Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

Significance Strict laboratory precautions against present day human DNA contamination are standard in ancient DNA studies, but contamination is already present inside many ancient human fossils from previous handling without specific precautions. We designed a statistical framework to isolate endogenous ancient DNA sequences from contaminating sequences using postmortem degradation patterns and were able to reduce high-contamination fractions to negligible levels. We captured DNA sequences from a contaminated Neandertal bone from Okladnikov Cave in Siberia and used our method to assemble its mitochondrial genome sequence, which we find to be from a lineage basal to five of six previously published complete Neandertal mitochondrial genomes. Our method paves the way for the large-scale genetic analysis of contaminated human remains. 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.