Ancient DNA: Methods and Protocols

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