A typical ancient bone might yield DNA fragments that average only fifty to eighty nucleotides in length — compared to the chromosomes of a living cell, which can be hundreds of millions of nucleotides long.

Reconstructing genetic information from this kind of material is like trying to reconstruct a novel from shredded paper confetti, where most of the confetti comes from completely different books.

The techniques that Svante Pääbo and his colleagues at the Max Planck Institute developed to address this problem are genuinely revolutionary.

They involve, among other things:

Extracting DNA from the denser inner portions of bones — particularly the petrous bone, a dense region inside the skull behind the ear that has been shown to preserve ancient DNA far better than other skeletal elements.

Using specialized “capture” techniques that selectively extract human DNA from a mixed sample full of microbial contamination — essentially setting molecular traps that catch only the human genetic sequences.

Sequencing the captured fragments millions of times and using statistical analysis to build a consensus picture of what the original genome looked like, compensating for damage and error through redundancy.

Applying bioinformatic techniques developed specifically for damaged, ancient sequences that can distinguish genuine ancient mutations from DNA damage artifacts.

For Kennewick Man, the petrous bone was a crucial resource.

When Eske Willerslev’s team applied these techniques to samples taken from that bone, they recovered enough high-quality ancient DNA to conduct a meaningful genomic analysis — a staggering achievement given the age and environmental history of the remains.