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
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