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This study deals with the contribution of the genetic variant lactase persistence among Neolithic people from the Baltic Island Öland. Skeletal remains from twelve individuals went through DNA sequencing in order to find the mutation that allows adult individuals to digest milk sugar. The twelve individuals were chosen from two different Neolithic sites, where the archaeological and isotopic data suggest that the individuals from Köpingsvik were hunters and gatherers and the individuals from Resmo were early farmers. The individuals with the genetic variant lactase persistence can be described with selection and genetic flow.  Only five individuals produced results and the mutation was found in two of the subjects. All the individuals who were successfully sequenced came from Resmo, whereasno individuals from Köpingsvik yielded any results.

<p>The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock.</p><p>In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones.</p><p>Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.</p>

The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock. In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones. Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.

The transition from a hunter-gatherer lifestyle to a farming lifestyle, i.e. the Neolithisation, is arguably the most important event in human prehistory. While the geography and dating of the Neolithisation is well known, the process is still under debate, especially if it occurred through diffusion of ideas or with migrating farmers. The process accelerated when alternative use of domesticated animals increased. Especially the use of dairy products, and the consumption of unprocessed milk, appears to be of importance. As milk consumption (lactose digestion) is dependent upon genetic components, it is debated whether the genetic disposition allowed for dairy production to evolve, or if the usages of dairy products added selection pressure that eventually lead to present day allele frequencies. Molecular genetics have the potential to solve this and similar questions, but only if the contamination problem, where authentic DNA can be distinguished from modern contaminating DNA, can be resolved. Here I investigate the nature and extent of contamination with modern human DNA in museum specimens and explore several approaches to minimise this contamination and to authenticate DNA results from ancient humans. I use real-time quantification, pyrosequencing and FLX-generated clonal sequencing assays to generate data on ancient humans and ancient dogs. I further use the techniques to study the development of lactase persistence and the nature of animal domestication. The results presented show that sample-based contamination is extensive, but can be minimised if treated with bleach. I retrieved authentic HVSI sequences from 30 Neolithic hunter-gatherers and farmers from Sweden, of which eighteen also yielded nuclear data indicating that the farmers had a higher frequency of the allele linked to lactase persistence compared to the hunter-gatherers. I conclude that genetic data from ancient humans as well as from ancient animals can be retrieved and used, but only under high stringency.

Viking-age boat grave burials are a less common but still repeatedly used way to bury the dead during the late Iron Age. Boat burials are exceptional in many aspects, not only due to placing the individual in a boat with numerous burial gifts including animals, but also by burying the individual without prior cremation, a common practice during the Iron Age. The aim of this thesis is to genetically analyse inhumation boat graves and compare the genetic composition of the ancient individuals with modern populations through population genetic analyses. This will highlight these particular human remains in a mobility context. A total of 11 individuals was analysed, but only one yielded enough DNA for further statistical analyses. This one individual proved genetically exceptionally well preserved. The results clearly show that the individual (a female) has a genetic affinity to populations in northern Europe. However, the results do not discriminate between modern Baltic/Scandinavian populations, depending on the statistical test.

Cette étude a pour objet la mise en évidence de traces d'ADN bactérien pathogène dans des échantillons animaux et humains anciens, et ainsi améliorer les connaissances sur l'évolution des maladies au cours du temps. En parallèle, nous avons étudié les phénomènes de dégradation de l'ADN dans le sol sur des cadavres de souris enterrées après avoir été contaminées par des bactéries non pathogènes. Cette étude des processus taphonomiques s'est étalée sur trois ans et a permis de montrer une disparition rapide des bactéries simulantes, remplacé par l'ADN des bactéries du sol, qui colonisent rapidement la dépouille et dégradent tant l'ADN endogène (murin) qu'exogène (bactérien). Cette disparition rapide explique la grande difficulté à mettre en évidence des pathogènes dans des échantillons anciens, à de rares exceptions près. Notre étude n'a pas permis de détecter d'agents pathogènes particuliers dans les échantillons que nous avons étudié, mais nous avons mis en évidence l'intérêt d'analyser certains types de restes pour accéder à une information génétique préservée. Le tartre dentaire indique est un bon indicateur de la flore buccale de l'hôte et les kystes calcifiés assurent une bonne préservation de l'ADN endogène, moins soumis à contamination et digestion par les bactéries de l'environnement. Les kystes présentent en règle générale une teneur en ADN endogène supérieure à tous les autres tissus étudiés. / The aim of this study was the identification of pathogenic bacterial DNA traces in ancient animal and human samples, and thus improve knowledge of past diseases that affect humankind over time. In parallel, we studied the DNA degradation phenomena in the soil on the buried corpses of mice after being contaminated by non-pathogenic bacteria. This study of taphonomic processes was spread over three years and has shown a rapid disappearance of simulant bacteria, replaced with the DNA of soil bacteria that colonize the body quickly after burial and degrade both the endogenous DNA (murine) that exogenous (bacteria). This quick degradation can explain the high difficulty to detect and identify bacterial pathogens in old samples, with very few exceptions. Despite the fact in our study we were not able to detect specific pathogens in the samples we have studied, we have shown the interest to analyze certain types of remnants to access preserved and informative genetic data. Dental calculus is a good indicator of the oral flora of the host and calcified cysts ensure good preservation of the endogenous DNA, less subject to contamination and digestion by bacteria from the environment. Cysts generally have an endogenous DNA content higher than all other tissues examined.

The Pacific is the part of the world that was last settled by humans. The colonization occurred in different stages which can be discerned through various methods, one of them DNA analysis of humans as well as other species of animals and plants associated with human settlement. The direction of human migration is traditionally believed to have taken a west-eastern direction, originating in the area near Taiwan and spreading eastward until reaching the islands of Remote Oceania. However, there are also strong indications of an east-western route of interaction, with recent DNA studies confirming prehistoric human contact between South American and Polynesian peoples. The aim of this paper is to investigate the current research on human settlement of the Pacific focusing on the genetic analyses of humans as well as animals and plants believed to have accompanied the human settlers. It is to be hoped that this research survey will shed new light on the subject of geographical origins of Pacific migration and the early interactions and settlement patterns that ensued. / Oceanien blev den sista världsdelen att befolkas av människan. Koloniseringen ägde rum i flera steg som kan studeras med olika metoder, däribland DNA-analys av människor samt andra arter av djur och växter vilka förknippas med mänsklig migration. Kolonisationen av Stilla Havet gick enligt den vedertagna forskningen i en väst-östlig riktning, med utgångspunkt från området kring Taiwan och vidare österut till Bortre Oceanien. Det finns emellertid även starka indikationer på öst-västliga interaktioner mellan polynesier och sydamerikansk ursprungsbefolkning. Syftet med denna uppsats är att undersöka det aktuella forskningsläget med fokus på genetiska analyser av människor såväl som av de djur och växter som tros ha följt människorna. Förhoppningen är att denna forskningsöversikt ska kasta nytt ljus över frågan om det geografiska ursprunget för den oceaniska expansionen och de tidiga migrationsmönster och interaktioner den gav upphov till.

The analysis of kinship from ancient DNA (aDNA) data has the potential to provide insight into social structures of prehistoric societies. Kinship analysis is gaining popularity as optimised wet-lab methods allow for studies with sample sizes on the level of whole cemeteries. However, the specifics of ancient DNA require different methods than what would be used for modern DNA. A common way is to use the sites that are identical-bydescent (IBD), however, detecting these is often a challenging task since it is not easy to determine whether a shared locus between two individuals is inherited from the ancestor or if another factor caused the similarity. Most methods used in the field are able to identify up to 2nd or 3rd degree relatives from aDNA data but do not distinguish between different types of relationship for the same degree, for instance not being able to differentiate between parentoffspring and full sibling-sibling relationship in first degree. The aDNA kinship methods often use either of window-based or single-site approaches, however, these two approaches have not been compared formally before in terms of effectivity and efficiency. In this work, READv2 is presented as a re-implementation of a popular kinship analysis method for aDNA studies with additional features such as accepting .bed files as input, which take up less space than the previous input type, plain-text .tped files. It is shown that the new version works more efficiently in terms of runtime. However, the memory requirements seem to be increased with the new implementation. Furthermore, a window-based approach is compared with the single-site approach of READv2, as well as varying window sizes, with benchmarked simulation data which contains approximately 700 individuals with known 1st degree, 2nd degree and 3rd degree relationships. According to the comparison, the sensitivity of the method does not vary between the approaches and different window sizes for high coverages. However, the single-site approach has been shown to be the superior one by a small margin for lower coverages. In addition to these, using the variance of non-shared alleles in windows along the genome has been used to implement a method to differentiate different first-degree relationships, parent-offspring and siblings. The method is tested with an independent dataset from the 1000 Genomes Project which shows that the proposed method is able to work with different datasets with varying sets of SNPs. Nevertheless, the first-degree classification method requires further analyses to determine the stress-point where the True Positive rates for both categories start to drop. Additionally, some necessary changes and decisions are required for READv2 to be a user-friendly method that can be used by other researchers. The preliminary release of READv2, including example data as well as instructions to install the necessary packages and to run the algorithm can be found in https://github.com/GuntherLab/READv2/releases/tag/READ.

In recent years, archaeogenetic studies have been widely discussed in popular media and they have raised many questions, especially regarding cultural identity and ethnicity. This thesis discusses reconstructions based on ancient human remains and how they are related to the current academic hegemony and political circumstances in Europe. People of Britain have reacted particularly strongly to the reconstruction of the Cheddar Man, exhibited in the Natural History Museum in London. Based on this and few other reconstructions of ancient individuals, the ethical issues behind human reconstructions are analyzed and how museums and popular media as the public spaces displaying these pieces of art should deal with such issues as cultural heritage, human origins, and identity. / Under de senaste åren har arkeogenetiska studier diskuterats allmänt i populära media och de har väckta väckts många frågor speciellt kring kulturell identitet och etnicitet. Denna studie diskuterar rekonstruktioner baserat på forntida mänskliga kvarlevor och hur de är relaterade till den nuvarande akademiska hegemonin och den politiska omständigheter i Europa. Människor i Storbritannien har reagerat särskilt starkt på rekonstruktionen av Cheddar-mannen, utställd i ”Natural History Museum” i London. Med utgångspunkt i denna och ytterligare några rekonstruktioner av forntida individer analyseras etiska frågor bakom mänskliga rekonstruktioner och hur museer och populära medier ska hanterar frågor om kulturarv, mänskligt ursprung och identitet.