Genomic insights into Late Neolithic and Early Bronze Age populations of modern-day Switzerland

aDNA research on human remains provides great opportunities to study past populations regarding their genetic history and processes that shaped modern-day populations. The topic of this dissertation was to further improve specific techniques for aDNA analysis, such as specific target enrichment and authentication of the retrieved sequences, and to use these improved methods to investigate the population history of modern-day Switzerland. In the first paper, issues in estimating contamination were addressed which represents a major problem in aDNA research. The level of contaminating DNA in the mtDNA can easily be assessed but this estimate might not be representative in case of extreme differences between the amount of mtDNA and nDNA. In this study, it is shown that petrous bones contain more nuclear DNA in relation to their mitochondrial DNA content and that this causes the mitochondrial and nuclear contamination rates to be most similar. In the second study, different methods for specific target enrichment were compared to determine the most efficient one. Statistical analyses were used to compare their performance regarding enrichment efficiency, specificity, and reproducibility. Results indicate that the commercial myBaits® kit utilising RNA baits is the most suitable for the work on aDNA and that in-solution approaches, in general, are advantageous. The third study focuses on the genetic transitions detected in the 5th millennium BP in Europe and particularly in modern-day Switzerland. The main aspects of the study are ancestry components, admixture dates, and social structure. In this study, results show that a steppe-like ancestry component arrives in Switzerland in around 4700 BP and that the relative amount decreases after a sudden steep increase. Furthermore, female individuals with relatively young radiocarbon dates but with zero steppe ancestry who were likely causing this decline could be identified.1. Introduction 1.1 The field of ancient DNA research 1.2 aDNA authentication 1.3 Specific target enrichment for aDNA sequencing libraries 1.4 Genetic transitions in Europe 1.5 The end of the Neolithic in what is now Switzerland 2. Aims and Objectives 3. Methods 4. Results 4.1 New strategy in authenticating genomic DNA from ancient female individuals 4.2 Identification of the best method for target enrichment in ancient DNA 4.3 Population genetics analysis of Late and Final Neolithic individuals from what is now Switzerland 5. Discussion 5.1 DNA preservation and target enrichment (papers I, II & III) 5.2 Authentication and assessment of data quality (papers I & III) 5.3 Population history of present-day Switzerland (paper III) 6. Outloo