Ancient DNA: Methods and Protocols by Beth Shapiro Read Free Book Online

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Chapter 3
    DNA Extraction of Ancient Animal Hard Tissue
    Samples via Adsorption to Silica Particles
    Nadin Rohland
    Abstract
    A large number of subfossil and more recent skeletal remains, many of which are stored in museums and private collections, are potentially accessible for DNA sequence analysis. In order to extract the small amount of DNA preserved in these specimens, an effi cient DNA release and purifi cation method is required. In this chapter, I describe an effi cient and straightforward purifi cation and concentration method that uses DNA adsorption to a solid surface of silica particles. Comparative analysis of extraction methods has shown that this method works reliably for ancient as well as younger, museum-preserved specimens.
    Key words: Ancient DNA , DNA extraction , Bones , Teeth , Museum-specimen , Silica , Column 1. Introduction
     
    The most abundant faunal remains are partial skeletons. Bones and teeth are the hardest tissues of vertebrates and can persist for hundreds of thousands of years without fossilization if sediments or permafrost shield them from unstable environmental conditions.
    When environmental conditions are unfavorable for microbial life that would otherwise metabolize the hard tissue, this can lead to the preservation of DNA molecules within these ancient skeletons.
    Such conditions are common to permafrost regions, where large numbers of preserved faunal remains have been found. In more moderate climatic ecosystems, well-preserved skeletal remains can be found within sediment deposits in natural shelters such as caves.
    Three major obstacles impede DNA analyses of ancient skeletal remains. First, the total amount of DNA preserved in very old bones and teeth is likely to be very small, and often the DNA fragments that do remain are highly damaged ( 1 ) . The same may be Beth Shapiro and Michael Hofreiter (eds.), Ancient DNA: Methods and Protocols , Methods in Molecular Biology, vol. 840, DOI 10.1007/978-1-61779-516-9_3, © Springer Science+Business Media, LLC 2012
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    true for modern specimens that have been treated with chemical preservatives to prepare them for long-term storage in museums.
    Second, if DNA is preserved in ancient bones or teeth, it is often contaminated with DNA from bacteria, fungi, or other