High-altitude cave used by Tibetan Buddhists reveals Denisovan fossil

For more than a century, we’ve had the opportunity to study Neanderthals—their bones, the objects they left behind, and their distribution across Eurasia. So when we finally sequenced their genome and discovered that we shared a genetic heritage, it was easy to put the findings into context. By contrast, we had no idea how similar we were to Neanderthals. Denisova man This was the case when DNA sequencing from a little finger bone revealed that another relative of modern humans roamed Asia in the recent past.

Since then, we’ve learned little about these discoveries. The frequency of their DNA in modern human populations suggests 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 a very educated guess about what they looked like. On Wednesday, an international group of researchers described discoveries in a Tibetan cave inhabited by Denisovans that tell us more about these relatives: what they ate. And that seems to be anything they could get their hands on.

Baishia karst cave

These discoveries come from a site called the Baixia Karst Cave, which is located on a cliff in the northeastern Tibetan Plateau. It is at a high elevation (over 3,000 meters or nearly 11,000 feet) but borders an open, high plain, as you can see in the image below.

Oddly enough, this caught the attention of the paleontological community because the cave was a pilgrimage site for Tibetan monks, one of whom discovered a partial lower jaw that was eventually donated to a university. There, people struggled to understand how it fit in with the human population until analyses of the proteins preserved inside it eventually suggested that it belonged to a Denisovan. It is now called “Neanderthal.” Lower jaw is oldThis fossil remains the largest fossil we have discovered to date.

Since then, excavations at the site have uncovered 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 had been inhabiting the cave regularly for at least 100,000 years, meaning they were living at high altitudes during the last two glacial periods.

The new work focuses on bones, many of which were too fragmented to be conclusively identified as a species. To do this, the researchers purified protein fragments from the bones, which contain large amounts of collagen. These fragments were then separated by mass, a technique called mass spectrometry, which works well even with incredibly small amounts of proteins that have survived 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 at a given mass. So, if mass spectrometry finds a signal at that mass, you can compare the possible amino acid combinations it produces to known collagen sequences to find matches. Some of these matches will end up in places where collagens from different types have distinct amino acid sequences, allowing you to determine which type the bone came from.

When used in this way, the technique is called zooarchaeology using mass spectrometry, or ZooMS. In the case of the work described in the new paper, it was able to identify nearly 80 percent of the bone fragments tested.