The geographic extent of Denisovan populations, inferred from the genetic traces they left in modern human populations, was considerable. Modern people in Papua New Guinea, Indigenous Australians, and some groups in the Philippines carry approximately 3 to 6 percent Denisovan DNA—a higher proportion than the Neanderthal DNA found in non-African modern humans generally. This suggests that Denisovans and modern humans interbred somewhere in Southeast Asia or Oceania, far from the Siberian cave where the only physical remains have been found. Modern Tibetans carry a specific Denisovan-derived gene variant, EPAS1, that helps regulate the body’s response to low oxygen levels at high altitudes—a functional inheritance from a people who may have occupied high-altitude environments for thousands of generations.
The Denisovan genome, sequenced from the Denisova Cave remains, shows evidence of a small effective population size and limited genetic diversity, suggesting that the group was not numerically large. They were, at any given time, probably a sparse population spread across a vast territory—the kind of thin human presence that leaves few physical traces even when it is present across thousands of kilometers and tens of thousands of years.
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## Recognizing a Hominin Bone
The challenge that faced researchers working with the Denisova Cave material was fundamental: how do you find a hominin bone when it looks like nothing in particular?
The answer, developed by researchers at the University of Oxford and at the University of Manchester, was a method called ZooMS—Zooarchaeology by Mass Spectrometry. The technique works by analyzing collagen, the protein that makes up the structural matrix of bone. Collagen’s amino acid sequence varies between species: not dramatically, but enough that a mass spectrometer can detect the differences in the pattern of protein fragments produced when collagen is digested with an enzyme.