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  • © 2019

Ancient DNA

Methods and Protocols

Editors:

  1. Beth Shapiro

    1. Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Axel Barlow

    1. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

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  3. Peter D. Heintzman

    1. Tromsø University Museum, UiT—The Arctic University of Norway, Tromsø, Norway

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  4. Michael Hofreiter

    1. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

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  5. Johanna L. A. Paijmans

    1. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

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  6. André E. R. Soares

    1. Laboratório Nacional de Computação Científica, Petrópolis, Brazil

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  • Includes cutting-edge, fully updated techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1963)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-x
    PDF

  2. Setting Up an Ancient DNA Laboratory

    • Tara L. Fulton, Beth Shapiro
    Pages 1-13

  4. Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step

    • Hannes Schroeder, Peter de Barros Damgaard, Morten E. Allentoft
    Pages 21-24

  5. Extraction of Highly Degraded DNA from Ancient Bones and Teeth

    • Jesse Dabney, Matthias Meyer
    Pages 25-29

  6. Sampling and Extraction of Ancient DNA from Sediments

    • Laura S. Epp, Heike H. Zimmermann, Kathleen R. Stoof-Leichsenring
    Pages 31-44

  7. Extraction of Ancient DNA from Plant Remains

    • Nathan Wales, Logan Kistler
    Pages 45-55

  8. DNA Extraction from Keratin and Chitin

    • Paula F. Campos, M. Thomas P. Gilbert
    Pages 57-63

  9. Double-Stranded Library Preparation for Ancient and Other Degraded Samples

    • Kirstin Henneberger, Axel Barlow, Johanna L. A. Paijmans
    Pages 65-73

  10. A Method for Single-Stranded Ancient DNA Library Preparation

    • Marie-Theres Gansauge, Matthias Meyer
    Pages 75-83

  11. Sequencing Library Preparation from Degraded Samples for Non-illumina Sequencing Platforms

    • Renata F. Martins, Marie-Louise Kampmann, Daniel W. Förster
    Pages 85-92

  12. Whole-Genome Capture of Ancient DNA Using Homemade Baits

    • Gloria González Fortes, Johanna L. A. Paijmans
    Pages 93-105

  13. Generating RNA Baits for Capture-Based Enrichment

    • Noah Snyder-Mackler, Tawni Voyles, Jenny Tung
    Pages 107-120

  14. Hybridization Capture of Ancient DNA Using RNA Baits

    • André E. R. Soares
    Pages 121-128

  15. Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA

    • Johanna L. A. Paijmans, Gloria González Fortes, Daniel W. Förster
    Pages 129-139

  17. Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA

    • Ruth V. Nichols, Emily Curd, Peter D. Heintzman, Beth Shapiro
    Pages 149-161

  18. Authentication and Assessment of Contamination in Ancient DNA

    • Gabriel Renaud, Mikkel Schubert, Susanna Sawyer, Ludovic Orlando
    Pages 163-194

  20. Back Matter

    Pages 215-216
    PDF
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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. The volume 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.
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Keywords

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Editors and Affiliations

  • Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, USA

    Beth Shapiro

  • Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Axel Barlow, Michael Hofreiter, Johanna L. A. Paijmans

  • Tromsø University Museum, UiT—The Arctic University of Norway, Tromsø, Norway

    Peter D. Heintzman

  • Laboratório Nacional de Computação Científica, Petrópolis, Brazil

    André E. R. Soares

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Bibliographic Information

  • Book Title: Ancient DNA

  • Book Subtitle: Methods and Protocols

  • Editors: Beth Shapiro, Axel Barlow, Peter D. Heintzman, Michael Hofreiter, Johanna L. A. Paijmans, André E. R. Soares

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9176-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9175-4Published: 15 March 2019

  • eBook ISBN: 978-1-4939-9176-1Published: 15 March 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: X, 216

  • Number of Illustrations: 10 b/w illustrations, 5 illustrations in colour

  • Topics: Genetics and Genomics, Evolutionary Biology

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Buy it now

eBook USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book USD 159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

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