Instead of amplifying specific target regions of ancient DNA — which required knowing in advance what you were looking for and which amplified contaminants just as effectively as the authentic ancient material — shotgun sequencing read all the DNA in a sample, ancient and contaminating alike, and then used computational methods to distinguish the authentic ancient material from contamination.

The key insight that made this possible is that authentic ancient DNA has specific characteristics that contaminating modern DNA lacks: it is shorter (degraded into smaller fragments), it has characteristic chemical modifications at the ends of fragments, and its sequence reflects the genome of the ancient individual rather than any modern person.

By analyzing the length distribution, damage patterns, and genomic context of the sequenced fragments, researchers can identify and retain the authentic ancient material while excluding contamination.

By 2010, when Pääbo’s team published the first Neanderthal genome — and identified the first evidence that modern humans and Neanderthals had interbred — the field had matured enough to produce results of sufficient quality to make such claims credible.