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

Proc Natl Acad Sci U S A

Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden.

Published: February 2014

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.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926038PMC
http://dx.doi.org/10.1073/pnas.1318934111DOI Listing

Publication Analysis

Top Keywords

dna
8
dna modern
8
dna sequences
8
modern human
8
dna fragments
8
separating endogenous
4
endogenous ancient
4
ancient dna
4
modern day
4
day contamination
4

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!