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Palaeogenomic and Biostatistical Analysis of Ancient DNA Data from Mesolithic and Neolithic Skeletal Remains

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Palaeogenomic and Biostatistical Analysis of Ancient DNA Data from Mesolithic and Neolithic Skeletal Remains Palaeogenomic and Biostatistical Analysis of Ancient DNA Data from Mesolithic and Neolithic Skeletal Remains Dissertation submitted in fulfilment of the requirements for the degree Doktor der Naturwissenschaften at Faculty of Biology Johannes Gutenberg University Mainz Zuzana Hofmanov´a Mainz, 2016 Abstract Palaeogenomic data have illuminated several important periods of human past with surprising im- plications for our understanding of human evolution. One of the major changes in human prehistory was Neolithisation, the introduction of the farming lifestyle to human societies. Farming originated in the Fertile Crescent approximately 10,000 years BC and in Europe it was associated with a major population turnover. Ancient DNA from Anatolia, the presumed source area of the demic spread to Europe, and the Balkans, one of the first known contact zones between local hunter-gatherers and incoming farmers, was obtained from roughly contemporaneous human remains dated to ∼6th mil- lennium BC. This new unprecedented dataset comprised of 86 full mitogenomes, five whole genomes (7.1–3.7x coverage) and 20 high coverage (7.6–93.8x) genomic samples. The Aegean Neolithic pop- ulation, relatively homogeneous on both sides of the Aegean Sea, was positively proven to be a core zone for demic spread of farmers to Europe. The farmers were shown to migrate through the central Balkans and while the local sedentary hunter-gathers of Vlasac in the Danube Gorges seemed to be isolated from the farmers coming from the south, the individuals of the Aegean origin infiltrated the nearby hunter-gatherer community of Lepenski Vir. The intensity of infiltration increased over time and even though there was an impact of the Danubian hunter-gatherers on genetic variation of Neolithic central Europe, the Aegean ancestry dominated during the introduction of farming to the continent. Acknowledgements First of all, I would like to thank my supervisor, Prof. Joachim Burger for giving me the opportunity to be his PhD student for this challenging project and for his guidance and wisdom during my time in Mainz. I also could not stress enough how important was for me the environment created by the members of the Palaeogenetic Group in Mainz. In the beginning, they were my colleagues and I enjoyed fruitful collaborations, inspiring discussions and active encouragement but they soon became my close friends and I will always be grateful for the privilege of getting to know them. I am also grateful to the BEAN and PAT teams whose knowledge and scientific excellence inspired me and pushed me further. Special thanks to those who on the short notice invested their time, effort and knowledge into our joint articles. Especially, I would like to thank Krishna Veeramah for his comments and assistance with our joint SI chapter and Mathias Currat whose example of patient scientific reasoning during my stay at his lab helped me more than he probably realises. My work would be also hard without dedication of my students, Florian Gumboldt, Hannah Dehoust, Laura Winkelbach and Ilektra Schulz, who taught me a lot through our interactions. My deepest gratitude goes to my loving family. To my parents who always supported me in whatever direction I fancied to go next, to my brother who could always put things into perspective and to my beloved husband who not only encouraged me in my dreams but made my dreams his. M´amv´asmoc r´ada! Contents Abstract ............................................. ii Acknowledgements..................................... .... iii 1Introduction ....................................... 1 1.1 Palaeogenomics as a tool for studying past populations . 2 1.2 Main prehistoric demographic events in a view of palaeogenomics . 3 1.2.1 Last Glacial Maximum . 4 1.2.2 Neolithic Transition . 4 1.2.3 Population influx from the Pontic Steppe . 6 1.2.4 Challenges in palaeogenomic applications . 7 2 The skeletal material and its archaeological background . 9 2.1 Anthropological and archaeological background . 10 2.2 The Balkans in Meso-Neolithic Transition . 11 2.2.1 Lepenski Vir . 11 2.2.2 Vlasac . 15 2.2.3 Padina ........................................ 17 2.2.4 OstrovulCorbului ................................. 17 2.2.5 Vinˇca ......................................... 17 2.2.6 Grivac......................................... 18 2.2.7 SultanaMaluRo¸su.................................. 18 2.3 Neolithic in NW Anatolia . 19 2.3.1 Aktopraklık . 20 2.3.2 Barcın H¨oy¨uk . 21 2.3.3 Catalh¨oy¨uk . 22 2.4 Isotopic analysis . 22 3Methods ........................................... 26 3.1 Sample Preparation . 26 3.2 Extraction ......................................... 27 3.3 Library preparation . 28 3.4 Quality assessment of samples . 29 3.5 Sexdetermination ................................... 29 3.6 Quantitativereal-timePCR. 29 3.7 Whole-genomesequencing.............................. 30 3.8 Nuclearcapture ...................................... 30 3.9 Mitochondrialcapture................................ 32 3.10Readprocessing .................................... 32 3.11 Analysis of mitochondrial dataset . 33 3.11.1 Contamination rate . 34 3.12 Y chromosomal variation . 35 iv 3.13 Nuclear data analysis . 35 3.13.1 f3-statistics . 35 3.13.2Dstatistics ...................................... 36 3.13.3 Admixture proportions . 36 4AncientDNAanalysis.................................... 38 4.1 Evaluation of Anatolian and Danubian extraction success rate and ancient DNA quality andquantity ......................................... 38 4.2 Sexdetermination ................................... 39 4.3 Maternal insight into population makeup of Meso-Neolithic Balkans and NW Anatolia 41 4.3.1 Mitochondrial haplogroups identified for Mesolithic individuals from the Danube Gorges (∼9,500-6,200 cal BC) . 41 4.3.2 Mitochondrial haplogroups identified in the Transition period (∼6,200-6,000/5,950 cal BC) of Lepenski Vir . 43 4.3.3 Mitochondrial haplogroups identified for Neolithic and post-Neolithic indivi- duals from NW Anatolian and the Balkans . 44 4.3.4 Diversities indices comparison for farmers and hunter-gatherers . 47 4.4 Quality of nuclear dataset obtained . 53 4.5 Using f-statistics to infer shared drift in Anatolians and Danubians . 57 4.5.1 Mesolithic Danubian genomes compared to modern and ancient reference po- pulations ....................................... 57 4.5.2 Differences among Danubian samples . 59 4.5.3 Placing Danubians in the context of other hunter-gatherer genomes . 62 4.5.4 Genetic structure of Western hunter-gatherers . 64 4.5.5 Relationship of Greek and Anatolian genome samples to other ancient and mo- dernpopulations................................... 67 4.5.6 Genetic Structure of Aegean Neolithic populations . 67 4.5.7 The Aegean as the source for early farming populations in Europe . 69 4.5.8 The relationship between Neolithic Aegeans and Chalcolithic Anatolians . 70 4.5.9 Hunter-gatherer contributions to farming societies . 82 4.5.10 Differences between Danubian and WHG heritage in farming societies . 82 4.5.11 Patterns of allele correlations among Anatolian and Danubian capture samples and reference populations . 89 4.5.12 Intrapopulation genetic structure in Anatolia . 90 4.5.13 Intrapopulation genetic structure in the Danube Gorges . 93 4.5.14 Relationships between Danubians and Anatolians . 96 4.5.15 Confirming D statistics results on the capture dataset . 112 4.6 Ancestral components of studied populations . 113 4.6.1 NW Anatolian samples form an ancestral cluster to Neolithic farmers in Europe 113 4.6.2 CHG affinities to farmers . 114 4.6.3 Yamnaya signal in Late Neolithic . 114 4.6.4 Danubians during Neolithic Transition . 115 v 4.7 Remarks on Y chromosomal variation . 121 5Discussion ......................................... 123 5.1 Population demographics during the spread of farming . 123 5.1.1 Western Anatolia as a core zone for Neolithic spread to Europe . 123 5.1.2 Neolithic NW Anatolians in a context of known regional genetic variation . 124 5.1.3 Mesolithic settlements in the Danube Gorges . 126 5.1.4 The Balkans in a time of change . 127 5.2 Implication for understanding of Neolithisation . 129 5.2.1 Summaryofdifferencesbetweensites . 130 5.2.2 Comparison to archaeological models . 130 5.2.3 Hypothesis of the Neolithic spread through the Aegean and the Balkans . 132 5.3 Methodological considerations . 134 5.3.1 Processing of old and damaged samples . 134 5.3.2 Sexdetermination .................................. 135 5.3.3 Comparison to the context . 136 5.3.4 Different datasets could lead to different conclusions . 137 6Conclusion .......................................... 139 References ......................................... 140 Supplementarymaterial................................. 157 Additionalfiles........................................ 180 vi 1 Introduction The great events of world history are, at bottom, profoundly unimportant. In the last analysis, the essential thing is the life of individual. This alone makes history, here alone do the great transformations take place, and the whole future, the whole history of the world, ultimately springs as a gigantic summation from these hidden source in individuals. CG Jung, The Meaning of Psychology for Modern Man, 1934 By comparing DNA of different people, it is possible to observe patterns in genetic variation, and the main objectives are usually differences between populations that can be interpreted in relation to the past. For instance, similarities between two populations can be indicative of connections between them
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