The team drilled a small hole into the base of Cheddar Man’s skull to reach the petrous bone and extracted bone powder from it. This was not a destructive process in any meaningful sense for the overall skeleton — the hole was small and precisely placed — but it was the key to everything that followed. The powder contained ancient DNA that had survived, protected by the density of the petrous bone and the cool stability of the cave environment, for approximately ten thousand years.
The success of the extraction was not guaranteed. No ancient DNA from a British individual of this age had been successfully sequenced before. The cave conditions that preserved the DNA — the cool, relatively stable temperature and humidity of the limestone interior — were favorable, but favorable conditions are not the same as certainty. The researchers were attempting something that had not been achieved with a British specimen of this antiquity.
The extraction worked. The DNA was there.
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## Sequencing the Oldest British Genome
The sequencing method the team used was shotgun sequencing — an approach that fragments the available DNA and sequences all of it, producing millions of short reads that computational methods then assemble against a reference genome to build a picture of the original sequence.
Shotgun sequencing of ancient DNA presents specific challenges that don’t arise in the same way with modern samples. Ancient DNA is typically highly fragmented — the original double-stranded molecules have been broken into short pieces by millennia of chemical and enzymatic degradation. The fragments also carry characteristic patterns of chemical damage at their ends that can cause sequencing errors if not properly accounted for. Modern ancient DNA methods include computational steps to identify and correct for these damage patterns.