Ancient DNA Methods and Protocols

About this book

This fully updated second edition explores protocols that address the most challenging aspects of experimental work in ancient DNA, such as preparing ancient samples for DNA extraction, the DNA extraction itself, and transforming extracted ancient DNA molecules for sequencing library preparation. Ancient DNA: Methods and Protocols also examines the analysis of high-throughput sequencing data recovered from ancient specimens, which, because of the degraded nature of ancient DNA and common co-extraction of contaminant DNA, has challenges that are unique compared to data recovered from modern specimens.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Ancient DNA: Methods and Protocols, Second Edition aims to serve both experts and beginners by presenting protocols in a manner that makes them easily accessible for everyday use in the lab.

Contents

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. Foerster
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. Foerster
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

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