signalisotopique de l’oxygène enregistré dans les dents de bovinés fossiles. Ainsi, l’analyse dedents de Bison priscus provenant de l’aven de Coudoulous (Lot, France) a permis dereconstituer les variations saisonnières de température au cours de l’avant-dernier épisodeglaciaire (MIS 6) au Pléistocène moyen, lorsque la région servait de terrain de chasse àHomo neanderthalensis. Le climat était à cette époque plus froid de 4°C en moyenne, maisavec des saisons nettement plus contrastées. Ainsi, si les températures estivales étaientidentiques aux valeurs actuelles, les températures hivernales étaient plus basses de 6-7°C.En milieu marin, les variations saisonnières de température affectent uniquement leseaux de surface. Les plaques dentaires de myliobatidés, un groupe de raies pélagiquesvivant principalement entre 0 et 100 mètres de profondeur, sont un outil potentiel pourreconstituer la paléosaisonnalité. L’étude de plaques dentaires de Myliobatis et deRhinoptera actuels montre que la composition isotopique des dents de ces animauxenregistre des variations de température et de δ18O des eaux de surface. Ainsi, il est doncpossible de reconstituer les caractéristiques des masses d’eau traversées par l’animal. Cetoutil a également un intérêt paléoécologique car il permet de mettre en évidence d’éventuelscomportements migratoires, comme chez certains myliobatidés actuels. L’étude despécimens d’Aetomylaeus provenant du Pliocène de Montpellier (Hérault, France) montredes températures 5°C plus élevées par rapport aux v aleurs actuelles. / The oxygen isotopic composition of the vertebrate tooth enamel is a reliable proxy toreconstruct paleotemperatures based on the dependence of the δ18O of the tooth apatite onthe δ18O of body fluids, on the δ18O of the drinking water, and on the environmentaltemperature. The improvement and the miniaturization of the analytical procedures allowedincreasing the resolution of the reconstructed signal, from paleotemperature variations overgeological times to seasonal variations during the tooth growth. However seasonal variationsof the enamel δ18O do not only depend on temperature variations but can also be influencedby other climatic parameters such as rainfall distribution over the year, or by biological andecological parameters such as tooth mineralization process, diet, physiology or migratorypatterns.Biological parameters can be estimated based on the study of extant relatives inmodern faunas. For example, data on tooth formation and mineralization processes inmodern bovids allow a better understanding of the oxygen isotopic signal recorded in fossilbovid teeth. Thus reconstruction of seasonal variations of temperature during the penultimateglacial episode (MIS 6) has been made possible from the analysis of Bison priscus teethfrom the aven of Coudoulous (Lot, France). Climate was 4°C colder during the middlePleistocene when Europe was still Homo neanderthalensis hunting ground, and seasonswere more contrasted than today. Summer temperatures were similar to modern values, butwinter temperatures were 6-7°C colder.In marine environments, seasonal variations of temperature only affect surfacewaters. Myliobatids are pelagic rays living mostly between 0 and 100 m depth, thus theoxygen isotopic composition of myliobatid dental plates is a potential proxy to reconstruct thepaleoseasonality. The isotopic analysis of modern Myliobatis and Rhinoptera samplesconfirmed that variations of the sea-surface temperature (SST) and the δ18O of seawater arerecorded in the δ18O of myliobatid teeth. Thus it is possible to reconstruct the variations ofseawater temperature during a part of the animal’s life, but it also allows pointing outmigratory patterns in some myliobatid species. Reconstructions of seasonal variations ofSST during the middle Pliocene in Montpellier (Hérault, France) from the δ18O of myliobatiddental plates yielded paleotemperatures 5°C higher than modern values.

Humans evolved in a world of giant creatures. Current evidence suggests that most ice age megafauna went extinct around the transition to our current Holocene epoch. The ecological reverberations associated with the loss of over 65% of Earth’s largest terrestrial animals transformed ecosystems and human lifeways forever thereafter. However, there is still substantial debate as to the cause of this mass extinction. Evidence variously supports climate change and anthropogenic factors as primary drivers in the restructuring of the terrestrial biosphere. Much of the ongoing debate is driven by the insufficient resolution accessible via macro-remains. To help fill in the gaps in our understandings of the Pleistocene-Holocene transition, I utilized the growing power of sedimentary ancient DNA (sedaDNA) to reconstruct shifting signals of plants and animals in central Yukon. To date, sedaDNA has typically been analyzed by amplifying small, taxonomically informative regions. However, this approach is not ideally suited to the degraded characteristics of sedaDNA and ignores most of the potential data. Means of isolating sedaDNA have also suffered from the use of overly aggressive purification techniques resulting in substantial loss. To address these limitations, I first experimentally developed a novel means of releasing and isolating sedaDNA. Secondly, I developed a novel environmental bait-set designed to simultaneously capture DNA informative of macro-scale ecosystems. When combined, we identify a substantial improvement in the quantity and breadth of biomolecules recovered. These optimizations facilitated the unexpected discovery of horse and mammoth surviving thousands of years after their supposed extirpation. I followed up these results by extracting DNA from multiple permafrost cores where we confirm the late survival signal and identify a far more complex and high-resolution dataset beyond those identifiable by complementary methods. I was also able to reconstruct mitochondrial genomes from multiple megafauna simultaneously solely from sediment, demonstrating the information potential of sedaDNA. / Dissertation / Doctor of Philosophy (PhD) / A new addition to the rapidly growing field of palaeogenetics is environmental DNA (eDNA) with its immense wealth of biomolecules preserved over millennia outside of biological tissues. Organisms are constantly shedding cells, and while most of this DNA is metabolized or otherwise degraded, some small fraction is preserved through sedimentary mineral-binding. I experimentally developed new ancient eDNA methods for recovery, isolation, and analysis to maximize our access to these biomolecules and demonstrate that this novel approach outperforms alternative protocols. Thereafter, I used these methods to extract DNA from ice age permafrost samples dating between 30,000–6,000 years before present. These data demonstrate the power of ancient eDNA for reconstructing ecosystem change through time, as well as identifying evidence for the Holocene survival of caballine horse and woolly mammoth in continental North America. This late persistence of Pleistocene fauna has implications for understanding the human ecological and climatological factors involved in the Late Pleistocene mass extinction event. This effort is paralleled with megafaunal mitogenomic assembly and phylogenetics solely from sediment. This thesis demonstrates that environmental DNA can significantly augment macro-scale buried records in palaeoecology.