Ancient DNA: Methods and Protocols [Hardcover]

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. Setting Up an Ancient DNA Laboratory.- Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate.- Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Pre-Digestion Step.- Extraction of Highly Degraded DNA from Ancient Bones and Teeth.- Sampling and Extraction of Ancient DNA from Sediments.- Extraction of Ancient DNA from Plant Remains.- DNA Extraction from Keratin and Chitin.- Double-Stranded Library Preparation for Ancient and Other Degraded Samples.- A Method for Single-Stranded Ancient DNA Library Preparation.- Sequencing Library Preparation from Degraded Samples for Non-Illumina Sequencing Platforms.- Whole-Genome Capture of Ancient DNA Using Homemade Baits.- Generating RNA Baits for Capture-Based EnrilÓy