Group of Dongju Zhang (Lanzhou University)
For over a century, we’ve had the opportunity to study Neanderthals: their bones, the stuff they left behind, their spread across Eurasia. When we finally sequenced their genome and discovered that we shared a genetic legacy with them, it was easy to put the discoveries into context. By contrast, we had no idea that Denisovans existed until DNA sequencing from a tiny finger bone revealed that another relative of modern humans had roamed Asia in the recent past.
We’ve learned little since then. The frequency of their DNA in modern human populations suggests they were probably concentrated in East Asia. But since then, we’ve only discovered fragments of bone and a few teeth, so we can’t even make educated guesses about what they might have looked like. On Wednesday, an international group of researchers described finds from a cave on the Tibetan Plateau that was once occupied by Denisovans that tell us a little more about these relatives: what they ate. And that seems to be all they could get their hands on.
The Baishiya Karst Cave
The finds come from a site called the Baishiya Karst Cave, which is located on a cliff in the northeast of the Tibetan Plateau. It is at a high altitude (over 3,000 meters or nearly 11,000 feet), but it borders a high open plain, as you can see in the photo below.
Oddly enough, it came to the attention of the paleontological community because the cave was a place of pilgrimage for Tibetan monks, one of whom discovered part of a mandible that was eventually donated to a university. There, people struggled to understand exactly how it fit into human populations until finally analysis of the proteins preserved inside indicated that it belonged to a Denisovan. It is now called the Xiahe mandible, and remains the most substantial Denisovan fossil yet discovered.
Group of Dongju Zhang (Lanzhou University)
Since then, excavations at the site have yielded a large collection of animal bones, but none have been identified as Denisovan. However, sequencing of environmental DNA preserved in the cave revealed that the Denisovans had regularly occupied the cave for at least 100,000 years, meaning they survived at high altitudes during the last two glacial cycles.
The new work focuses on the bones, many of which are too fragmentary to be definitively assigned to a species. To do this, the researchers purified fragments of proteins from the bones, which contained large amounts of collagen. These fragments were then separated based on their mass, a technique called mass spectrometry, which works well even with the incredibly small volumes of proteins that survive for hundreds of thousands of years.
Mass spectrometry is based on the fact that there are only a limited number of combinations of amino acids, often just one, that will produce a protein fragment of a certain mass. So if mass spectrometry finds a signal at that mass, you can compare the possible amino acid combinations that produced it to known collagen sequences to find matches. Some of these matches will ultimately be in places where collagen from different species has different sequences of amino acids, allowing you to determine what species the bone came from.
When used this way, the technique is called zooarchaeology by mass spectrometry, or ZooMS. And in the case of the work described in the new paper, it identified nearly 80 percent of the bone fragments tested.
