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1
Gilbert, Marcus Thomas Pius. "An assessment of the use of human samples in ancient DNA studies". Thesis, University of Oxford, 2003. http://ora.ox.ac.uk/objects/uuid:434e285b-bf62-41fe-8250-5f4273f38152.
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This thesis addresses gaps that exist in the theory and knowledge of ancient DNA (aDNA). Much of the underlying basis of the field has been neglected in the excitement that followed the first aDNA studies. Therefore the results of many studies have been based on untested assumptions about the nature of post mortem DNA damage, sample preservation, contamination, and the efficacy of sample decontamination techniques. The validity of such results is questionable if the assumptions prove false. Hydrolytic post mortem DNA damage may modify recovered aDNA sequences. This thesis reports new insights into the biochemical basis of, predisposition of certain sequences and nucleotide positions towards, and subsequent effects of, such damage. Parallels of post mortem damage with in vivo mutation also enable insights into DNA sequence evolution. The long-term survival of DNA, and contamination of samples with exogenous DNA are two related problems characteristic to aDNA. The survival of endogenous DNA within bone, teeth and hair samples, the susceptibility of such samples to contamination, and the efficacy of decontamination techniques used to remedy such problems are investigated. The results highlight serious flaws in using bone and teeth as a DNA source. In contrast, the results demonstrate that hair may present a valuable DNA source for future studies. Numerous studies have reported the retrieval of ancient pathogen DNA from human samples. Analyses of the DNA content within teeth extracted from putative victims of the 2nd plague argue that such studies are at great risk from DNA degradation, and contamination arising due to environmental microorganisms. An extrapolation of these results using basic physical and chemical theory is used to evaluate the potential survival of aDNA in ancient Egyptian remains. This suggests that positive results from such samples are unlikely.
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Johansson, Tom. "Archaeology and aDNA in Oceania : Debates on migration patterns the past 50 years". Thesis, Uppsala universitet, Institutionen för arkeologi och antik historia, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-296506.
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The aim of this thesis is to investigate how discussions in archaeology and genetics influence the consensus on human origins and migrations in the South Pacific. By analyzing the genetic research on chicken- and sweet potato-DNA, I present a general overview of how genetics and archaeology shape the understanding of how humans have colonized the Pacific. By deconstructing a review on how the Pacific was settled based on aDNA, I analyze a geneticist’s perspective on archaeological problems. Through this analysis I suggest how archaeology should be approached on a theoretical level in order to be relevant in understanding human migrations in the Pacific. I propose that archaeology’s strength lie in interpreting material culture through an agency perspective in order to reach a dimension not obtainable by biological perspectivesSyftet med denna uppsats är att undersöka hur diskussioner i arkeologi och genetik påverkar hur vi ser på mänskliga migrationer i Oceanien. Genom att analysera den genetiska forskning som gjorts på kyckling och sötpotatis ges en övergripande bild av hur genetik och arkeologi formar den förståelse som finns för hur människan koloniserat Söderhavet. Genom att dekonstruera en sammanställning av den genetiska forskning som gjorts på mänskligt DNA i Oceanien analyseras en genetikers synsätt på arkeologiska problemställningar. Genom analysen i denna uppsats föreslår jag hur arkeologi borde arbeta på ett teoretiskt plan för att vara relevant i hur vi förstår Oceaniens migrationsmönster. Jag föreslår att arkeologins styrka ligger i att tolka den materiella kulturen genom ett agency-perspektiv för att komma åt en dimension av migrationsproblematiken som inte går att nås genom biologiska perspektiv.
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Yang, Dongya. "DNA diagnosis of thalassemia from ancient Italian skeletons /". *McMaster only, 1997.
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Mathias, Neal. "Y chromosome DNA polymorphisms and human evolution". Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333355.
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Naxerova, Kamila. "Tracing human cancer evolution with hypermutable DNA". Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11253.
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Metastasis is the main cause of cancer morbidity and mortality. Despite its clinical significance, several fundamental questions about the metastatic process in humans remain unsolved. Does metastasis occur early or late in cancer progression? Do metastases emanate directly from the primary tumor or give rise to each other? How does heterogeneity in the primary tumor relate to the genetic composition of secondary lesions? Addressing these questions in representative patient populations is crucial, but has been difficult so far. Here we present a simple, scalable PCR assay that enables the tracing of tumor lineage in patient tissue specimens. Our methodology relies on somatic variation in highly mutable polyguanine (poly-G) repeats located in non-coding genomic regions. We show that poly-G mutations are present in a variety of human cancers. Using colon carcinoma as an example, we demonstrate an association between patient age at diagnosis and tumor mutational burden, suggesting that poly-G variants accumulate during normal division in colonic stem cells. We further show that poorly differentiated colon carcinomas have fewer mutations than well-differentiated tumors, possibly indicating a shorter mitotic history of the founder cell in these cancers. We collect multiple spatially separated samples from primary carcinomas and their metastases and use poly-G fingerprints to build well-supported phylogenetic trees that illuminate each patient's path of progression. Our results imply that levels of intra-tumor heterogeneity vary significantly among patients.
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Johnson, Sarah. "Comparative Resistomics of Ancient and Modern Human Microbiomes". Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1707269/.
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Increased exposure to antibiotics has led to the dissemination of genes conferring resistance to antimicrobial metabolites throughout human microbiomes globally via horizontal gene transfer (HGT). This has resulted in the emergence of new resistant strains leading to a rising epidemic of deaths from previously treatable infections. Evidence suggests that before the age of anthropogenic antibiotic use, microbes living within a community produced antibiotic metabolites and, subsequently, maintained such genes for several useful functions and a balance of diversity in nature. The question of the origin of these resistant genes is difficult to answer, but with continued advancements in ancient genomic analysis, researchers have developed methods of acquiring a more accurate representation of the microbiome associated with our human ancestors by extracting fossilized microbial specimens from dental calculus and directly sequencing the metagenomes. This thesis outlines the production of taxonomic and functional profiles of 20 different human and non-human oral microbiome samples using metagenomics tools originally developed for living individuals, altered for use with ancient microbial specimens. Putative antimicrobial resistant (AMR) genes derived from these profiles were reconstructed and conserved functional regions were identified. From the data that is available regarding the human microbiome from a range of time points throughout history dating back to Neanderthal specimens, it is possible to elucidate relationships between these AMR genes and to better understand the evolutionary trajectory of antibiotic resistance.
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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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Chandler, Helen C. "Using ancient DNA to link culture and biology in human populations". Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.404074.
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Endicott, Phillip. "Ancient DNA and human population genetics in island South East Asia". Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670170.
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Faltyskova, Zuzana. "Human dispersals to Tierra del Fuego revealed by ancient mitochondrial DNA". Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709073.
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Cascini, Manuela. "Evolution of marsupial biodiversity". Thesis, Queensland University of Technology, 2020. https://eprints.qut.edu.au/197697/1/Manuela_Cascini_Thesis.pdf.
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This thesis explored the evolutionary trajectory of marsupials, focusing primarily on the Australasian marsupial fauna, and used a phylogenetic inference approach that combines molecular, ecological and fossil data sets. A first study provided the most complete and accurate (to-date) species-level marsupial phylogeny by using the most taxonomically complete set of nuclear and mitochondrial loci. In a second study, DNA and fossils from extinct and modern taxa were used to infer the evolution of macropods. A third project inferred the most complete (to-date) time-calibrated phylogeny of Diprotodontia. By incorporating fossil data, this last project revealed apparent competitive displacement of Vombatiformes (koala and wombats) by Macropodiformes (kangaroos) from the Late Miocene onwards, and a long (~25 million year) lag in the evolution of herbivory among marsupials compared to placental mammal faunas.
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D'Abbadie, Marc François. "Directed evolution of polymerases with altered substrate specificities : the paradigm of ancient DNA". Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613870.
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Ramsey, Heather C. "Comparisons of mitochondrial DNA from ancient and modern Miami Indian populations". Virtual Press, 1999. http://liblink.bsu.edu/uhtbin/catkey/1133738.
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The purpose of this research endeavor was to determine the extent of genetic relatedness between an ancient and modern Miami Indian population. The modern Miami Indian nation in Indiana is currently in the process of regaining the federal recognition which was lost in the mid 1800's when part of the tribe was forced to relocate. A close genetic relationship between a modern and known ancient population could considerably strengthen the case to regain federal recognition. The human skeletal remains used for this experiment were excavated after partial exposure by flooding between 1989-1993 along the banks of the Mississinewa River in Wabash County. Through ethnohistoric dating techniques, the remains have been shown to represent a Miami Indian population living between 1790-1820. In order to yield amplifiable DNA several methods of isolation were attempted and compared. CTAB and phenol/chloroform/isoamyl alcohol (24:24:1) and a silica based purification method provided the best results yielding approximately 50-100 ng of amplifiable DNA from 3 of the 4 individuals. Purification of the DNA was found to be necessary following both isolation (Elu-Quik) prior to PCR amplification and after PCR but prior to sub-cloning(Gene-Clean). Regions of the mitochondrial DNA (mtDNA) genome of isolated DNA were amplified using primers which are specific for the HIizcIl and AIui regions of the mtDNA genome. Although the mtDNA proved to be somewhat amplifiable, it was still too fragmented to be cloned, which prevented genetic analysis and comparison of the two populations. As a result, a discussion of alternative methods for looking at relatedness between populations has been included.Department of Biology
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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’EuropeThe 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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Miller, K. W. P. "Molecular genetic analysis of human populations in Orkney and the North Atlantic region". Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242555.
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McGinley, Susan. "The Co-Evolution of a Beetle and a Plant: DNA Evidence Shows Survival of Ancient Association". College of Agriculture and Life Sciences, University of Arizona (Tucson, AZ), 2004. http://hdl.handle.net/10150/622212.
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Rudd, Mary Katharine. "Organization, evolution and function of alpha satellite DNA at human centromeres". Case Western Reserve University School of Graduate Studies / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=case1091493781.
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Rudd, M. Katharine. "Organization, evolution and function of alpha satellite DNA at human centromeres". Connect to text online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=case1091493781.
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Bodiba, Molebogeng K. "Ancient DNA analysis of the Thulamela remains : deciphering the migratory patterns of a Southern African human population". Diss., University of Pretoria, 2014. http://hdl.handle.net/2263/45931.
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Bio-archaeology is the study of biological remains found at sites of archaeological interest. It is an interdisciplinary science employing different scientific fields including physical anthropology, geography, archaeology and genetics. Genetic analysis includes ancient DNA (aDNA) studies, now a specialised field in genetics. This approach was used to analyse human skeletal material of eight individuals from various Iron Age archaeological sites in southern Africa. Included in this sample is a naturally mummified individual from Tuli, in Botswana. The context of the specimens found in the Limpopo Province (Thulamela), as well as their cultural links with the Zimbabwe Culture Complex (which includes Mapungubwe and Khami) suggests that some gene exchange might have occurred. While this is not the first aDNA study on southern African samples, it is the first aDNA study based on southern African Iron Age human individuals and also included a naturally mummified individual.
Morphometric and morphological analyses have indicated the age at death, sex and health status of the individuals, and the context in which they were found has helped in assessing their cultural affinity. Bone samples were analysed in a specialized aDNA laboratory at the Centre for Evolutionary Medicine in Switzerland. Following DNA extraction, ancestry-specific mitochondrial DNA was amplified from all samples and was compared to that of modern sub-Saharan Africans whose data were accessed from GenBank.
Some individuals show (maternal) genetic similarities to present-day Sotho/Tswana groups. The male individual from Thulamela aligns somewhat more with the groups from the west and the female with the eastern peoples. Two Early Iron Age individuals from Happy Rest presented some similarities to the Khoesan peoples. Genetic-sex determination efforts were inconclusive for all individuals.
The purpose of this study was to place the Thulamela individuals within the context of the genetic diversity in South Africa. It was noted that the introduction of genetic material from the early Sotho/Tswana was gradual in the case of Thulamela. Two other individuals from Happy Rest, who were contemporaries of each other, showed very little genetic variation and it can be said that their maternal DNA was of the same (possibly Khoesan) origin. Further resolution in haplotype assignment will be done in future. These temporally and spatially dispersed individuals can only provide a glimpse into the population interactions of the Iron Age that may have partially shaped the immense genetic diversity of present-day southern Africa.Dissertation (MSc)--University of Pretoria, 2014.
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Daskalaki, Evangelia. "Archaeological Genetics - Approaching Human History through DNA Analysis". Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-211156.
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There are a variety of archaeological questions, which are difficult to assess by traditional archaeological methods. Similarly, there are genetic and population genetic questions about human evolution and migration that are difficult to assess by studying modern day genetic variation. Archaeological genetics can directly study the archaeological remains, allowing human history to be explored by means of genetics, and genetics to be expanded into historical and pre-historical times. Examples of archaeological questions that can be resolved by genetics are determining biological sex on archaeological remains and exploring the kinship or groups buried in close proximity. Another example is one of the most important events in human prehistory – the transition from a hunter-gatherer lifestyle to farming - was driven through the diffusion of ideas or with migrating farmers. Molecular genetics has the potential to contribute in answering all these questions as well as others of similar nature. However, it is essential that the pitfalls of ancient DNA, namely fragmentation, damage and contamination are handled during data collection and data analysis. Analyses of ancient DNA presented in this thesis are based on both mitochondrial DNA and nuclear DNA through the study of single nuclear polymorphisms (SNPs). I used pyrosequencing assays in order to identify the biological sex of archaeological remains as well as verifying if fragmented remains were human or from animal sources. I used a clonal assay approach in order to retrieve sequences for the HVRI of a small family-like burial constellation from the Viking age. By the use of low coverage shotgun sequencing I retrieved sequence data from 13 crew members from the 17th century Swedish man-of-war Kronan. This data was used to determine the ancestry of the crew, which in some cases was speculated to be of non-Scandinavian or non-European origin. However, I demonstrate that all individuals were of European ancestry. Finally, I retrieved sequence data from a Neolithic farmer from the Iberian Peninsula, which added one more facet of information in exploring the Neolithization process of Europe. The Neolithic Iberian individual was genetically similar to Scandinavian Neolithic farmers, indicating that the genetic variation of prehistoric Europe correlated with subsistence mode rather than with geography.
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Hernando, Herráez Irene 1985. "Evolutionary insights into human DNA methylation". Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/392140.
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DNA methylation is a crucial epigenetic modification involved in numerous biological processes. However, despite its functional importance, the evolutionary history of this modification and the mechanisms diving such changes are poorly understood. The aim of this thesis is to provide a better understanding of DNA methylation in the context of human recent evolution. We identified and described hundreds of regions presenting a human-specific DNA methylation pattern compared to great apes. We also analyzed for the first time the relationship between DNA methylation changes and sequence evolution at both nucleotide and protein level. In summary, this research reveals new insights into the evolutionary properties of DNA methylation and the interpretation of inter-species non-coding variationLa metilación del ADN es una modificación epigenética implicada en numerosos procesos biológicos. Sin embargo, a pesar de su relevancia funcional, se sabe muy poco sobre su historia evolutiva y los mecanismos que generan estos cambios. El objetivo de esta tesis es proporcionar una mejor compresión de la metilación del ADN en el contexto de la evolución humana reciente. Hemos identificado y descrito cientos de regiones que presentan un patrón de metilación especifico de humanos. Así mismo, hemos analizado por primera vez la relación entre los cambios en metilación y la evolución de la secuencia tanto a nivel nucleotídico como proteico. En resumen, esta investigación revela nuevos conocimientos sobre las propiedades evolutivas de la metilación del ADN y la interpretación de la variación no codificante entre especies.
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Ferrando-Bernal, Manuel 1990. "Analysis of co-ancestry links in modern and ancient human populations". Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2021. http://hdl.handle.net/10803/672475.
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The aim of this thesis is to apply Identity by Descent (IBD) methodology to identify ancestry connections among individuals from genetically similar populations. Recombination events diminish the likelihood to detect IBDs. As most of the aDNA samples date from 2,000 years ago or more, this methodology has rarely been applied to these studies. In this thesis we detect IBD among modern individuals from similar Bantu populations and among modern Europeans with an historical individual (700 years ago) from the Iberian peninsula, which was sequenced to a high coverage. Our results show that IBDs can be used to detect the genomic structure in genetically close populations. For example, they can be used to show high degrees of endogamy caused by isolation or to identify ancestral connections among individuals belonging to different populations that otherwise would be difficult to see with other more commonly used methods.
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Wilkins, Helen. "The evolution of the built environment : complexity, human agency and thermal performance". Thesis, The University of Sydney, 2006. https://hdl.handle.net/2123/29246.
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The thermal environments created by buildings provide the context within which social life operates. Adjustable built environments generate diverse thermal conditions. That is, they possess the thermal capacity to produce enhanced levels of thermal choices and thermal control. Classes and assemblages of buildings that generate diverse thermal environments will increase the range of social options that the building milieu can accommodate, compared with less adjustable classes and assemblages, because they are more readily able to accommodate changing social options and circumstances. A relationship therefore exists between the thermal operational adjustability (combining thermal choices and thermal control) associated with classes of buildings and the capacity for operational adjustability possessed by communities. This means that a class of building or an assemblage of buildings, eg. a ‘pueblo’ form, that provides a highly adjustable milieu is more likely to be occupied for longer periods of time, because it can accommodate more internal social changes prior to undergoing a system—level alteration into a different class of building or settlement. Conversely, an inflexible building milieu is more likely to be occupied for shorter periods of time prior to a system-level alteration, in which change will be observed in the class of building or settlement.
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Goidts, Violaine. "Identification of large-scale DNA copy number differences between human and non-human primate genomes and their role in mediating evolutionary rearrangements". [S.l. : s.n.], 2006. http://nbn-resolving.de/urn:nbn:de:bsz:289-vts-56317.
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Linardopoulou, Elena. "Structure, function and evolution of human subtelomeres /". Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/8120.
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Anderson, Jon Paul. "Molecular diversity and evolution of human immunodeficiency virus type 1 /". Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/8049.
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Lizzo, Giulia. "Towards comparative epigenomics in hominids : a study of DNA methylation detection in ancient human and chimp bones". Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCC180.
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Les modifications épigénétiques sont des modulateurs importants de l'expression des gènes qui peuvent être associés à des changements phénotypiques et utilisés pour suivre l'évolution des éléments cis-régulateurs. Parmi les différents types de marqueurs épigénétiques, la méthylation de l'ADN est conservée dans le temps et peut être mesurée dans des échantillons anciens. Nous visons à réaliser une étude comparative approfondie de l'évolution de la méthylation de l'ADN dans les tissus minéralisés de la lignée des hominidés. Nous établissons ainsi des cartes de méthylation évolutives de référence en utilisant des échantillons post-mortem d'os humains et de chimpanzés, datés jusqu'à 110 ans, pour s'assurer qu'ils ont subi des transformations diagénétiques suffisantes pour imiter la situation taphonomique rencontrée dans les os anciens. En outre, cette étude inclut différents types d'os afin de réduire le bruit dû à la variabilité inter-osseuse. Différentes approches de cartographie de la méthylation ont été utilisées pour identifier celles qui conviennent le mieux à ces échantillons. Le séquençage au bisulfite des génomes entiers (BS) ou la représentation réduite BS (RRBS) ne sont pas appropriés pour les échantillons anciens en raison de la présence fréquente d'un excès important d'ADN environnemental. Nous avons donc exploré à la fois du BS ciblée par Bisulfite Patch-PCR, et une méthode haut-débit d'enrichissement de la fraction méthylée (MBD-seq). Les deux techniques nécessitent des adaptations aux caractéristiques des échantillons anciens, y compris une faible quantité d'ADN endogène, une contamination élevée de l'ADN environnemental et une fragmentation de l'ADN. Les résultats obtenus illustrent les forces et les inconvénients des stratégies choisies pour les échantillons anciensEpigenetic modifications are important modulators of gene expression that can be associated to phenotypic changes and used to track the evolution of cis-regulatory elements. Among the different types of epigenetic marker, DNA methylation is conserved over time and can be measured in ancient samples. We aim at performing an in-depth comparative study of the evolution of DNA methylation patterns in mineralized tissues of the hominine lineage. We are thus establishing reference evolutionary methylation maps using post-mortem samples of human and chimpanzee bones up to 110 years old, to ensure that they have experienced sufficient diagenetic transformations to mimic the taphonomic situation encountered in ancient bones. Furthermore, this study includes different types of bones in order to reduce noise due to inter-bone variability. Different methylation mapping approaches were used to identify those best suited to such samples. Whole genome bisulfite sequencing (BS) or reduced representation BS (RRBS) are not suitable for ancient samples due to the frequent presence of a vast excess of environmental DNA. We thus explored both high-throughput targeted BS using Bisulfite Patch-PCR, and a methylation-based enrichment method (MBD-seq). Both techniques require adaptations to ancient sample characteristics, including low quantity of endogenous DNA, high environmental DNA contamination and DNA fragmentation. The results obtained illustrate strengths and drawbacks of the chosen strategies for ancient samples
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Potter, Amiee Bell. "The genetic affinities of the prehistoric people of San Clemente Island, California : an analysis of ancient DNA /". view abstract or download file of text, 2004. http://wwwlib.umi.com/cr/uoregon/fullcit?p3136440.
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Thesis (Ph. D.)--University of Oregon, 2004.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 153-168). Also available for download via the World Wide Web; free to University of Oregon users.
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Zeng, Jia. "The evolutionary significance of DNA methylation in human genome". Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/50308.
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In eukaryotic genomes ranging from plants to mammals, DNA methylation is a major epigenetic modification of DNA by adding a methyl group exclusively to cytosine residuals. In mammalian genomes such as humans, these cytosine bases are usually followed by guanine. Although it does not change the primary DNA sequence, this covalent modification plays critical roles in several regulatory processes and can impact gene activity in a heritable fashion. What is more important, DNA methylation is essential for mammalian embryonic development and aberrant DNA methylation is implicated in several human diseases, in particular in neuro-developmental syndromes (such as the fragile X and Rett syndromes) and cancer. These biological significances disclose the importance of understanding genomic patterns and function role of DNA methylation in human, as a initial step to get to know the epigenotype and its manner in connecting the phenotype and genotype.
Two key papers back in 1975 independently suggested that methylation of CpG dinucleotides in vertebrates could be established de novo and inherited through somatic cell divisions by protein machineries of DNA methyltransferases that recognizes hemi-methylated CpG palindromes. They also indicated that the methyl group could be recognized by DNA-binding proteins and that DNA methylation directly silences gene expression. After almost four decades, several key points in these foundation papers are proved to be true. Take the mammalian genome for example, there are several findings indicating the epigenetic repression of gene expression by DNA methylation. These include X-chromosome inactivation, gene imprinting and suppressing the proliferation of transposable elements and repeat elements of viral or retroviral origin. In addition to these, many novel roles of DNA methylation have also been revealed. For example, DNA methylation can regulate alternative splicing by preventing CTCF, an evolutionarily conserved zinc-finger protein, binding to DNA. By using the technique of fluorescence resonance energy transfer (FRET) and fluorescence polarization, DNA methylation has also been shown to increase nucleosome compaction through DNA-histone contacts. What is more important, DNA methylation is essential for mammalian embryonic development and aberrant change of DNA methylation has been related to disease such as cancer. However, it is also notable there are several lines of evidence contradicting the relationship between DNA methylation and gene silencing. For example, comparison of DNA methylation levels in human genome on the active and inactive X chromosomes showed reduced methylation specifically over gene bodies on inactive X chromosomes. Not only in human, DNA methylation is found to be usually targeted to the transcription units of actively transcribed genes in invertebrate species. These results prove that the function of DNA methylation is challenging to be unravel. Besides, due to the development of sequencing technique, whole genome DNA methylation profiles have been detected in diverse species. Comparing genomic patterns of DNA methylation shows considerable variation among taxa, especially between vertebrates and invertebrates. However, even though extensive studies reveal the patterns and functions of DNA methylation in different species, in the mean time, they also highlight the limits to our understanding of this complex epigenetic system.
During my Ph.D., in order to perform in-depth studies of DNA methylation in diverse animals as a way to understand the complexity of DNA methylation and its functions, I dedicated my efforts in investigating and analyzing the DNA methylation profiles in diverse species, ranging from insects to primates, including both model and non-model organisms. This dissertation, which constitutes an important part of my research, mainly focuses on the DNA methylation profile in primates including human and chimpanzee. In general, I will use three chapters to elucidate my work in generating and interpreting the whole genome DNA methylation data. Firstly, we generated nucleotide-resolution whole-genome methylation maps of the prefrontal cortex of multiple humans and chimpanzees, then comprehensive comparative studies for these DNA methylation maps have been performed, by integrating data on gene expression as well. This work demonstrates that differential DNA methylation might be an important molecular mechanism driving gene-expression divergence between human and chimpanzee brains and also potentially contribute to the human-specific traits, such as evolution of disease vulnerabilities. Secondly , we performed global analyses of CpG islands (CGIs) methylation across multiple methylomes of distinctive cellular origins in human. The results from this work show that the human CpG islands can be distinctly classified into different clusters solely based upon the DNA methylation profiles, and these CpG islands clusters reflect their distinctive nature at many biological levels, including both genomic characteristics and evolutionary features. Moreover, these CpG islands clusters are non-randomly associated with several important biological phenomena and processes such as diseases, aging, and gene imprinting. These new findings shed lights in deciphering the regulatory mechanisms of CpG islands in human health and diseases. At last, by utilizing the DNA methylome from human sperm and genetic map generated from the International HapMap Consortium project, we investigated the hypothesis suggesting a potential role of germ line DNA methylation in affecting meiotic recombination, which is essential for successful meiosis and various evolutionary processes. Even thought the results imply that DNA methylation is a important factor affecting regional recombination rate, the strength of correlation between these two is not as strong as the previous report. Besides, high-throughput analyses indicate that other epigenetic modifications, tri-methylation of histone 3 lysine 4 and histone 3 lysine 27 are also global features at the recombination hotspots, and may interact with methylation to affect the recombination pattern simultaneously. This work suggests epigenetic mechanisms as additional factors affecting recombination, which cannot be fully explained by the DNA sequence itself. In summary, I hope the results from these work can expand our knowledge regarding the common and variable patterns of DNA methylation in different taxa, and shed light about the function role and its major change during animal evolution.
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Xu, Ke. "Comparative genomic and epigenomic analyses of human and non-human primate evolution". Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/52935.
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Primates are one of the best characterized phylogenies with vast amounts of comparative data available, including genomic sequences, gene expression, and epigenetic modifications. Thus, they provide an ideal system to study sequence evolution, regulatory evolution, epigenetic evolution as well as their interplays. Comparative studies of primate genomes can also shed light on molecular basis of human-specific traits. This dissertation is mainly composed of three chapters studying human and non-human primate evolution. The first study investigated evolutionary rate difference between sex chromosome and autosomes across diverse primate species. The second study developed an unbiased approach without the need of prior information to identify genomic segments under accelerated evolution. The third study investigated interplay between genomic and epigenomic evolution of humans and chimpanzees.
Research advance 1: evolutionary rates of the X chromosome are predicted to be different from those of autosomes. A theory based on neutral mutation predicts that the X chromosome evolves slower than autosomes (slow-X evolution) because the numbers of cell division differ between spermatogenesis and oogenesis. A theory based on natural selection predicts an opposite direction (fast-X evolution) because newly arising beneficial mutations on the autosomes are usually recessive or partially recessive and not exposed to natural selection. A strong slow-X evolution is also predicted to counteract the effect of fast-X evolution. In our research, we simultaneously studied slow-X evolution, fast-X evolution as well as their interaction in a phylogeny of diverse primates. We showed that slow-X evolution exists in all the examined species, although their degrees differ, possibly due to their different life history traits such as generation times. We showed that fast-X evolution is lineage-specific and provided evidences that fast-X evolution is more evident in species with relatively weak slow-X evolution. We discussed potential contribution of various degrees of slow-X evolution on the conflicting population genetic inferences about human demography.
Research advance 2: human-specific traits have long been considered to reside in the genome. There has been a surge of interest to identify genomic regions with accelerated evolution rate in the human genome. However, these studies either rely on a priori knowledge or sliding windows of arbitrary sizes. My research provided an unbiased approach based on previously developed “maximal segment” algorithm to identify genomic segments with accelerated lineage-specific substitution rate. Under this framework, we identified a large number of human genomic segments with clustered human-specific substitutions (named “maximal segments” after the algorithm). Our identified human maximal segments cover a significant amount of previously identified human accelerated regions and overlap with genes enriched in developmental processes. We demonstrated that the underlying evolutionary forces driving the maximal segments included regionally increased mutation rate, biased gene conversion and positive selection.
Research advance 3: DNA methylation is one of the most common epigenetic modifications and plays a significant role in gene regulation. How DNA methylation status varies on the evolutionary timescale is not well understood. In this study, we investigated the role of genetic changes in shaping DNA methylation divergence between humans and chimpanzees in their sperm and brain, separately. We find that for orthologous promoter regions, CpG dinucleotide content difference is negatively correlated with DNA methylation level difference in the sperm but not in the brain, which may be explained by the fact that CpG depleting mutations better reflect germline DNA methylation levels. For the aligned sites of orthologous promoter regions, sequence divergence is positively correlated with methylation divergence for both tissues. We showed that the evolution of DNA methylation can be affected by various genetic factors including transposable element insertions, CpG depleting mutations and CpG generating mutations.
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Chassaing, Olivier. "Organisation génétique des populations d'esturgeon européen Acipenser sturio : passé, présent, futur". Thesis, Montpellier 2, 2010. http://www.theses.fr/2010MON20252/document.
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L'esturgeon européen Acipenser sturio (Linnaeus, 1758) était un poisson commun de nos fleuves jusqu'au début du 20e siècle. Toutes ses populations sont maintenant éteintes sauf une qui survit dans le bassin Gironde-Garonne-Dordogne en France. Les données disponibles sur l'espèce restent très partielles car elles proviennent quasi exclusivement de cette population relictuelle. Au cours de cette thèse, plus d'une centaine d'échantillons anciens d'esturgeons restes archéologiques ou spécimens naturalisés conservés dans les muséums d'histoire naturelle ont été analysé grâce aux méthodes de la paléogénétique. Ces analyses génétiques ont été réalisées sur l'ADN mitochondrial (surtout la Dloop) ainsi que sur cinq loci microsatellites qu'il a été nécessaire d'adapter aux méthodes d'étude de l'ADN ancien. Les données paléogénétiques obtenues ont permis d'étudier : 1) les relations de l'esturgeon européen avec les autres espèces d'esturgeons vivant ou ayant vécu en Europe, en particulier l'esturgeon de l'Adriatique A. naccarii et l'esturgeon atlantique A. oxyrinchus. 2) la diversité génétique de l'esturgeon européen sur l'ensemble de son ancienne aire de répartition. 3) la diversité génétique d'une population d'esturgeon européen au cours du temps la population du Rhône, d'une période où elle était florissante jusqu'à son extinction. L'ensemble de ces données ont été discuté à la lumière de la conservation de l'espèce, qui est aujourd'hui en danger critique d'extinctionThe European sturgeon Acipenser sturio (Linnaeus, 1758) was a common fish of our rivers until the beginning of the 20th century. All populations are now extinct except one which survives in the Gironde-Garonne-Dordogne basin in France. Data available on this species are only partial because they only stem from this relictual population. During this thesis, more than one hundred ancient sturgeon samples archaeological remains or naturalized museum specimens were analysed by paleogenetics means. These genetics anlyses were carried out on mitochondrial DNA (mainly the Dloop) and five microsatellites loci which were adapted to ancient DNA methodologies. Paleogenetics data that we obtained were used to study : 1) A. sturio interactions with other sturgeon species which live or lived in Europe, especially the Adriatic sturgeon A. naccarii and the atlantic sturgeon A. oxyrinchus. 2) the genetic diversity of A. sturio all over its former geographical range. 3) genetic diversity of a population of the European sturgeon through time the Rhone River population from a period it was flourishing until its extinction. All these data were considered in the light of the species conservation, since A. sturio is now critically endangered
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Dudar, J. Christopher. "Reconstructing population history from past peoples using ancient DNA and historic records analysis : the Upper Canadian pioneers and land resources /". *McMaster only, 1998.
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López, de Rioja Víctor. "Population range expansions, with mathematical applications to interacting systems and ancient human genetics". Doctoral thesis, Universitat de Girona, 2019. http://hdl.handle.net/10803/667171.
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The thesis studies from an analytical and computational perspective, and by using reaction-diffusion equations, the spatiotemporal evolution of different populations.
First, the dynamics of the T7 bacteriophage infecting the E. coli bacteria is studied. By adding the delayed time in diffusion and reaction terms, as well as new mathematical terms biologically sound, we can achieve results that accurately match the experimental propagation speeds.
Secondly, different mathematical models are proposed to correctly understand the expansion of VSV in Glioblastoma. The only model capable of this explanation is the system which understands the delay time for the processes of diffusion and reaction.
Finally, the Neolithic transition through Europe is explained by studying ancient genetic DNA samples alongside mathematical simulations. Focusing on haplogroup K, the model is built by analyzing the two Neolithic diffusion mechanisms: demic and cultural. The simulations show that the transition is basically demic, with only 2% of the Neolithic farmers interacting culturallyAquesta tesi estudia des d’un punt de analític i computacional, gràcies a les equacions de reacció-difusió, l’evolució espaciotemporal de diferents poblacions que interactuen entre elles. El primer article estudia la dinàmica del bacteriòfag T7 infectant el bacteri E. coli. Gràcies a la incorporació del temps de retard en els termes de difusió i reacció, així com de nous termes matemàtics amb sentit biològic, aconseguim uns resultats que s’ajusten millor a les velocitats de propagació. El segon article aplica diferents models matemàtics per entendre millor l’expansió del VSV en Glioblastomes. L'únic model capaç d'explicar de manera correcte el sistema té en compte el temps de retard per als processos de difusió i reacció. L’últim article explica la transició del Neolític a través d’Europa utilitzant mostres genètiques antigues i simulacions matemàtiques. Centrant-nos en l’haplogrup K, el model es construeix tenint en compte els dos mecanismes de difusió neolítica: dèmica i cultural. Les simulacions mostren que la transició és bàsicament dèmica, on només el 2% dels neolítics interaccionen culturalment
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Sampietro, Bergua Mª Lourdes. "Genetic Analysis of the prehistoic peopling of Western Europe: Ancient DNA the role of contamination". Doctoral thesis, Universitat Pompeu Fabra, 2007. http://hdl.handle.net/10803/79128.
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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.
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Gaentzsch, Ricarda E. G. "Establishment and maintenance of the DNA methylation pattern in the human alpha-globin cluster". Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:fecf70d2-4845-4f42-b890-c163a1020eec.
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DNA methylation is an epigenetic modification that plays an important role in development and differentiation. The patterns of DNA methylation are largely established in early embryogenesis and maintained during development. Abnormal DNA methylation patterns have been associated with many human diseases, including cancer. Despite its importance, little is currently known about the mechanisms that determine DNA methylation patterns throughout the genome. To shed light on the molecular mechanisms that regulate DNA methylation, this study investigates whether DNA methylation patterns are established and maintained normally when human DNA is placed into a heterologous murine environment as opposed to its natural, endogenous chromosomal environment. Here, a previously generated transgenic mouse model, containing 117 kb of human DNA bearing the human α-globin cluster and all of its known regulatory elements, was analysed. The pattern of DNA methylation of the endogenous human α-globin cluster was compared with that of the transgenic cluster in the background of mouse embryonic stem cells (ESCs) and tissues. It was found that, although the normal human DNA methylation pattern was largely established and maintained in a mouse background, the region immediately around the human α-globin genes themselves is generally less methylated in mouse compared to human ESCs. It was found that regions adjacent and up to 2kb from the CpG islands (CGIs), so-called CGI shores, were unusually hypomethylated: this seems to be the result of an extension of CGIs in humanised mouse (hm) ESCs compared to human (h) ESCs. Furthermore, this hypomethylation appeared to increase during development in both erythroid and non-erythoid cells. To identify any cis-regulatory sequences responsible for the hypomethylated state of human CGI shores in the mouse, 2-4 kb human test sequences containing the CGI associated with the human α-globin 2 (α2) gene and its adjacent hypomethylated shore were re-integrated into the mouse α-globin locus via recombination-mediated cassette exchange (RMCE). Human CGI shores became hypomethylated in the context of the re-integrated test sequences, indicating that the appearance of hypomethylation is determined by the underlying human DNA sequence in the test fragments. In summary, the data presented here reveal that human CGIs become extended when placed in a mouse background leading to hypomethylation of human CGI shores in the mouse compared to the pattern of methylation at the normal endogenous human locus. These findings suggest that species-specific factors determine DNA methylation near CGIs. The transgenic mouse model provides an excellent system to dissect out species-specific regulation of CGI shore methylation. Furthermore, this study lays the foundation for future experiments addressing the role of DNA methylation in regulating human gene expression in the murine context, and examining the validity of transgenic mouse models for the study of human gene regulation.
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Wang, Ke [Verfasser], Stephan [Gutachter] Schiffels, Matthias [Gutachter] Steinrücken y Christina [Gutachter] Warinner. "Investigating human population structure through time with new computational methods and ancient DNA data / Ke Wang ; Gutachter: Stephan Schiffels, Matthias Steinrücken, Christina Warinner". Jena : Friedrich-Schiller-Universität Jena, 2021. http://d-nb.info/1226217907/34.
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Moos, Sarah. "Analyzing the interconnectedness between space, place, and human interaction with the natural environment: "Ecological reawakening: Organic DNA and evolution"". Scripps College, 2009. http://ccdl.libraries.claremont.edu/u?/stc,51.
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I have organized this paper into four chapters: "The Environmental Situation," "Space and Place," "Art and the Natural Environment," and "Creating Work of My Own." Chapter 1 explains human beings' intrinsic interconnection to the natural environment, outlining why humans should be concerned about the current degraded state of the natural world. Chapter 2 discusses the concepts of space and place. It analyzes how human beings interact with and experience spaces, developing their sense of place - within physical, theoretical, and spiritual realms. It finally illustrates the importance that spaces and places have in humans' lives. Chapter 3 describes the Land Art phenomenon: its development, the different forms within it, and artists producing Land Artworks. The forms and artists included are those that have been inspirational for the development of my own work. It also emphasizes Land Art as a fundamental form for improving humans' relationship with the natural environment and the new realm of eco-feminism that resonates with Land Art ideals. Chapter 4 recounts the development of my art throughout my college career. It describes my work as site-specific, sculptural installations that use natural materials. It also states why this format is the most effective for my senior art thesis project. Focusing mainly on "Ecological Reawakening: organic DNA," it explains the mentality in designing, creating, installing, and completing the work. Overall, Chapter 4 emphasizes the work's two main goals: to demonstrate a new avenue for comprehending humankind's place within earth's environmental spaces, and to advocate for an environmental paradigm shift during the twenty-first century. Finally, Chapter 5 describes the transformation of "Ecological Reawakening: organic DNA" as it developed over time during the spring honors senior thesis course. It details my mentalities in adding living plant matter to the structure, incorporating a stool into the piece, and creating "Evolution," the digital photography composition that documents "Ecological Reawakening" and was included in the Scripps Senior Art Exhibition in the Ruth Chandler Williamson Gallery from May 1 – May 17, 2009.
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TASSI, Francesca. "Genome-based multidisciplinary approaches to the reconstruction of human demographic history". Doctoral thesis, Università degli studi di Ferrara, 2015. http://hdl.handle.net/11392/2389071.
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In my doctoral dissertation I summarize the scientific work leading to three papers in peer-reviewed journal, two submitted manuscripts. These entire studies share a common focus on human evolutionary history, but each of them address different scientific questions by means of a different combination of molecular and statistical methods.
Our cells contain a message from the past, written in their genomes; thus the study of genetic variation within and between populations can help us understand aspects of human demographic history over the past thousands of years, i.e. well beyond the time-limits of historical evidence.
Recently, extensive human genome data are becoming available, both from genome wide SNP data, and from the rapidly-increasing number of complete genome sequences, offering novel means of reconstructing human population history with a detail that was, until very few years ago, unthinkable. This abundant, and ever-growing amount of genomic data is of enormous relevant for understanding how and why human are different. Paper I (Barbujani et al., 2013) represents a review of human genetic variation and their implications for human evolutionary inference
Genetic data are indispensable to test hypothesis, generated in complementary discipline such as anthropology, linguistic and archaeology. Paper II (Tassi et al., submitted) and Paper III (Longobardi et al., submitted) provide examples of how it is possible to achieve a detailed picture of human history and evolution, taking advantage of archaeological and linguistic knowledge to interpret the genetic data.
For many years, studies of human genetic diversity have been necessarily limited to modern populations, severely limiting our ability to investigate the detail of past processes. Conversely, today, thanks to the advent of methods for reliably typing ancient DNA, it has been possible to increase our power to reconstruct historical demographic processes, and to explicitly test evolutionary hypotheses. In Paper IV (Ghirotto et al., 2013) and Paper V (Tassi et al., 2013) we analyzed ancient Etruscans sample and, within the ABC framework, we explicitly compared several models, differing for demographic and genealogical histories, to shed light on the origin and evolution of the Etruscans.
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Lamnidis, Thiseas C. [Verfasser], Stephan [Gutachter] Schiffels, Holger [Gutachter] Schielzeth y Anna-Sapfo [Gutachter] Malaspinas. "Exploring the effects of migration and admixture on human populations through time, using ancient DNA / Thiseas C. Lamnidis ; Gutachter: Stephan Schiffels, Holger Schielzeth, Anna-Sapfo Malaspinas". Jena : Friedrich-Schiller-Universität Jena, 2021. http://d-nb.info/1228432171/34.
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Seeliger, Martin [Verfasser], Helmut [Gutachter] Brückner y Olaf [Gutachter] Bubenzer. "Elaia, the maritime harbour city of ancient Pergamon (Turkey) – Coastal evolution and human impact over the past eight millennia. / Martin Seeliger. Gutachter: Helmut Brückner ; Olaf Bubenzer". Köln : Universitäts- und Stadtbibliothek Köln, 2016. http://d-nb.info/1112652124/34.
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Kline, Amanda Le. "Speculation on the Trajectory of Human Kind". The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1404324124.
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Rogers, Leland Liu. "Understanding ancient human population genetics of the eastern Eurasian steppe through mitochondrial DNA analysis| Central Mongolian samples from the Neolithic, Bronze Age, Iron Age and Mongol Empire periods". Thesis, Indiana University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10253175.
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This study is based on the extraction and sequencing of the mitochondrial DNA from 132 ancient human samples from central Mongolia dating to the Neolithic, Bronze Age, Iron Age (Xiongnu) and Mongol Empire periods. The data collected were compared to mtDNA gene pools from multiple published studies of ancient and modern human populations from across Eurasia with particular focus on Eurasian steppe populations. The results of these analyses support a model of human migration showing an original eastern population on the Neolithic Mongol Steppe that admixed with a western population, which had migrated onto the eastern Eurasian steppe zone during the Neolithic. This study demonstrates western Eurasian DNA on the eastern Eurasian steppe as far as the Mongol Steppe by the Late Neolithic, and reveals a significant western component in the Bronze Age population of Central Mongolia. It supports an indigenous population as the origin of the Xiongnu, confirms that the Xiongnu had a strongly admixed mtDNA gene pool, and indicates that a significant shift towards eastern mtDNA occurred between the Xiongnu Empire and Mongol Empire periods, which has continued up to the present.
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Long, Hannah Katherine. "Evolutionary usage and developmental roles of vertebrate non-methylated DNA". Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:78b14c1d-1fa3-46f1-815f-a8ba55579c43.
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Vertebrate genomes exhibit global methylation of cytosine residues where they occur in a cytosine-guanine dinucleotide (CpG) context and this epigenetic mark is generally thought to be repressive to transcription. Punctuating this pervasive DNA methylation landscape are short, contiguous regions of non-methylated DNA which are found at two thirds of mammalian gene promoters. These non-methylated regions exhibit CpG content close to expected levels as they escape the depletion of CpGs observed across the methylated fraction of the genome. The unique nucleotide properties of these CpG island (CGI) regions enable their identification by computational prediction in mammalian genomes. Owing to a lack of high-resolution genome-wide DNA methylation profiles in non-mammalian species, these CGI predictions have often been used as a proxy for non-methylated DNA in these organisms. In contrast to mammals, CGI predictions in cold-blooded vertebrates rarely coincide with gene promoters, leading to the belief that CGls are significantly divergent between vertebrate species, and that unique promoter-associated features may have been acquired during warmblooded vertebrate evolution. This thesis is primarily concerned with the location, establishment and biological function of non-methylated islands of DNA in vertebrate genomes. To experimentally determine genome-wide profiles of non-methylated DNA, a novel biochemical technique was established called biotinylated ZF-CxxC affinity purification (Bio-CAP), and development of this method is discussed in Chapter 3. Experimental analysis of non-methylated DNA profiles in this thesis initially addresses two main questions: (1) 'How does the non-methylated DNA landscape compare genome-wide for seven vertebrates considering distinct tissue types and developmental stages?' (2) 'How are vertebrate non-methylated regions of DNA defined and interpreted in the nuclear environment?' To address the first question, non-methylated DNA was profiled by Bio-CAP sequencing across the genomes of seven diverse vertebrate species, representing all major branch points of vertebrate evolution, and the results are discussed in Chapters 4 and S. Contrary to previously held dogma, experimentally determined nonmethylated islands of DNA (NMls) constitute an ancient epigenetic feature of vertebrate gene regulatory elements. However, despite having numerous high-resolution maps of vertebrate non-methylated DNA, the means by which NMls are identified and maintained in the nuclear environment remains poorly understood. To address the second question and identify features which determine the methylation state of DNA, exogenous DNA sequences were introduced into mouse embryonic stem (ES) c~.II~. Non-methylated DNA was profiled by Bio-CAP sequencing to investigate how different features, such as sequence-specific binding motifs, chromatin architecture and nucleotide composition of a given DNA sequence impact local DNA methylation patterns. Interestingly, the majority of exogenous promoters were appropriately non-methylated in mouse ES cells, germline and somatic cells suggesting that gene promoters have retained strong signals for the nonmethylated state across millions of years of evolution (discussed in Chapter 6). During mouse embryogenesis, genome-scale DNA demethylation and remethylation events occur to remodel the epigenetic landscape and loss of DNA methylation during this time leads to embryonic lethality. To investigate the biological function of non-methylated DNA, the third question addressed in this thesis is (3) 'What is the developmental importance of non-methylated islands of DNA during vertebrate embryogenesis?' To investigate this, members of the ZF-CxxC domain-containing family of chromatin modifiers were ablated in zebrafish embryos to perturb the chromatin landscape at NMls, and therefore interfere with their function during early development (Chapter 7). Early embryonic development and patterning was disrupted in knockdown embryos, suggesting that interpretation of non-methylated DNA and placement of chromatin modifications at NMls is essential for normal zebrafish embryogenesis. Together this work sheds light on the evolutionary origins of NMls, the mechanisms involved in the recognition and establishment of nonmethylated loci and provides an insight into the function of non-methylated DNA during early embryonic development.
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Zvénigorosky-Durel, Vincent. "Etude des parentés génétiques dans les populations humaines anciennes : estimation de la fiabilité et de l'efficacité des méthodes d'analyse". Thesis, Toulouse 3, 2018. http://www.theses.fr/2018TOU30260/document.
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L'étude des parentés génétiques permet à l'anthropologie d'identifier la place du sujet au sein des différentes structures dans lesquelles il évolue : l'individu est membre d'une famille biologique, d'un groupe social et d'une population. L'application des méthodes probabilistes classiques (établies pour répondre à des problématiques de médecine légale, comme la méthode des Likelihood Ratios (LR) ou " Rapports de vraisemblance ") aux données STR issues du matériel archéologique a permis la découverte de nombreux liens de parenté, qui ensemble constituent des généalogies parfois complexes. Notre pratique prolongée de ces méthodes nous a cependant amenés à identifier certaines limites de l'interprétation des données STR, en particulier dans les cas de parentés complexes, distantes ou consanguines, ou dans des populations isolées, méconnues ou disparues. Ce travail de thèse s'attache en premier lieu à quantifier la fiabilité et l'efficacité de la méthode des LR dans quatre situations : une population moderne avec une grande diversité allélique, une population moderne avec une faible diversité allélique, une population ancienne de grande taille et une population ancienne de petite taille. Les publications récentes font usage des marqueurs plus nombreux issus des nouvelles technologies de séquençage (NGS) pour mettre en place de nouvelles stratégies de détection des parentés, basées en particulier sur l'analyse des segments chromosomiques partagés par ascendance entre les individus (segments IBD). Ces méthodes ont rendu possible l'estimation plus fiable de probabilités de parenté dans le matériel ancien. Elles sont néanmoins inadaptées à certaines situations caractéristiques de la génétique des parentés archéologiques : elles ne sont pas conçues pour fonctionner avec une seule paire isolée d'individus et reposent, comme les méthodes classiques, sur l'estimation de la diversité allélique dans la population. Nous proposons donc une quantification de la fiabilité et de l'efficacité de la méthode des segments partagés à partir de données NGS, en s'attachant à déterminer la qualité des résultats dans les différentes situations qui correspondent à des tailles de population plus ou moins importantes et à une hétérogénéité plus ou moins grande de l'échantillonnage.[...]The study of genetic kinship allows anthropology to identify the place of an individual within which they evolve: a biological family, a social group, a population. The application of classical probabilistic methods (that were established to solve cases in legal medicine, such as Likelihood Ratios, or LR) to STR data from archaeological material has permitted the discovery of numerous parental links which together constitute genealogies both simple and complex. Our continued practice of these methods has however led us to identify limits to the interpretation of STR data, especially in cases of complex, distant or inbred kinship. The first part of the present work is constituted by the estimation of the reliability and the efficacy of the LR method in four situations: a large modern population with significant allelic diversity, a large modern population with poor allelic diversity, a large ancient population and a small ancient population. Recent publications use the more numerous markers analysed using Next generation Sequencing (NGS) to implement new strategies in the detection of kinship, especially based on the analysis of chromosome segments shared due to common ancestry (IBD "Identity-by-Descent" segments). These methods have permitted the more reliable estimation of kinship probabilities in ancient material. They are nevertheless ill-suited to certain typical situations that are characteristic of ancient DNA studies: they were not conceived to function using single pairs of isolated individuals and they depend, like classical methods, on the estimation of allelic diversity in the population. We therefore propose the quantification of the reliability and efficiency of the IBD segment method using NGS data, focusing on the estimation of the quality of results in different situations with populations of different sizes and different sets of more or less heterogeneous samples.[...]
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Pleuger, Elisa. "Evolution paléoenvironnementale du delta de la Medjerda et géoarchéologie du site d'Utique (Tunisie)". Thesis, Lyon, 2020. http://www.theses.fr/2020LYSE2017.
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La ville d'Utique est considérée comme l'un des trois premiers comptoirs phéniciens de Méditerranée occidentale. Selon la tradition littéraire, elle aurait été fondée en 1101 av J.-C., par des phéniciens venus de Tyr au Liban.Néanmoins, dans l'état actuel des recherches, aucun vestige archéologique ne remonte au delà du 9e siècle av. J.-C. Aux périodes phéniciennes et romaines, Utique était une importante ville marchande faisant face à la mer. Au cours des siècles, la ville a perdu son accès à la mer et son port s'est envasé. Malgré plus d'un siècle d'investigation par les archéologues et chercheurs associés, l'emplacement des structures portuaires de la ville aux périodes phénicienne et romaine reste inconnu, enfoui sous plusieurs mètres de sédiments.Partant de cette problématique archéologique, notre recherche s'est concentrée sur trois axes principaux : paléogéographique, géoarchéologique et palynologique. Basés sur l'étude pluridisciplinaire de carottages sédimentaires, les résultats ont montré que les fortes crues de l'Oued Medjerda, qui coulait au sud de la ville à l'époque romaine, ont été un facteur majeur du déclin d'Utique et de l'ensablement de son port. En effet, au moment de sa fondation, la ville était située sur un promontoire baigné par la mer, mais les sédiments transportés par la Medjerda ont progressivement scéllé la baie, laissant la pointe du promontoire d'Utique à 10 km à l'intérieur des terres. Une crise hydrologique majeure a été mise en évidence vers le 4e siècle ap J.-C. Celle-ci est corrélée à une augmentation des taux de sédimentation dans le bassin versant, ce qui semble correspondre à une dégradation climatique globale à la même époque. Les résultats mettent également en évidence, l'existence d'une longue façade maritime au nord du promontoire d'Utique aux époques phénicienne et romaine. Un environnement marin profond est attesté dans l'ancienne baie au 6e mill. av. J.-C. et la profondeur de la colonne d'eau le long de la façade nord était encore de 2 m autour des 4e _ 3e siècle av. J.C. La phase d'occupation phénicienne et romaine est caractérisée par une forte baisse des taxons forestiers, probablement due à des défrichements importants pour l'agriculture et le pastoralisme. L'olivier quant à lui est en augmentation, ainsi que les céréales. La crise érosive survenant à la fin de la période romaine s'accompagne d'une très forte augmentation de l'armoise, témoin d'une steppisation du paysage.Ce travail illustre la contribution de la géoarchéologie à une résolution d'une problématique archéologique majeure et à la compréhension des relations entre cette importante ville portuaire et son environnementUtica is considered, according to ancient literary tradition, as one of the fist three Phoenician foundations of the Western Mediterranean, supposedly founded in 1101 BC by Levantines from Tyre. Neverthelesss, until now, no archaeological remains date back beyond the 9th century BC. In the Phoenician and Roman periods, Utica was an important merchant coastal town, facing the sea. Over the centuries, the city has lost its access to the sea and the port has silted up. Despite more than a century of investigation, by archaeologist and associated researchers, the location of the city's harbour, dating from the Phenician and Roman periods, remains unknown, burried under several meters of sediment.Starting from this archaeological problem, our research focused on three main axes : paleogeographic, geoarchaeological and palynological. Based on the multidisciplinary study of sedimentary cores, the results showed that the strong floods of the Medjerda wadi, wich flowed south of the city during Roman times, were a major factor in the decline of Utica and the silting of its port. Indeed, at the time of its foundation, the city was located on a promontary bathed by the sea, but the sediments transported by the Medjerda gradually sealed the bay, leaving the tip of the Utica promontary 10 km in land. A major hydrological crisis was highlighted around the 4 th century AD. This correlated with an increased in sedimentation rates in the watershed, wich seems to correspond to an overall climatic degradation. The results also highlight the existence of a long maritime facade north of Utica promontary during the Phoenician and Roman eras. A deep maritime environment is attested in the ancient bay at 6th mill. BC and the depth of the water column along the north facade was still 2 m around the 4th - 3th centuries BC. Finally, the palynological study showed the existence of traces of human activities as early as the 3th mill. BC. The Phoenician and Roman occupation is characterized by a sharp drop in forest taxa, probably due a significant clearings for agriculture and pastoralism. The olive tree is increasing, as well as cereals. The erosive crisis occuring at the end of the Roman period was accompanied by a sharp increase of "Artemisia", witnessing a steppisation of the landscape.This work illustrates the contribution of geoarchaelogy to the resolution of a major archeological problem and to the understanding of the relationships between this important port city and its enviroment
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Monfouilloux, Sylvaine. "Etude de la structure et de l'évolution d'une région de translocations sous télomériques chez l'homme". Rouen, 1997. http://www.theses.fr/1997ROUES065.
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Les extrémités des chromosomes comportent le télomère puis la région sous télomérique. Ces deux domaines se distinguent des autres régions chromosomiques car ils évoluent par des échanges entre les chromosomes hétérologues. Le télomère est une structure spécialisée constituant la fin des chromosomes et indispensable à leur stabilité. Il joue un rôle important dans l'organisation spatiale des chromosomes en particulier dans l'agglutination des extrémités chromosomiques en périphérie nucléaire. La région sous télomérique, adjacente au télomère est très redondante entre les chromosomes hétérologues et se termine avec les séquences uniques spécifiques à chaque chromosome. Sa fonction ainsi que sa structure ne sont pas bien connues. Plusieurs familles de séquences répétées y sont présentes. Certaines sont localisées uniquement à proximité du télomère, d'autres comme les minisatellites sont en majorité localisées dans les derniers mégabases des chromosomes. Nous avons étudié en détail une région sous télomérique présente sur une dizaine de chromosomes chez tous les individus. Nous montrons qu'elle s'est propagée par des translocations successives de domaines chromosomiques terminaux de 80 a 200 Kb, impliquant des processus de recombinaison divers. Ces translocations se sont produites après la séparation de l'homme et du chimpanzé. La stabilité de la région apparaît variable suivant les chromosomes ce qui se traduit par un polymorphisme des localisations de la région entre les individus. Cette région sous télomérique a évolué de façon très différente entre l'homme et le chimpanzé. Nous proposons que cette évolution pourrait être conditionnée par la présence de gènes adjacents à la région sous télomerique. Nous avons en effet montré que des gènes ubiquitaires se trouvent à quelques dizaines de Kb en aval de la région sous télomérique. Leur expression pourrait être influencée par la chromatine adjacente, c'est à dire par la nature de la région sous télomérique. Nous proposons enfin que l'évolution de la région sous télomérique constitue un modèle pour l'étude de l'évolution du génome humain.
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Silvestrini, Milene 1972. "Ecology and evolution of Croton floribundus Spreng = how are the genetic diversity and structure of a pioneer tree species affected by natural and human disturbances? = Ecologia e evolução de Croton floribundus Spreng: como a diversidade e estrutura genética de uma espécie arbórea pioneira são afetadas por distúrbios naturais e antrópicos?" [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/315905.
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Orientadores: Flavio Antonio Maës dos Santos, Maria Imaculada ZucchiTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A estrutura genética espacial de populações de plantas pode variar ao longo dos estádios ontogenéticos, através das gerações e entre diferentes condições ambientais. Estas mudanças são direcionadas por fatores ecológicos e evolutivos. As espécies pioneiras apresentam histórias de vida e estruturas populacionais características que são afetadas principalmente pelas mudanças ambientais geradas por distúrbios naturais ou antrópicos. O objetivo deste trabalho foi investigar como as características do ciclo de vida, os processos ecológicos e fatores genéticos associados aos distúrbios afetam a diversidade e estrutura genética de populações de uma espécie arbórea pioneira. Nós estudamos Croton floribundus Spreng. (Euphorbiaceae), uma espécie arbórea pioneira abundante em clareiras e em áreas secundárias da Floresta Estacional Semidecidual, em duas áreas com níveis contrastantes de distúrbios antrópicos: uma floresta primária e uma floresta secundária em estádio inicial de sucessão. A fim de abordar a principal questão deste estudo, nós avaliamos o padrão de distribuição da espécie sob as diferentes condições ambientais geradas por distúrbios naturais e antrópicos (Capítulo I); testamos e caracterizamos iniciadores universais cloroplastidiais (cpSSR) para C. floribundus (Capítulo II); desenvolvemos e caracterizamos marcadores microssatélites nucleares (SSR) para C. floribundus bem como examinamos algumas características citogenéticas da espécie com o objetivo de testar a ocorrência de poliploidia e avaliar sua implicação para o uso dos marcadores SSR (Capítulo III); avaliamos a diversidade e estrutura genética de C. floribundus entre duas classes de tamanho e entre populações em uma floresta primária e uma floresta secundária em estádio inicial de sucessão (Capítulo IV). C. floribundus foi frequente e igualmente distribuído em clareiras de todos os tamanhos na floresta primária, mas sua estrutura populacional variou entre áreas com níveis contrastantes de distúrbio antrópico. Seis locos cpSSR foram otimizados e caracterizados em C. floribundus. O estudo citogenético permitiu a caracterização mais precisa dos locos SSR, bem como forneceu novos dados sobre a origem e a evolução da espécie. O número de bivalentes observados na meiose, n = 56 (2n = 8x = 112), mostrou a ocorrência de poliploidia em todas as populações estudadas. Altos níveis de diversidade genética foram encontrados para C. floribundus. A dispersão de sementes e as colonizações (e extinções) foram determinantes para a estrutura genética em fina escala encontrada nas populações de C. floribundus em ambos os tipos de florestas. Além disso, os efeitos destes processos associados aos distúrbios antrópicos parecem aumentar fortemente a diferenciação genética entre as populações na floresta em estádio inicial de sucessão. As análises de marcadores moleculares nucleares e cloroplastidias sugeriram que o fluxo gênico por pólen é responsável por manter a diversidade genética dentro das populações de C. floribundus tanto na floresta primária quanto na floresta secundária em estádio inicial de sucessão. Nesta última, o fluxo gênico por sementes parece ser igualmente importante. Os resultados obtidos mostraram que a dinâmica de clareiras, o processo de colonização e a dispersão de pólen e sementes afetam a diversidade e estrutura genética da espécie arbórea pioneira, aumentando-os ou diminuindo-os conforme o número de colonizadores, número de populações-fonte, as taxas de fluxo gênico e o nível de perturbação antrópica da área
Abstract: The spatial genetic structure of plant populations may vary across life stages, across generations and among different environmental conditions. These changes are driven by evolutionary and ecological forces. Pioneer tree species exhibit particular life histories and population structures that are mainly affected by environmental changes generated by natural or human disturbances. Our aim was to investigate how the life-history traits, ecological processes, and the genetic factors associated to natural and human disturbances can affect the genetic diversity and structure of populations of a pioneer tree species. We studied Croton floribundus Spreng. (Euphorbiaceae), a pioneer tree species abundant in gaps and secondary areas of the semi-deciduous tropical forest, in two areas with contrasting levels of human disturbance: a primary forest and an early successional forest. In order to address the main question of this study, we examined the pattern of distribution of the species under the different environmental conditions generated by natural and human disturbances (Chapter I); tested and characterized universal chloroplast microsatellite (cpSSR) primers for C. floribundus (Chapter II); developed and characterized nuclear microsatellite (SSR) markers for C. floribundus as well as examined some cytogenetic traits of the species in order to test for polyploidy and to evaluate its implications for the appropriate use of the SSR markers (Chapter III); and evaluated the genetic diversity and structure of C. floribundus between two size classes and among populations in the primary forest and in the early successional forest (Chapter IV). C. floribundus was widespread and equally distributed along the gap size range in the primary forest, but its population structure varied between areas with contrasting levels of human disturbance. Six universal cpSSR loci were optimized and characterized for C. floribundus. The cytogenetic study allowed the accurate characterization of SSR loci as well as provided new data on the origin and evolution of the species. The number of bivalents observed in meiosis n=56 (2n=8x=112) showed the occurrence of polyploidy in all populations studied. High genetic diversity levels were found for C. floribundus. Seed dispersal and colonizations (and extinctions) were determinants of the fine-scale genetic structure of C. floribundus in both forest types. Also, their effects associated to the human disturbances seem to strongly increase the genetic differentiation among populations in the early successional forest. Analysis of nuclear and chloroplast markers suggested that gene flow by pollen is responsible for maintaining the genetic diversity within populations of C. floribundus in both primary and early successional forests. In the latter, gene flow by seeds seem to be equally important. The results showed that gap dynamics, colonization process, and pollen and seed dispersal affect the genetic diversity and structure of the pioneer tree species by increasing or decreasing them depending mainly on the number of colonizers, the number of source populations, the gene flow rates, and the level of human disturbance of the area
Doutorado
Ecologia
Doutora em Ecologia
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Baker, Antoine. "Le programme spatio-temporel de réplication de l'ADN et son impact sur l'asymétrie de composition : d'une modélisation théorique à l'analyse de données génomiques et épigénétiques". Phd thesis, Ecole normale supérieure de lyon - ENS LYON, 2011. http://tel.archives-ouvertes.fr/tel-00682586.
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Deux processus majeures de la vie cellulaire, la transcription et la réplication, nécessitent l'ouverture de la double hélice d'ADN et agissent différemment sur les deux brins, ce qui génère des taux de mutation différents (asymétrie de mutation), et aboutit à des compositions en nucléotides différentes des deux brins (asymétrie de composition). Nous nous proposons de modéliser le programme spatio-temporel de réplication et son impact sur l'évolution des séquences d'ADN. Dans le génome humain, nous montrons que les asymétries de composition et de mutation peuvent être décomposées en deux contributions, l'une associée à la transcription et l'autre à la réplication. Celle associée à la réplication est proportionnelle à la polarité des fourches de réplication, elle-même proportionnelle à la dérivée du "timing" de réplication. La polarité des fourches de réplication délimite, le long des chromosomes humains, des domaines de réplication longs de plusieurs Mpb où le "timing" de réplication a une forme de U. Ces domaines de réplication sont également observés dans la lignée germinale, où ils sont révélés par une asymétrie de composition en forme de N, indiquant la conservation de ce programme de réplication sur plusieurs centaines de millions d'années. Les bords de ces domaines de réplication sont constituées d'euchromatine, permissive à la transcription et à l'initiation de la réplication. L'analyse de données d'interaction à longue portée de la chromatine suggère que ces domaines correspondent à des unités structurelles de la chromatine, au coeur d'une organisation hautement parallélisée de la réplication dans le génome humain.
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Saenz, Ruales Nancy. "Etude paléogénétique de deux sépultures collectives du Néolithique (mont Aimé, Bassin parisien, 3500-3000 av. J.C.)". Thesis, Toulouse 3, 2021. http://thesesups.ups-tlse.fr/4969/.
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En France, deux courants culturels sont entrés en contact dès le Néolithique ancien (6000-4700 av .J.-C.) : le courant Méditerranéen par le Sud et le courant Danubien par l'Est. Dans le cadre de ce travail de thèse, nous avons étudié deux sépultures collectives du Bassin parisien qui pourraient se trouver au point de rencontre de ces deux courants ; il s'agit des hypogées 1 et 2 du Mont-Aimé (Marne, France) utilisées à la fin du Néolithique (3500-3000 av. J.C.). Dans ces deux ensembles funéraires souterrains de construction analogue, des analyses génétiques ont été réalisées sur 30 des sujets inhumés. L'étude de STR (Short Tandem Repeats) autosomaux a permis la caractérisation du sexe des individus ainsi que la détermination de liens de proche parenté. L'analyse de STR et de SNP (Single Nucleotide Polymorphisms) du chromosome Y a non seulement permis de retracer les lignées paternelles mais aussi de comparer ces dernières à celles portées par d'autres populations anciennes et modernes. Enfin, le séquençage de la totalité de la molécule d'ADN mitochondrial a, de la même manière, permis l'étude de lignées maternelles. L'analyse combinée des données archéologiques et de l'ADN nucléaire a révélé les détails de la chronologie du site et démontré la présence de parentés génétiques au sein et entre les deux hypogées. Ces résultats contribuent ainsi à notre compréhension des similarités de structure entre les deux sépultures collectives, utilisées par des générations successives d'individus. L'étude des lignées uniparentales a montré une diversité d'haplotypes mitochondriaux caractéristiques du Néolithique européen mais a également mis en lumière l'homogénéité des haplotypes du chromosome Y, dont aucun n'est retrouvé dans d'autres populations anciennes ou modernes. Ce résultat suggère la présence, dans la population Néolithique du Bassin Parisien, de groupes humains porteurs de lignées maternelles typiques de la période et de lignées paternelles alors déjà rares et aujourd'hui disparues. Si la présence de ces lignées masculines, vraisemblablement issues du Paléolithique européen, ne permet pas de rattacher le groupe d'individus du Mont-Aimé à l'un ou l'autre des deux courants de migration européens, elle démontre la persistance d'un groupe d'hommes encore génétiquement non-assimilés à la fin du Néolithique. Ces analyses révèlent donc une histoire personnelle, celle de lignées paternelles demeurées majoritaires dans un groupe humain, alors même que celui-ci était progressivement incorporé à une population de nouveaux arrivantsIn France, two cultural currents came into contact from the early Neolithic (6000-4700 BC): the Mediterranean current from the south and the Danubian current from the east. As part of this thesis work, we studied two multiple burials in the Paris Basin which could be located at the meeting point of these two currents; these are hypogeum 1 and 2 of Mont-Aimé (Marne, France) used at the end of the Neolithic (3500-3000 BC). In these two underground burial complexes of similar construction, genetic analyzes were carried out on 30 of the buried subjects. The study of autosomal STRs (Short Tandem Repeats) allowed the characterization of the sex of individuals as well as the determination of close family ties. The analysis of STR and SNP (Single Nucleotide Polymorphisms) of the Y chromosome has not only made it possible to trace the paternal lines but also to compare them with those carried by other ancient and modern populations. Finally, the sequencing of the entire mitochondrial DNA molecule has similarly enabled the study of maternal lines. Combined analysis of archaeological data and nuclear DNA revealed details of the site's chronology and demonstrated the presence of genetic relatedness within and between the two hypogea. These results thus contribute to our understanding of the structural similarities between the two collective burials, used by successive generations of individuals. The study of uniparental lineages has shown a diversity of mitochondrial haplotypes characteristic of the European Neolithic but also shed light on the homogeneity of the Y chromosome haplotypes, none of which is found in other ancient or modern populations. This result suggests the presence, in the Neolithic population of the Paris Basin, of human groups carrying maternal lines typical of the period and paternal lines that were already rare and now extinct. If the presence of these male lineages, probably from the European Paleolithic, does not allow the group of individuals from Mont-Aimé to be linked to one or the other of the two European migration currents, it demonstrates the persistence of a group of men still genetically unassimilated at the end of the Neolithic. These analyzes, therefore, reveal a personal history, that of paternal lines which remained in the majority in a human group, even though the latter was gradually incorporated into a population of newcomers
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Ross, Jeremy D. "The Evolutionary History, Demographic Independence and Conservation Status of Two North American Prairie Bird Species: The Greater Prairie Chicken and the Lark Sparrow". Bowling Green State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1303855437.
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