1. Setting Up an Ancient DNA Laboratory Tara L. Fulton and Beth Shapiro 2. Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate Petra Korlevic and Matthias Meyer 3. Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Pre-Digestion Step Hannes Schroeder, Peter de Barros Damgaard, and Morten E. Allentoft 4. Extraction of Highly Degraded DNA from Ancient Bones and Teeth Jesse Dabney and Matthias Meyer 5. Sampling and Extraction of Ancient DNA from Sediments Laura S.
Epp, Heike H. Zimmermann, and Kathleen R. Stoof-Leichsenring 6. Extraction of Ancient DNA from Plant Remains Nathan Wales and Logan Kistler 7. DNA Extraction from Keratin and Chitin Paula F. Campos and M. Thomas P. Gilbert 8.
Double-Stranded Library Preparation for Ancient and Other Degraded Samples Kirstin Henneberger, Axel Barlow, and Johanna L.A. Paijmans 9. A Method for Single-Stranded Ancient DNA Library Preparation Marie-Theres Gansauge and Matthias Meyer 10. Sequencing Library Preparation from Degraded Samples for Non-Illumina Sequencing Platforms Renata Martins, Marie-Louise Kampmann, and Daniel W. Förster 11. Whole-Genome Capture of Ancient DNA Using Homemade Baits Gloria Gonzalez-Fortes and Johanna L.A.
Paijmans 12. Generating RNA Baits for Capture-Based Enrichment Noah Snyder-Mackler, Tawni Voyles, and Jenny Tung 13. Hybridization Capture of Ancient DNA Using RNA Baits André E.R. Soares 14. Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA Johanna L.A. Paijmans, Gloria Gonzalez-Fortes, and Daniel W.
Förster 15. Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis Saskia Wutke and Arne Ludwig 16. Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA Ruth V. Nichols, Emily Curd, Peter D. Heintzman, and Beth Shapiro 17. Authentication and Assessment of Contamination in Ancient DNA Gabriel Renaud, Mikkel Schubert, Susanna Sawyer, and Ludovic Orlando 18. Assembly of Ancient Mitochondrial Genomes without a Closely Related Reference Sequence Christoph Hahn.