Differentiating Ancient DNA from modern DNA contamination

[N]ew techniques were used in sequencing the genome of a young adult male known as the Markina Gora skeleton [...]
[...]
When compared with modern DNA, ancient DNA tends to show mutations at the end of molecules, the molecules break at different points in the DNA strand, and fragments of ancient DNA often are shorter than modern DNA fragments, Paabo and his Russian associates wrote in a recent issue of Current Biology.

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