Relevant bibliographies by topics / Paleogenomic

Academic literature on the topic 'Paleogenomic'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Paleogenomic"

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Clabby, Catherine. "Paleogenomic Puzzles." American Scientist 99, no. 3 (2011): 210. http://dx.doi.org/10.1511/2011.90.210.

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Dobrovolskaya, M. V., S. S. Kunizheva, T. V. Andreeva, and E. I. Rogaev. "Paleogenomic research in the context of modern Biomolecular Archaeology." VESTNIK ARHEOLOGII, ANTROPOLOGII I ETNOGRAFII, no. 1(56) (March 21, 2022): 244–49. http://dx.doi.org/10.20874/2071-0437-2022-56-1-21.

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Biomolecular Archaeology is a newly formed field of archaeological science. The 9th International Sympo-sium on Biomolecular Archaeology was held in June 2021 in Toulouse (France) with the participation of almost 500 delegates. Such conferences were originally organized in the beginning of the 21st c. for regular discussion the most relevant topics and the latest achievements in biomolecular archaeology. Thus, the materials of the symposium appear as a representative reflection of the processes taking place in modern science. Paleogenomics being one of the most actively developing components of biomolecular archaeology. The proposed review presents the most stri-king, in our opinion, reports on the topic, which enables understanding of the potential and prospects of modern pa-leogenomic research. Conclusions based on the results of paleogenomic studies are crucially important for the study of population formation, which makes it essential to comply with the rules of parity comprehensive research, which have been reflected in the publication of the basic ethical rules for organizing such studies.
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López-Sánchez, Paula, Javier C. Costas, and Horacio F. Naveira. "Paleogenomic Record of the Extinction of Human Endogenous Retrovirus ERV9." Journal of Virology 79, no. 11 (June 1, 2005): 6997–7004. http://dx.doi.org/10.1128/jvi.79.11.6997-7004.2005.

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ABSTRACT An outstanding question of genome evolution is what stops the invasion of a host genome by transposable elements (TEs). The human genome, harboring the remnants of many extinct TE families, offers an extraordinary opportunity to investigate this problem. ERV9 is an endogenous retrovirus repeatedly mobilized during primate evolution, 15 to 6 million years ago (MYA), which left a trace of over a hundred provirus-like copies and at least 4,000 solitary long terminal repeats (LTRs) in the human genome. Then, its proliferation ceased for unknown reasons, and the family went extinct. We have made a detailed reconstruction of its last active subfamily, ERV9_XII, by examining 115 solitary LTRs from it. These insertions were grouped into 11 sets according to shared nucleotide variants, which could be placed in a sequential order of 10 to 6 MYA. At least 75% of the subfamily was produced 8 to 6 MYA, during a stage of intense proliferation. With new analytical tools, we show that the youngest and most prolific sets may have been produced by effectively instantaneous expansions of corresponding single-sequence variants. The extinction of this family apparently was not a consequence of its slow gradual degeneration, but the outcome of the fixation of specific restrictive alleles in the human-chimpanzee ancestral population. Three species-specific insertions (two in humans and one in chimpanzees) were identified, further supporting that extinction took place when these two species were beginning to diverge. These are the only fixed differences of this kind so far observed between humans and chimpanzees, apart from those belonging to the human endogenous retrovirus K family.
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Nakatsuka, Nathan, Iosif Lazaridis, Chiara Barbieri, Pontus Skoglund, Nadin Rohland, Swapan Mallick, Cosimo Posth, et al. "A Paleogenomic Reconstruction of the Deep Population History of the Andes." Cell 181, no. 5 (May 2020): 1131–45. http://dx.doi.org/10.1016/j.cell.2020.04.015.

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Wales, Nathan, Jazmín Ramos Madrigal, Enrico Cappellini, Aldo Carmona Baez, José Alfredo Samaniego Castruita, J. Alberto Romero-Navarro, Christian Carøe, et al. "The limits and potential of paleogenomic techniques for reconstructing grapevine domestication." Journal of Archaeological Science 72 (August 2016): 57–70. http://dx.doi.org/10.1016/j.jas.2016.05.014.

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Mitchell, Kieren J. "Ancient DNA from the koala lemur puts Madagascar on the paleogenomic map." Proceedings of the National Academy of Sciences 118, no. 30 (July 22, 2021): e2110218118. http://dx.doi.org/10.1073/pnas.2110218118.

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Kistler, Logan, Roselyn Ware, Oliver Smith, Matthew Collins, and Robin G. Allaby. "A new model for ancient DNA decay based on paleogenomic meta-analysis." Nucleic Acids Research 45, no. 11 (May 9, 2017): 6310–20. http://dx.doi.org/10.1093/nar/gkx361.

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Sánchez-Quinto, Federico, Helena Malmström, Magdalena Fraser, Linus Girdland-Flink, Emma M. Svensson, Luciana G. Simões, Robert George, et al. "Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society." Proceedings of the National Academy of Sciences 116, no. 19 (April 15, 2019): 9469–74. http://dx.doi.org/10.1073/pnas.1818037116.

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Paleogenomic and archaeological studies show that Neolithic lifeways spread from the Fertile Crescent into Europe around 9000 BCE, reaching northwestern Europe by 4000 BCE. Starting around 4500 BCE, a new phenomenon of constructing megalithic monuments, particularly for funerary practices, emerged along the Atlantic façade. While it has been suggested that the emergence of megaliths was associated with the territories of farming communities, the origin and social structure of the groups that erected them has remained largely unknown. We generated genome sequence data from human remains, corresponding to 24 individuals from five megalithic burial sites, encompassing the widespread tradition of megalithic construction in northern and western Europe, and analyzed our results in relation to the existing European paleogenomic data. The various individuals buried in megaliths show genetic affinities with local farming groups within their different chronological contexts. Individuals buried in megaliths display (past) admixture with local hunter-gatherers, similar to that seen in other Neolithic individuals in Europe. In relation to the tomb populations, we find significantly more males than females buried in the megaliths of the British Isles. The genetic data show close kin relationships among the individuals buried within the megaliths, and for the Irish megaliths, we found a kin relation between individuals buried in different megaliths. We also see paternal continuity through time, including the same Y-chromosome haplotypes reoccurring. These observations suggest that the investigated funerary monuments were associated with patrilineal kindred groups. Our genomic investigation provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.
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Shapiro, B., and M. Hofreiter. "A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA." Science 343, no. 6169 (January 23, 2014): 1236573. http://dx.doi.org/10.1126/science.1236573.

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Hofmanová, Zuzana, Susanne Kreutzer, Garrett Hellenthal, Christian Sell, Yoan Diekmann, David Díez-del-Molino, Lucy van Dorp, et al. "Early farmers from across Europe directly descended from Neolithic Aegeans." Proceedings of the National Academy of Sciences 113, no. 25 (June 6, 2016): 6886–91. http://dx.doi.org/10.1073/pnas.1523951113.

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Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.
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Dissertations / Theses on the topic "Paleogenomic"

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Skoglund, Pontus. "Reconstructing the Human Past using Ancient and Modern Genomes." Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-206787.

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The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modern-day contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.
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Brunel, Samantha. "Paleogenomics of human population dynamics on the French territory between 7000 and 2000 before present." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC282.

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Ces derniers 10000 ans en Eurasie occidentale ont été marqués par des transitions culturelles qui ont profondément transformé les sociétés humaines : l’apparition et la diffusion du Néolithique, de l’Âge du Bronze et de l’Âge du Fer. La paléogénomique, en analysant les génomes anciens, s’est attelée à en décrire les processus démographiques sous-jacents dans diverses parties du continent. En France cependant, la fin de la Préhistoire est seulement connue par le biais de l’archéologie, et n’a pas encore été explorée par la génétique à l’échelle du territoire. Nous avons produit un large jeu de données comprenant les génomes mitochondriaux, marqueurs du chromosome Y et génotypes d’une sélection de loci nucléaires d’intérêt via une procédure d’enrichissement pour 193 individus datant du Mésolithique, Néolithique, Âge du Bronze et Âge du Fer à travers le territoire de la France actuelle. Nous avons également généré les génomes à faible couverture de 58 individus répartis sur les mêmes périodes et recouvrant partiellement ce panel. L’intégralité de ces résultats offre, pour la première fois, un aperçu des dynamiques des lignées maternelles et paternelles ainsi que du génome nucléaire sur une période recouvrant 5000 ans. Que ce soient les lignées parentales ou le génome, différentes dynamiques apparaissent entre le nord et le sud de la France durant le Néolithique, avec un degré variable d’incorporation des populations de chasseurs-cueilleurs autochtones dans les communautés de fermiers. Ils mettent également en évidence, peu avant le début de l’Âge du Bronze, un flux de gènes dominé par des hommes dont la signature génétique des bergers de la Steppe Pontique, une signature qui ensuite persiste durant l’Âge du Fer, alors que la population montre peu de différentiation à l’échelle du territoire français. Certains marqueurs phénotypiques observés au Néolithique arborent une fréquence proche de celle observée dans la population européenne actuelle, indiquant des épisodes de sélection positive pré-datant le Néolithique, tandis que d’autres montrent des fréquences différentes, signe d’une sélection en cours sur ces loci. Cette étude accroit notre compréhension de relations entre les différentes populations de la fin de la Préhistoire, à l’échelle de la France et de l’Europe
The last 10,000 years in Western Eurasia were marked by cultural transitions that profoundly transformed human societies: the advent of the Neolithic, the Bronze Age and the Iron Age. Paleogenomics, the analysis of ancient genomes, started to address the underlying demographic processes in various parts of the continent. In France, however, Late Prehistory is only known from the rich archaeological records and not yet explored through genetics at a territory-wide scale. We generated a large dataset comprising the complete mitochondrial genomes, Y chromosome markers and genotypes on a number of nuclear loci of interest obtained through a DNA enrichment approach of 193 Mesolithic, Neolithic, Bronze Age and Iron Age individuals sampled across the territory of present-day France. It was complemented with the low-coverage genomes of 58 individuals partially overlapping this dataset. This panel provides, for the first time, a high-resolution 5,000-year transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Both parental lineages and genomic data revealed different dynamics in the North and the South of the French territory during the Neolithic, with varying degrees of incorporation of autochthonous hunter-gatherers lineages into farming communities. They also revealed a mostly male-driven gene flow from individuals deriving part of their ancestry from the Pontic Steppe at the onset of the Bronze Age, a signature that then persisted through the Iron Age. The various nuclear phenotypic markers we studied evolved differently. While some harbor present-day European frequencies already at the Neolithic epoch indicating ancient episodes of positive selection of these specific traits, others show different evolutionary stages throughout the Neolithic and the Bronze Age allowing us the establish more clearly the origin and evolution of the phenotypic traits that characterize the present-day European population. This study further expands our understanding of the relationship between populations during late Prehistory in France and across Europe
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Olalde, Marquínez Íñigo 1987. "From the Mesolithic to the Bronze Age: unraveling 5.000 years of European population history with paleogenomics." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/403608.

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The general objective of this thesis is to use ancient genomic data to study the European prehistory. Thanks to the latest advances in DNA sequencing technologies, the field of ancient DNA has suffered a profound transformation and has entered in the so-called paleogenomic revolution. The retrieval of genome-wide genetic information from ancient human remains is now routinely achieved, allowing us to study past processes with a level of resolution that geneticists hardly imagined a decade ago. When we conceived this project in the second half of 2012, only one ancient human genome from Europe, that of the Tyrolean Iceman, was available and therefore many key events in our history remained obscure. We decided to fill this gap and recovered genome-wide data from 55 ancient Europeans that lived from 6,000 to 2,000 BCE. I present in this thesis the results we obtained from the analysis of this remarkable amount of genetic information.
El objetivo de esta tesis es usar datos genómicos antiguos para estudiar la prehistoria europea. Gracias a los últimos avances en secuenciación de ADN, el campo del ADN antiguo ha sufrido una profunda transformación y ha entrado en la llamada revolución paleogenómica. La recuperación de información genética nuclear a partir de restos humanos antiguos está ahora al alcance de muchos laboratorios, permitiéndonos estudiar el pasado con una resolución que los genetistas nunca habrían imaginado hace una década. Cuando este proyecto fue concebido durante la segunda mitad del año 2012, sólo un genoma humano antiguo europeo había sido secuenciado y por tanto muchos acontecimientos clave de la prehistoria quedaban por esclarecer. Para paliar esta situación, nos propusimos recuperar datos genómicos de 55 humanos que vivieron en Europa entre el 6000 y el 2000 AEC. En esta tesis presento los resultados obtenidos tras analizar esta extraordinaria cantidad de información genética.
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Gelabert, Xirinachs Pere 1991. "Paleogenomics applied to the study of ancient infectious diseases : tracing the signals of the eradicated European malaria." Doctoral thesis, Universitat Pompeu Fabra, 2018. http://hdl.handle.net/10803/665491.

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La malària és una malaltia infecciosa causada per diverses espècies de protozous del gènere Plasmodium, capaces d’infectar eritròcits humans. La malària és probablement la patologia infecciosa que ha causat més morts al llarg de tota la història de l’espècie humana. Encara avui dia és un problema de salut pública global, agreujat per la creixent aparició de soques de Plasmodium resistents als tractaments farmacològics. L'origen de la majoria d’espècies de Plasmodium és africà. Espècies com P. vivax s’han expandit arreu per mitjà de moviments migratoris complexes, els quals romanen encara parcialment desconeguts degut a la manca de seqüències de Plasmodium europeus. Aquesta expansió probablement originada en el Neolític, ha seguit sempre moviments migratoris humans, deixant variants de resistència al Plasmodium en les poblacions humanes que hi han estat exposades. En aquest treball es presenta la seqüència de les soques europees de P. vivax i P. falciparum que han estat usades per traçar els moviments migratoris dels patògens així com per datar l’expansió del P. vivax. No gens menys el genotipat de variants de resistència en individus europeus antics mostra un impacte genètic limitat de la malària, suggerint amb una introducció recent del Plasmodium al continent.
Malaria is an infectious disease caused by several protozoa species of the Plasmodium genus, capable to infect human erythrocytes. Malaria is probably the infectious pathology responsible of the larger amount of deaths among all human history. Still nowadays it is a major public health concern, which is aggravated due to the emergence and spread of Plasmodium strains resistant to current drug treatments. Most of Plasmodium species have an African origin. Parasites like P. vivax have colonized the world following complex migrating movements, partially unclear due to the lack of European Plasmodium genomes. The Plasmodium expansion, probably associated with the Neolithic onset, has been a strong selective pressure for the exposed human populations. Here we present the genomes of eradicated European strains of P. vivax and P. falciparum, which have been used to trace the migrating movements of these pathogens, as well as for dating the P. vivax dispersal. A genetic screen of malaria resistance variants in ancient European populations has revealed very low rates of genetic adaptive variants, which might be explained by a very recent introduction of malaria in Europe.
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Luhmann, Nina [Verfasser], Jens [Akademischer Betreuer] Stoye, and Cedric [Akademischer Betreuer] Chauve. "Phylogenetic assembly of paleogenomes integrating ancient DNA data / Nina Luhmann ; Jens Stoye, Cedric Chauve." Bielefeld : Universitätsbibliothek Bielefeld, 2017. http://d-nb.info/1128818523/34.

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Cuenca, Cambronero Maria. "Documenting long-term impact of eutrophication and climate change on the keystone species Daphnia using resurrection ecology and paleogenomics." Thesis, University of Birmingham, 2018. http://etheses.bham.ac.uk//id/eprint/8275/.

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Dramatic loss of biodiversity in the last two decades has been associated with human activities. Yet, we understand little of the mechanisms that enable species persistence to anthropogenic environmental changes over evolutionary time. Here, we measured ecological and evolutionary responses of a population of Daphnia magna to multiple anthropogenic stressors over evolutionary time, and assessed the role of historical exposure in adaptive response to recurring environmental stress. D. magna is a keystone grazer in freshwater standing waters and a driver of ecosystem dynamics. As part of its life cycle, Daphnia produces dormant embryos that arrest their development entering dormancy and creating a long-term documentation of evolutionary responses to environmental change. Resurrected dormant stages are maintained as clonal lines in the laboratory, providing us with the unique opportunity of disentangling the role of phenotypic plasticity and genetic adaptation in population responses to environmental stress. We studied phenotypic, physiological, and molecular responses that enabled a population of D. magna to persist across major pollution events. We found that adaptive responses to multiple environmental stressors are not predictable from the responses to single stressors. We also discovered that historical exposure to stress prior to dormancy provides an evolutionary advantage when the stress recurs. However, this advantage is contingent upon the type and severity of environmental stressor. We discovered that response to environmental stress is underpinned by extensive epistasis and pleiotropy, suggesting that standing genetic variation is the clay of evolution in this species.
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Dios, Martínez Toni de 1994. "Recovery of pathogen genomes from ancient human samples : individual cases, disease and epidemics." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2021. http://hdl.handle.net/10803/671369.

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Infectious diseases have affected humanity since its apparition in Africa 300,000 years ago. Demographic changes associated to the Neolithic transition, and ensuing population movements, have facilitated the emergence and expansion of those diseases around the world. The usage of ancient DNA has allowed us to have a snapshot of ancient pathogens’ genomes. In this thesis I present the genomes of different ancient pathogens associated to a global disease, to an historical individual case and to past epidemics. In the first case, we retrieve the partial genome of a European Plasmodium falciparum strain, which hints the arrival of the parasite to Europe during antiquity. We also take a look at French revolutionary Jean-Paul Marat’s condition, in order to shed light to his mysterious condition. Finally, we analyse an ancient Salmonella enterica Paratyphi C strain, which suggests that, although infections by this particular serovar are fairly scarce in the present, in the past could have been the responsible agent of epidemics around the globe.
Les malalties infeccioses han afectat a l’ésser humà des de la seva aparició a Àfrica fa 300,000 anys. Canvis demogràfics associats a la transició neolítica, i posteriors moviments poblacionals, han afavorit l’aparició i dispersió d’aquestes malalties al voltant del mon. L’ús de ADN antic permet obtenir una finestra temporal des d’on observar com eren aquests patògens en el passat. En aquesta tesi presento els genomes d’una sèrie de patògens antics associats a malalties, casos individuals històrics i epidèmies. En el cas de la malaltia, recuperem un genoma parcial d’una soca Europea erradicada de Plasmodium falciparum, la qual dóna indicis de l’arribada del paràsit a Europa durant l’antiguitat. Fem una ullada també al cas del revolucionari francès Jean Paul Marat amb la intenció d’esbrinar l’origen de la seva condició. Finalment analitzem una soca de Salmonella enterica Paratifoide C que podria suggerir que aquest patogen, actualment escàs, era el responsable d’epidèmies al voltant del mon.
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Fischer, Claire-Elise. "Apports de l’archéogénétique à l’étude des groupes du Second âge du Fer en France : Approche multi-scalaire." Thesis, Bordeaux, 2019. http://www.theses.fr/2019BORD0332.

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En Europe tempérée, et plus particulièrement en France, l’âge du Fer se découpe en deux périodes : le Premier (800-400 BC) et le Second âge du Fer (400-25 BC). Ce dernier est souvent associé aux cultures celtiques, dont l’unité a été montrée à travers l’étude de l’art celtique. Cependant, cette apparente unité est à présent rediscutée au travers des travaux récents en archéologie. Si la diversité culturelle est bien connue du point de vue de l’archéologie, elle est encore peu abordée du point de vue biologique. Ce travail propose donc l’analyse paléogénétique et paléogénomique inédite d’individus issus de trois nécropoles du Nord de la France, distribuées le long de la vallée de la Seine, axe d’échanges majeur entre Manche et Bourgogne. Un total de 106 haplogroupes, 87 haplotypes mitochondriaux ainsi que 15 lignées paternelles ont été caractérisés. En outre, 12 génomes à faible couverture ont été obtenus. À l’échelle locale, les données obtenues ont été systématiquement confrontées aux données biologiques et archéologiques disponibles, permettant de mettre en évidence des fonctionnements distincts. La nécropole d’Urville-Nacqueville (Normandie) semble accueillir une population cosmopolite, alors que celle de Gurgy ‘Les Noisats’ (Yonne) est vraisemblablement utilisée par une communauté locale. Les cas de Barbuise ‘Les Grèves de Frécul’ (Yonne) et d’Urville-Nacqueville révèlent par ailleurs la complexité de l’organisation sociale de ces groupes de l’âge du Fer au travers de la structuration de l’espace funéraire. Bien que ces nécropoles accueillent des communautés diverses, elles partagent une importante diversité mitochondriale, une absence de regroupement basé sur des liens maternels et une faible diversité des lignées paternelles. Ces résultats forment un faisceau d’indices supportant un système matrimonial de type patrilocal et une filiation de type patrilinéaire, cohérents avec les données de la littérature. À l’échelle régionale, les résultats montrent que les sites situés en basse vallée de la Seine partagent plus d’affinités avec les groupes du sud de l’Angleterre alors que ceux de la haute vallée de la Seine sont plus proches des populations de l’est de la France et occupent une position intermédiaire entre le nord et le sud de la France, mettant ainsi en évidence une structuration génétique de ces groupes en fonction de leur localisation le long de cet axe fluvial. Enfin, à l’échelle continentale, les résultats montrent que les communautés de l’âge du Fer d’Europe de l’ouest forment un cluster génétique cohérent et présentent une continuité génétique avec les groupes de l’âge du Bronze. Les données acquises s’accordent avec les hypothèses archéologiques privilégiant une transition économique, politique et/ou climatique pour expliquer la transition entre l’âge du Bronze et l’âge du Fer, en accord avec l’évolution locale des groupes perçue au niveau génétique
In Europe, and more precisely in France, the Iron Age is divided into two periods: the First (800-400 BC) and the Late Iron Age (400-25 BC). This one is often associated with Celtic cultures, which have been shown to be unified through the study of Celtic art. But this apparent unity is now being questioned through recent archaeological work. While cultural diversity is well known from an archaeological point of view, it is still poorly addressed from a biological point of view. The aim of this work is to provide an unprecedented palaeogenetic and palaeogenetic analysis of individuals from three necropolises in northern France, distributed along the Seine valley, a major axis of exchange between the English Channel and Burgundy. A total of 106 haplogroups, 87 mitochondrial haplotypes and 15 paternal lines were characterized. Furthermore, 12 genomes with low coverage were obtained. At the local level, a systematic comparison of the data obtained with the available biological and archaeological records was carried out, which revealed different ways of functioning. The necropolis of Urville-Nacqueville (Normandy) appears to have a cosmopolitan population, while the one of Gurgy "Les Noisats" (Yonne) is most likely being used by a local community. The cases of Barbuise "Les Grèves de Frécul" (Yonne) and Urville-Nacqueville also reveal the complexity of the social organization of these Iron Age groups through the organisation of the funeral space. Although these necropolises host diverse communities, they share a high mitochondrial diversity, an absence of grouping based on maternal ties and a low diversity of paternal lines. These results form a cohesive set of evidence supporting a patrilocal matrimonial system and a patrilineal filiation, consistent with the data in the literature. At the regional level, the results show that sites located in the lower Seine Valley share more affinities with groups in the south of England, while those in the upper Seine Valley are closer to the populations of eastern France and occupy an intermediate position between the north and south of France, highlighting a genetic structure of these groups based on their location along this river axis. Finally, on a continental scale, the results show that the Iron Age communities of Western Europe form a consistent genetic cluster and show genetic continuity with the Bronze Age groups. The data obtained are consistent with archaeological hypotheses that focus on an economic, political and/or climatic transition to explain the Bronze Age to Iron Age transition, in agreement with the local evolution of the groups as perceived at the genetic level
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Oliva, Adrien. "Quantifying and reducing biases in paleogenomic research." Thesis, 2022. https://hdl.handle.net/2440/136013.

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The emergence of high-throughput DNA sequencing technologies has enabled the sequencing of genomes at unprecedented rates and low costs. In parallel, paleogenomics research, which extends the study of ancient DNA molecules to whole genomes, has led to a number of transformative discoveries in evolutionary biology, environmental sciences, and even medicine. However, ancient DNA has a number of properties that make it challenging to investigate, including short fragment length, contamination, and damage, which are often exacerbated at genomic scales. It is now clear that numerous biases are pervasive in paleogenomics investigations, and their influence on downstream inferences is undeniable. In this thesis, I present results from a series of interrelated empirical studies that investigate issues related to reference bias and reproducibility in paleogenomics, providing the relevant historical and technical background in the introduction. In Chapter 1 of this thesis, I benchmark a range of short read alignment methods and algorithms available to paleogenomicists and quantify the impact of reference bias on downstream inferences. I show that the current standard alignment method in the paleogenomics field, i.e., using the BWA-aln software with specific settings developed during the early stages of paleogenomics, is still one of the best available tools for minimising the impact of reference bias. However, reference bias can be decreased even further when using NovoAlign software and an augmented version of the linear reference that incorporates known variants using IUPAC characters. In Chapter 2, I extend this investigation to include the recently developed variation graph methods to paleogenomic datasets, and assess its impact on a series of contentious population genetics inferences when compared to the two best performing 4 traditional (linear) alignment methods identified in chapter 1. Consistent with the results from chapter 1, the added variation captured by variation graphs make them less susceptible to reference bias than linear alignments (including IUPAC augmented methods). I also show that changes in bioinformatic parameters and sample choice can lead to subtle but significant differences in statistical inferences that could impact interpretations. Therefore, in the third chapter, I emphasise the importance of reproducibility in paleogenomic research, and make a series of recommendations regarding the minimum reported information required across all key steps of data processing and analyses to ensure reproducibility of paleogenomic results. Finally, in the discussion chapter, I summarise my findings and discuss their implications for the field of paleogenomics as well as potential directions for future research. Ultimately, this knowledge should help improve the reliability and robustness of paleogenomic inferences, leading to an improved understanding of population history and evolutionary phenomena.
Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 2022
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Books on the topic "Paleogenomic"

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Lindqvist, Charlotte, and Om P. Rajora, eds. Paleogenomics. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-04753-5.

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Rajora, Om P., and Charlotte Lindqvist. Paleogenomics: Genome-Scale Analysis of Ancient DNA. Springer, 2019.

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Book chapters on the topic "Paleogenomic"

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Thalmann, Olaf, and Angela R. Perri. "Paleogenomic Inferences of Dog Domestication." In Population Genomics, 273–306. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/13836_2018_27.

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Marciniak, Stephanie, and Hendrik N. Poinar. "Ancient Pathogens Through Human History: A Paleogenomic Perspective." In Population Genomics, 115–38. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/13836_2018_52.

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Veeramah, Krishna R. "Primate Paleogenomics." In Population Genomics, 353–73. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/13836_2018_47.

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Caramelli, David, Lucio Milani, Roscoe Stanyon, and Carles Lalueza Fox. "Towards Neanderthal Paleogenomics." In Vertebrate Paleobiology and Paleoanthropology, 219–21. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-0492-3_20.

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Irving-Pease, Evan K., Hannah Ryan, Alexandra Jamieson, Evangelos A. Dimopoulos, Greger Larson, and Laurent A. F. Frantz. "Paleogenomics of Animal Domestication." In Population Genomics, 225–72. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/13836_2018_55.

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Bennett, E. Andrew, Olivier Gorgé, Thierry Grange, Yolanda Fernández-Jalvo, and Eva-Maria Geigl. "Coprolites, Paleogenomics and Bone Content Analysis." In Azokh Cave and the Transcaucasian Corridor, 271–86. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-24924-7_12.

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Salse, Jérôme. "Paleogenomics as a Guide for Traits Improvement." In Genomics of Plant Genetic Resources, 131–72. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-7572-5_7.

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Salse, Jérôme. "Brachypodium Paleogenomics: From Genome Evolution to Translational Research in Grass Crops." In Genetics and Genomics of Brachypodium, 71–80. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/7397_2015_2.

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Lan, Tianying, and Charlotte Lindqvist. "Paleogenomics: Genome-Scale Analysis of Ancient DNA and Population and Evolutionary Genomic Inferences." In Population Genomics, 323–60. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/13836_2017_7.

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Faure, Denis, and Dominique Joly. "Degraded and Paleogenomic DNA." In Insight on Environmental Genomics, 79–91. Elsevier, 2016. http://dx.doi.org/10.1016/b978-1-78548-146-8.50008-3.

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Conference papers on the topic "Paleogenomic"

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HAWKS, JOHN. "PALEOGENOMICS AND THE VOCAL AUDITORY CHANNEL IN ARCHAIC HUMANS." In Proceedings of the 9th International Conference (EVOLANG9). WORLD SCIENTIFIC, 2012. http://dx.doi.org/10.1142/9789814401500_0074.

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Bottjer, David J. "PALEOGENOMICS AND PLATE TECTONICS: REVOLUTIONS IN THE EARTH AND BIOLOGICAL SCIENCES." In GSA Annual Meeting in Denver, Colorado, USA - 2016. Geological Society of America, 2016. http://dx.doi.org/10.1130/abs/2016am-279983.

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Thompson, Jeffrey R., Eric M. Erkenbrack, Elizabeth Petsios, and David J. Bottjer. "PALEOGENOMICS OF ECHINOIDS AND THE EVOLUTION OF ECHINOID GENE REGULATORY NETWORKS." In GSA Annual Meeting in Denver, Colorado, USA - 2016. Geological Society of America, 2016. http://dx.doi.org/10.1130/abs/2016am-282588.

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