Separating endogenous ancient DNA from modern-day contamination: application to a Siberian Neandertal
2014 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 6, 2229-2234 p.Article in journal (Refereed) Published
One of the main impediments for obtaining DNA sequences from ancient humanskeletons 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 post-mortem degradation (PMD)—summarized in a PMD 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 the Okladnikov cave in Siberia in order 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.
Place, publisher, year, edition, pages
2014. Vol. 111, no 6, 2229-2234 p.
Research subject Evolutionary Genetics
IdentifiersURN: urn:nbn:se:uu:diva-206755DOI: 10.1073/pnas.1318934111ISI: 000330999600045OAI: oai:DiVA.org:uu-206755DiVA: diva2:645387