Multiple extraction blanks — samples of extraction reagents processed through the full extraction procedure without any ancient material — are run alongside genuine samples to detect any contamination that might be introduced by the reagents themselves.

Multiple negative PCR controls — reactions that include all reagents but no DNA — are run to detect contamination of the amplification step.

Any contamination signal in the controls indicates that the results from the genuine samples must be interpreted cautiously.

The specific detection of genuinely ancient sequences relies on the characteristic pattern of chemical damage that accumulates in DNA over time.

Cytosine deamination — the conversion of cytosine bases to uracil at the ends of DNA fragments — produces a specific pattern of sequence mismatches relative to the reference genome that is present in genuinely ancient sequences but not in modern contamination.