The petrous bone, which was used as the primary DNA source for the Cheddar Man genome, is particularly valuable in this context precisely because its density limits microbial invasion. The dense structure of the petrous creates a protected microenvironment for the ancient DNA that is more contamination-resistant than the trabecular bone of long bones or the more porous tissue of teeth roots. Drilling into the petrous to extract bone powder from the interior, rather than working with the specimen’s surface, further minimizes the contribution of any surface contamination.
The research team would have applied all of these standard protocols and controls, and the resulting genome data would have been examined for contamination indicators before the phenotype analysis was conducted. This does not mean that the ancient DNA work is infallible — contamination can sometimes be subtle and difficult to detect — but it means that the skeptical question “could the DNA be contaminated?” has a substantive answer: the field has well-developed methods for detecting and controlling contamination, and a reputable research team using the petrous bone from a specimen with good preservation conditions would have applied those methods.
—
## Isotope Analysis and What Physical Chemistry Can Add
While the DNA analysis provided the population genetics and phenotype predictions that attracted the most attention, there is a separate set of scientific techniques that can add information about ancient individuals that genetics cannot provide: isotope analysis.
Isotope analysis examines the ratios of certain stable isotopes preserved in bones and teeth to extract information about diet and geographic origin. The technique is based on the fact that different foods and different geographic locations have characteristic isotope signatures that become incorporated into the body’s hard tissues as the person grows and eats.