The specific DNA that is most useful in studies of ancient specimens tends to come from the pulp cavity of the tooth — the soft tissue space in the center of the tooth that in living individuals contains nerves, blood vessels, and the cells responsible for dentine production.

Even after these soft tissues have long since decomposed, the mineral walls of the pulp cavity can retain traces of the DNA that was once contained in those cells.

The extraction process for ancient DNA from a tooth sample involves carefully sampling the dentine by drilling into the tooth — typically through the root, to minimize damage to the morphologically informative crown — and then subjecting the powdered material to a series of chemical treatments designed to break down the remaining mineral structure and release the DNA it contains.

The DNA that is released is a complex mixture: some fraction of it is genuinely ancient, derived from the original occupant of the tooth; some fraction may be modern contamination, introduced by the researchers who handled the specimen or by environmental sources; and some fraction may be degraded to the point where it cannot be reliably sequenced.