After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

中文翻译：

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竞争性绘图可以识别和排除古代动物基因组数据集中的人类 DNA 污染

经过十多年的现场采集、实验室方法和高通量测序的进步，污染仍然是古代 DNA 研究中的一个关键问题。目前，人类和微生物污染 DNA 仍然对古代 DNA 数据的经济高效测序和准确解释提出了挑战。在这里，我们研究是否可以在古代动物测序数据集中发现人类污染 DNA。我们确定了不同水平的人类污染，即使在序列读取已映射到动物参考基因组之后，这种污染仍然持续存在。这种污染有可能影响一系列下游分析。我们提出了一种基于竞争性绘图的快速而简单的方法，该方法可以识别并消除古代动物 DNA 数据集中的人类污染，而真实古代数据的损失有限。这种方法可能是古代 DNA 领域的一个重要工具。