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    Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains

    199310_117749_journal.pone.0086827.pdf (904.6Kb)
    Access Status
    Open access
    Authors
    Wales, N.
    Andersen, K.
    Cappellini, E.
    Avila-Arcos, M.
    Gilbert, Thomas
    Date
    2014
    Type
    Journal Article
    
    Metadata
    Show full item record
    Citation
    Wales, N. and Andersen, K. and Cappellini, E. and Avila-Arcos, M. and Gilbert, T. 2014. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains. PLoS ONE. 9 (1): Article ID e86827.
    Source Title
    PLoS ONE
    DOI
    10.1371/journal.pone.0086827
    ISSN
    19326203
    Remarks

    This article is published under the Open Access publishing model and distributed under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ Please refer to the licence to obtain terms for any further reuse or distribution of this work.

    URI
    http://hdl.handle.net/20.500.11937/23723
    Collection
    • Curtin Research Publications
    Abstract

    Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.

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