Specific methods were developed for identifying authentic ancient DNA.

Ancient DNA has characteristic damage patterns: particular chemical modifications at specific positions in the sequence that result from the slow hydrolysis of cytosine over thousands of years.

These damage patterns serve as a kind of molecular authentication — they confirm that a sequence is genuinely ancient rather than a modern contaminant.

Modern software tools can identify and filter for these patterns, dramatically improving the reliability of ancient genome reconstruction.

The choice of what material to sequence matters enormously.