High altitude cave used by Tibetan Buddhists yields a Denisovan fossil

For more than a century, we had the opportunity to study Neanderthals – their bones, the objects they left behind, their distribution throughout Eurasia. So when we finally sequenced their genomes 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 small finger bone revealed that another relative of modern humans roamed Asia in the recent past.

Since then, we’ve learned quite a bit more. The frequency of their DNA in modern human populations suggests that they were likely concentrated in East Asia. But we’ve only discovered bone fragments and a few teeth since then, so we can’t even make very informed guesses about what they might have looked like. On Wednesday, an international team of researchers described findings from a cave on the Tibetan Plateau that had been occupied by the Denisovans, which tell us a little more about these relatives: what they ate. And that seems to be all they can get their hands on.

Baishiya Karst Caves

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

Surprisingly, it came to the attention of the paleontology community because the cave was a place of pilgrimage for Tibetan monks, one of whom discovered a part of the lower jaw that was eventually given to a university. There, people tried to figure out exactly how it fit into the human population until finally analysis of the proteins stored inside it showed that it belonged to a Denisovan. Now called the Xiahe mandible, it remains the most essential Denisovan fossil we have discovered to date.

Since then, excavations at the site have turned up a large collection of animal bones, but none that have been identified as Denisovan. Sequencing the environmental DNA preserved in the cave, however, revealed that Denisovans had occupied the cave regularly for at least 100,000 years, meaning they were surviving at high altitude 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 protein fragments from bones, which contain large amounts of collagen. These fragments were then separated by their mass, a technique called mass spectrometry that works well even with extremely small volumes of proteins that survive over 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 combinations of amino acids that produce it with known collagen sequences to find matches. Some of these matches will end up being in places where collagens from different species have distinct amino acid sequences, allowing you to determine which species the bone came from.

When used in 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 that were tested.