Introduction

One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation-summarized in a postmortem degradation score-which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.

Publications

  1. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal.
    Cite this
    Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Pääbo S, Krause J, Jakobsson M, 2014-02-01 - Proceedings of the National Academy of Sciences of the United States of America

Credits

  1. Pontus Skoglund
    Developer

    Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Sweden

  2. Bernd H Northoff
    Developer

  3. Michael V Shunkov
    Developer

  4. Anatoli P Derevianko
    Developer

  5. Svante Pääbo
    Developer

  6. Johannes Krause
    Developer

  7. Mattias Jakobsson
    Investigator

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Summary
AccessionBT000014
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByMattias Jakobsson