DNA & genetics

Why the petrous bone is the gold standard for ancient and degraded DNA

The dense bone around the inner ear preserves far more human DNA than teeth or long bones. What the studies found, how it is sampled without destroying a skull, and its limits in hot climates.

Forensic Science Pakistan23 October 20263 min read

Most of the DNA recovered from old bone is not human. Soil bacteria and fungi colonise the skeleton after death, and in a typical ancient sample only about 1% of the DNA, or less, comes from the person. Since 2014, one part of the skull has changed what is possible: the petrous part of the temporal bone, which houses the inner ear.

The otic capsule

The petrous bone is a dense wedge at the base of the skull. Inside it, the otic capsule surrounds the cochlea and the balance organs. It is among the densest bone in the body, and it barely remodels after it forms in early life, so the cells and DNA trapped in it are well sealed from groundwater and microbes.

What the studies found

In 2014, Gamba and colleagues sequenced 13 prehistoric individuals from Hungary using petrous bones and reported consistently high yields of human DNA. In 2015, Pinhasi and colleagues compared three parts of ten petrous bones, dated between about 10,000 and 1,800 years ago:

Spongy trabecular bone: the poorest source.
Dense bone around the otic capsule: a moderate source.
The dense part within the otic capsule: the share of human DNA was up to 65 times higher than the surrounding dense bone and up to 177 times higher than the spongy part.

Precision matters: grinding up the whole petrous bone mixes the rich inner part with poorer bone and wastes most of its advantage.

The limit: hot climates

The same study found that samples from hot regions, both arid and humid, yielded less than 1% human DNA even from the best part of the bone, although damage patterns showed some of it was genuinely ancient. For work in Pakistan and the rest of South Asia, that means the petrous bone is still the best choice, but success is never guaranteed and sequencing depth must be planned accordingly.

Sampling without destroying the skull

Skulls carry anthropological and cultural value, so cutting into them is avoided where possible. The cranial base drilling method described by Sirak and colleagues in 2017 reaches the inner ear through the base of an intact skull. It yielded somewhat less DNA than direct sampling of the same individual’s other petrous bone, but still more than any bone from below the skull. When remains are already fragmented, a loose petrous bone can be cut open and the otic capsule drilled directly.

Extracting very short DNA

Ancient DNA is broken into fragments mostly a few dozen base pairs long, and cytosines lose an amino group over time and read as thymines, a change concentrated at the ends of molecules. That damage pattern helps prove the DNA is genuinely old rather than modern contamination. Extraction methods such as the silica protocol published by Dabney and colleagues in 2013 digest bone powder at 37 °C and are designed to keep fragments as short as about 30 base pairs, which standard clinical kits discard.

From prehistory to casework

Ancient populations: the first genome from an Indus Valley Civilisation site, a woman buried at Rakhigarhi and published in 2019, is reported to have come mainly from petrous bone.
Disaster victim identification: the petrous bone sits deep in the skull base and often survives fire and impact that destroy other tissue.
Old and unidentified remains: skeletons from graves and cold cases where long bones and teeth have failed.

When even petrous DNA is too scarce for a nuclear profile, laboratories fall back on mitochondrial DNA. Read more about the field on our ancient DNA page.