A high mountain cave used by Tibetan Buddhists yields a Denisovan fossil

For more than a century, we have had the opportunity to study Neanderthals – their bones, the objects they left behind, their distribution in Eurasia. So, when we finally sequenced their genome and discovered that we share a genetic heritage with them, it was easy to put the discoveries into context. In contrast, we had no idea Denisovans existed when DNA sequencing from a little finger bone revealed that another relative of modern humans roamed Asia in the recent past.

We’ve learned a little more since then. The frequency of their DNA in modern human populations suggests that they were probably concentrated in East Asia. But since then we’ve only discovered bone fragments and a few teeth, so we can’t even make a very informed guess at what they might have looked like. An international team of researchers on Wednesday described findings from a cave on the Tibetan Plateau inhabited by Denisovans that tell us something more about these relatives: what they ate. And it seems that’s all they can get their hands on.

Baishiya Karst Cave

The finds come from a site called Baishiya Karst Cave, which is perched on a cliff in the northeast of the Tibetan Plateau. It is at a high altitude (over 3,000 meters or almost 11,000 feet) but borders a high open plain as you can see in the picture below.

Strangely enough, it came to the attention of the palaeontological community because the cave was a pilgrimage site for Tibetan monks, one of whom discovered part of the lower jaw, which was eventually given to the university. There, people tried to understand exactly how it fit into the human population, until finally analysis of the proteins preserved in it showed that it belonged to a Denisovan. Now called the Xiahe mandible, it remains the most significant Denisovan fossil yet discovered.

Excavations at the site have since turned up a large collection of animal bones, but none have been identified as Denisovan. However, sequencing of environmental DNA preserved in the cave revealed that Denisovans occupied the cave regularly for at least 100,000 years, meaning they survived at altitude during both of the last two ice 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 protein fragments from bones that contain large amounts of collagen. These fragments were then separated by mass, a technique called mass spectrometry that works well even with incredibly small volumes of proteins that survive for hundreds of thousands of years.

Mass spectrometry relies on the fact that there are only a limited number of amino acid combinations—often just one—that will produce a protein fragment of a given mass. So if mass spectrometry finds a signal at that mass, you can compare the possible amino acid combinations that produce it to known collagen sequences to find a match. Some of these matches end up in places where collagens from different species have different amino acid sequences, allowing you to determine what species the bone is from.

When used in this way, the technique is called zooarchaeology using 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 that were tested.