Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden.
Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2229-34. doi: 10.1073/pnas.1318934111. Epub 2014 Jan 27.
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.
从古代人类骨骼中获取 DNA 序列的主要障碍之一是，在许多化石样本和实验室试剂中存在污染的现代人类 DNA 分子。然而，从古代标本中分离出的 DNA 片段显示出一种由错配损伤引起的特征性 DNA 损伤模式，这种损伤模式与当今的 DNA 序列不同。在这里，我们开发了一个评估序列是否源自具有死后降解特征的模型的框架——以死后降解分数来概括——这使得鉴定不太可能源自现代来源的 DNA 片段成为可能。我们将这种方法应用于西伯利亚奥克拉德尼科夫洞穴的一个受污染的尼安德特人标本，从现代人类污染物中分离出其内源性 DNA，并表明重建的线粒体基因组序列与西方尼安德特人的变异更为密切相关，而这在以前的分析中是无法分辨的。我们的方法为分析受污染的化石材料的基因组开辟了可能性。
