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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.[...]

In this paper I report on a study whose principal aim is to understand the development and decline of the southern Peruvian Nasca culture in the upper Río Grande de Nasca drainage, and its cultural and biological affinities to the preceding Paracas culture. Ancient DNA analyses were conducted on over 300 pre-Columbian individuals from various cemeteries in southern Perú, from periods ranging from the Formative Period to the Middle Horizon. Our results show that the Nasca populations are close related to those of the preceding Paracas culture, and combined with archaeological data, suggest that the Nasca culture was autochthonous to the Río Grande drainage. Furthermore, one can observe how changes in socioeconomic complexity influence the genetic diversity. The pre-Columbian coastal populations of southern Perú differ significantly from both ancient highland and all present-day Peruvian populations. The genetic differentiation between the main cultural areas of western South America seems to fade with the Middle Horizon. / Se presenta aquí un estudio cuyo objetivo principal es la comprensión del desarrollo y decadencia de la cultura Nasca en la parte alta de la cuenca del Río Grande de Nasca, así como sus afinidades biológicas y culturales con su antecesora, la cultura Paracas. Se realizaron análisis de ADN antiguo en más de 300 individuos procedentes de varios cementerios prehispánicos del sur del Perú correspondientes a un lapso que se inicia en el Período Formativo y alcanza el Horizonte Medio. Los resultados muestran que las poblaciones nasca son cercanas a las de su cultura precedente. Esta información, combinada con los datos arqueológicos, sugiere que la cultura Nasca se desarrolló, de manera autóctona, en la cuenca del Río Grande. Más aún, se puede observar que los cambios socioeconómicos de este período influyeron en la diversidad genética. Las poblaciones prehispánicas costeñas del sur del Perú difieren, significativamente, de las antiguas poblaciones de la sierra y de las poblaciones peruanas actuales. La diferenciación genética entre las principales áreas culturales de la parte oeste de Sudamérica parece desaparecer en el Horizonte Medio.

Even though the analysis of DNA from archaeological bone comes with some major limitations, it constitutes the most directmeans of investigating prehistoric population dynamics. The interdisciplinary contextualization of genetic data with the archaeological and palaeoecological record helps to reconstruct past population histories and the demography of ancient populations. For South America, palaeogenetic studies have become increasingly important. Here we review the existing ancient DNA data from pre-Columbian individuals to assess their potential to contribute to our understanding of early South American population history. The spatial and temporal distribution of ancient South American populations analysed to date is very uneven and the data resolution of the analysed genetic markers is low. Nevertheless, the data suggest that there were population dynamic processes accompanying cultural development in Western South America. With the new methodologies and better sampling strategies employed in current paleogenetic projects and more effective interdisciplinary cooperations it will be soon possible to achieve a better understanding of the peopling of the continent and the succeeding population history. / Aún cuando el análisis de ADN de huesos arqueológicos tiene algunas grandes limitaciones, constituye la manera más directa de investigar eventos prehistóricos de dinámica poblacional. La contextualización interdisciplinaria de los datos genéticos con los registros arqueológico y paleoecológico permite reconstruir las historias poblacionales pasadas y la demografía de sociedades antiguas. Por otro lado, el número de estudios paleogenéticos en Sudamérica se está incrementando. En este artículo revisamos los datos de ADN antiguo de individuos prehispánicos que existen en la actualidad con la finalidad de evaluar su potencial para contribuir a nuestro entendimiento de la historia temprana del poblamiento de Sudamérica. La distribución espacial y temporal de las poblaciones sudamericanas antiguas muestreadas a la fecha es muy irregular y la resolución de los marcadores genéticos analizados esbaja. Sin embargo, los datos sugieren que existieron procesos de dinámica poblacional que acompañaron el desarrollo cultural de la parte oeste de Sudamérica. Con las nuevas metodologías y mejores estrategias de muestreo que se emplean hoy en día en los proyectos de paleogenética, y con una cooperación interdisciplinaria más efectiva, pronto será posible lograr un mejor entendimiento del poblamiento del continente, así como de los hechos sucesivos de su historia poblacional.

The aim of this diploma thesis was the initial genetic analysis of early mediaeval burial site from Mlekojedy polycultural locality (Litoměřice District, Czech Republic). Autosomal STR markers were chosen because of the following reasons. The high degree of polymorphism of these markers and the high extent of heterozygosity favor the use of STRs instead of mitochondrial DNA for the structural analysis of small populations. Usefulness of STR typing for validation purposes was demonstrated many times before. We used primers for miniSTRs to obtain the fullest results. Nuclear DNA was extracted from 35 % of bone samples and 91 % of teeth. We detected lower PCR amplification success rate of fragments longer than 150 bp and very high rate of allele drop-out which is sign of degraded DNA. Twelve reliable genotypes were determined for TH01 marker. Observed allele frequency and genetic diversity values were discussed in comparison with recent populations and other aDNA studies of burial sites. Keywords: ancient DNA, STR markers, miniSTR, early medieval burial site, Czech population

This thesis focuses on new haplotype-based methods for analyzing ancient DNA (aDNA) data. Methods based on allele frequency have so far dominated the aDNA world and have been the primary workhorse that drives most of the exciting discoveries from aDNA in the past decade. However, it suffers from two shortcomings: first, it has low resolution for decoding the demography of the recent past because the widely used in-solution capture enrichment panel (1240k panel) mostly consists of common variants, which is not particularly informative about recent population history; second, it can produce biased results due to deep population structure. Haplotype-based methods (e. g., imputation, phasing) and their downstream tasks (e. g., identity-by-descent segments calling) have long been applied to DNA data collected from modern populations and have greatly advanced many areas of human genetics, including both medical and population genetics. However, progress has been lagging in the aDNA world. This thesis presents three new haplotype-based methods that open new avenues for aDNA data analysis. Chapter 2 introduces hapCon, a new method for estimating contamination rate in aDNA sequencing data that implicitly performs imputation on the haploid male X chromosome. Because hapCon’s ability to use linkage disequilibrium (LD) to draw information from neighboring sites and to use the Li&Stephen’s haplotype copying model to draw information from a large reference panel, it consistently outperforms previously published methods by producing estimates with much lower variance. Section 2.4 also introduces how hapCon can be extended to estimate contamination rate from runs of homozygosity (ROH), which allows it to be applied to female samples that contain 50cM or more ROH blocks as well. Chapter 3 introduces ancIBD, a new method for detecting identity-bydescent (IBD) segments from aDNA data with 0.25x coverage (WGS data) or 1x coverage (1240k data). The model was designed by Harald Ringbauer, my PhD supervisor, during his postdoc. I was mainly responsible for simulations and extending it to detecting IBD2 segments and to IBD detection on X chromosomes. Chapter 4 presents TTNe, a new method to estimate effective population size (Ne) trajectory from time-series IBD segments. This is particularly handy for the aDNA community because samples collected from the same site often date to different time periods. However, as most models are designed to work with modern DNA, they assume all samples are contemporaneous. Using simulations, we show that utilizing IBD sharing in time series has increased resolution to infer recent fluctuations in effective population sizes compared to methods that only use contemporaneous samples. Finally, we developed an approach for estimating and modeling IBD detection errors in empirical IBD analysis. To showcase the practical utility of TTNe, we applied it to two time transects of ancient genomes, individuals associated with the Copper Age Corded Ware Culture (CWC) and Medieval England. In both cases, we found evidence of a growing population, a signal consistent with archaeological records. Chapter 5 discusses possible directions for improving the works presented in this thesis.

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 perspectives / Syftet 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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The mitochondrion is a tiny organelle that is the power supplier of the cell and vital to the functioning of the body organs. Additionally it contains a small circular genome of about 16 kb, present in many copies which makes the mitochondrial DNA more viable than nuclear DNA. Mitochondrial DNA is also maternally inherited and thus provides a direct link to maternal relatives. These two properties are of particular use for forensic samples, which only contain limited or degraded amounts of DNA, and for historical samples (ancient DNA). This thesis presents work on the mitochondrial DNA in the hypervariable regions (HV) I and II, in both contemporary and historical samples. Forensic genetics makes use of mitochondrial DNA analysis in court as circumstantial evidence, and population databases are used for the calculation of evidence value. Population samples (299) across Sweden have been analysed in order to enrich the EDNAP mtDNA database (EMPOP) (paper I). The application of mitochondrial DNA analysis allowed for analysis of historical skeletal remains: Copernicus, 1473-1543 (paper II), Karin Göring, 1888-1931 (paper III) and Medieval bones, 880-1000 AD, from a mass grave found in Sigtuna, Sweden (paper IV). The thesis also includes analyses of bones and teeth from the shipwrecked crew of the Vasa warship, 1628, samples from the Vasa museum, Stockholm, Sweden (paper V). Overall, the varying age of the samples and the different conservation environments (soil and water) accounted for variations in quality, but still allowed for successful DNA analysis.

Cette thèse a premièrement permis le développement d’une méthode de détection non-enzymatique de l’ADN. Les techniques enzymatiques couramment utilisées, comme la Polymerase Chain Reaction (PCR), échouent souvent dans l’analyse d’échantillons anciens ou transformés. L’ADN subit en effet de nombreuses dégradations post mortem, parmi lesquelles certaines bloquent les enzymes ADN-polymérases. Notre méthode combine hybridation et détection par SERRS (Surface Enhanced Resonant Raman Scattering), permettant la détection et la quantification de séquences d’ADN dégradées réfractaires à l’analyse par PCR. De nouvelles perspectives s’ouvrent donc en paléogénétique. Cette thèse aborde également le rôle des surfaces minérales dans l’origine des acides nucléiques. Les surfaces minérales pourraient avoir piégé et concentré les briques élémentaires de ces biopolymères, contribuant ainsi à leur construction. Les travaux existants se sont concentrés sur des minéraux comme la montmorillonite, qui n’était cependant pas abondante à l’Hadéen/Archéeen. La minéralogie de la Terre primitive aurait plutôt été dominée par les phyllosilicates ferromagnésiens. Nous avons étudié l’adsorption de nucléotides sur des minéraux plus cohérents avec le contexte géologique, en variant les paramètres environnementaux. Ce travail permet de préciser le mécanisme d’adsorption des nucléotides sur les surfaces minérales, ainsi que les conditions de l’origine du matériel génétique. / The first goal of this thesis was the development of a non-enzymatic DNA detection method. Current enzymatic techniques such as Polymerase Chain Reaction (PCR) often fail in analyzing ancient or processed samples. Indeed DNA undergoes numerous post-mortem degradations, among which some are known to block the bypass of DNA-polymerases. Our method combines hybridization and SERRS (Surface Enhanced Resonant Raman Scattering) spectroscopy, and allows the detection and quantification of degraded DNA sequences that are refractory to PCR analysis. This novel detection method therefore opens new perspectives, especially in paleogenetics. This thesis also aims at studying the role of mineral surfaces in the origin of nucleic acids. Mineral surfaces might have trapped and concentrated the elementary bricks of those biopolymers, thus contributing in their formation. Previous work has focused on minerals such as montmorillonite, although it might not have been abundant during the Hadean/Archean. The primitive Earth’s mineralogy would have been preferentially dominated by Fe-Mg rich phyllosilicates. We have therefore studied the adsorption of nucleotides on minerals we think are relevant to the geological context, and have varied the environmental conditions. This work allows characterizing the adsorption mechanism of nucleotides on mineral surfaces, as well as environmental conditions of the origin of genetic material.