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Introduction Destination: 1 Item: Title: 2. Materials and Methods Destination: 1 Children: Item: Title: 2.1. Ancient DNA Extraction Destination: 1 Item: Title: 2.2. Processing of Sequencing Data and Mapping to the Human Genome Destination: 1 Item: Title: 2.3. Assessing the Authenticity of the Human Genomic Data Destination: 1 Item: Title: 2.4. Assessing the Genetic Sex and Degree of Contamination Destination: 1 Item: Title: 2.5. Mitochondrial DNA and Y-Chromosome Haplogroup Determination Destination: 1 Item: Title: 2.6. Kinship Analysis Destination: 1 Item: Title: 2.7. Analysing Population Structure via Clustering Algorithms Destination: 1 Item: Title: 2.8. Ancestry Modelling Destination: 1 Item: Title: 2.9. Processing of Sequencing Data and Mapping of Ancient Microbes Destination: 1 Item: Title: 2.10. Assessing the Authenticity of the Ancient Microbial DNA Destination: 1 Item: Title: 2.11. Phylogenetic Analysis of T. forsythia Destination: 1 Item: Title: 2.12. Phylogenetic Dataset Filtering Destination: 1 Item: Title: 2.13. Tip Calibrated Dating Destination: 1 Item: Title: 2.14. Phylogenetic Analysis of T. denticola and P. gingivalis Destination: 1 Item: Title: 2.15. T. forsythia Pan-Genome Analysis Destination: 1 Item: Title: 3. Results Destination: 1 Children: Item: Title: 3.1. Human DNA Analysis Destination: 1 Children: Item: Title: 3.1.1. Assessing aDNA Reliability Destination: 1 Item: Title: 3.1.2. Uniparental Markers and Kinship Relationships Destination: 1 Item: Title: 3.1.3. Human Genetic Data Exploration Destination: 1 Children: Item: Title: 3.1.4. f-Statistics Ancestry Modelling Destination: 1 Item: Title: 3.2. Microbiome Analysis Destination: 1 Children: Item: Title: 3.2.1. Red Complex Bacteria Detection and Authentication Destination: 1 Item: Title: 3.2.2. Tannerella Forsythia Phylogeny and Clade Dating Destination: 1 Item: Title: 3.2.3. Presence of Virulence or Lifestyle-Related Tannerella Genes Destination: 1 Item: Title: 3.2.4. T. denticola and P. gingivalis Trees Destination: 1 Item: Title: 4. Discussion Destination: 1 Item: Title: 5. Conclusions Destination: 1 Item: Title: 6. 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