Contamination is a real and persistent challenge in ancient DNA work, and the field developed stringent protocols over decades specifically because early studies sometimes produced results that later turned out to reflect modern DNA contamination rather than authentic ancient sequences. The early history of ancient DNA research is in part a story of learning how to identify and exclude contaminated samples.
Contamination in ancient DNA work comes from several sources. The most significant is human contamination: researchers handling skeletal material transfer small amounts of their own DNA to the specimen, and if the specimen itself contains low amounts of ancient DNA, the modern human DNA from handling may come to dominate the sample. There is also environmental contamination from microbes and other organisms that have colonized the bone over thousands of years.
Modern ancient DNA laboratories address this problem through multiple strategies. They typically work in dedicated clean-room facilities with positive air pressure, extensive UV sterilization, full-body suits and double gloves, and strict protocols for who enters the space and when. Researchers handling ancient specimens are typically genotyped so that their DNA can be recognized and excluded from the data if contamination occurs. Extraction protocols are designed to degrade modern DNA on the specimen’s surface while recovering the protected ancient DNA from the interior of the bone.
Computational methods are also applied to distinguish authentic ancient DNA from modern contamination. Ancient DNA carries characteristic chemical damage at the ends of its fragments — principally, cytosine residues near fragment ends are converted to uracil by a spontaneous deamination reaction over time, creating a detectable signature that modern DNA does not have. Software programs that model this damage pattern can identify authentic ancient sequences and flag sequences that lack the expected damage pattern as likely modern contaminants.