High-altitude cave used by Tibetan Buddhists yields a Denisovan fossil

For well over a century, we had the opportunity to study Neanderthals—their bones, the items they left behind, their distribution across Eurasia. So, when we finally obtained the sequence of their genome and discovered that we share a genetic legacy with them, it was easy to place the discoveries into context. By contrast, we had no idea Denisovans existed until sequencing DNA from a small finger bone revealed that yet another relative of modern humans had roamed Asia in the recent past.

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

The Baishiya Karst Cave

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

Oddly, it came to the attention of the paleontology community because the cave was a pilgrimage site for Tibetan monks, one of whom discovered a portion of a lower jaw that eventually was given to a university. There, people struggled to understand exactly how it fit with human populations until eventually analysis of proteins preserved within it indicated it belonged to a Denisovan. Now called the Xiahe mandible, it remains the most substantial Denisovan fossil we've discovered to date.

The Ganjia Basin borders the cliffs that contain the Baishiya Karst Cave.

Credit: Dongju Zhang’s group (Lanzhou University)

Since then, excavations at the site had turned up a large collection of animal bones, but none that had been identified as Denisovan. Sequencing of environmental DNA preserved in the cave, however, revealed that the Denisovans had occupied the cave regularly for at least 100,000 years, meaning they were surviving at altitude during both of the last two glacial cycles.

The new work focuses in on the bones, many of which are too fragmentary to be definitively assigned to a species. To do so, the researchers purified fragments of proteins from the bones, which contain large amounts of collagen. These fragments were then separated according to their mass, a technique called mass spectrometry, which works well even with the incredibly small volumes of proteins that survive over hundreds of thousands of years.

The interpretation of the mass spectrometry data relies on the fact that there are only a limited number of combinations of amino acids—often only one—that will produce a protein fragment of a given mass. So, if the 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 matches. Some of these matches will end up being in places where collagens from different species have distinct sequences of amino acids, allowing you to determine what species the bone came from.

When used this way, the technique is termed 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.

The Denisovan diet

The ZooMS analysis showed that a lot of species eventually met their end in the Baishiya Karst Cave or were at least dragged there after dying. The single most common species was a bharal, or blue sheep, which is widespread across the Himalayas. But yaks, horses, and gazelles also appeared, along with two species of deer. These are consistent with the open grasslands near the site at present, but also suggest there may have been some small patches of wooded shrublands present as well.

There was also a range of smaller and larger species, including a woolly rhinoceros, flying squirrels, and porcupines. Predators included the spotted hyena, wolf, and snow leopard, and birds like the pheasant and golden eagle.

Obviously, some of these are extremely unlikely to have ended up in a cave on their own. But characterization of the bones show that many of them have signs of muscle being cut away and/or having been broken open to extract the marrow. Combined, rodent and predator damage appear on only 1 percent of the bones, while clear signs of butchering are present on nearly 20 percent. A handful also show signs of being worked into tools.

The lack of predator damage suggests that, in many cases, the people who occupied the cave weren't simply scavenging someone else's kills to get their food. In addition, the frequency of the species changes over time, with an increasing number of sheep in the more recent layers, suggesting that the Denisovans there were becoming more specialized hunters.

Another Denisovan bone

One of the bones didn't belong to any of the groups mentioned above. Instead, it clearly belonged to a human relative. Careful collagen sequencing from the bone showed that it clustered in with Denisovan populations found elsewhere, making it one of the larger bone samples we've ever obtained from them. Unfortunately, it's still just a fragment of a rib that's only 5 centimeters long.

Intriguingly, the bone came from a layer within the cave where environmental DNA hadn't indicated the Denisovans were present. Whether this is a matter of the Denisovans having become less frequent visitors or a matter of the preservation of environmental DNA isn't clear. But it does indicate the Denisovans were present on the Tibetan Plateau as recently as 30,000 years ago.

So, while we've learned a bit more about these relatives of ours, we still have no idea what they looked like. And any plants in their diet weren't preserved in the cave, so the study only provides a partial picture of their eating habits.

Still, the finds show that the Denisovans lived in a harsh, high-altitude climate over two distinct glacial periods, indicating that they were very adept survivalists. And it appears that they passed at least one of the things that helped them handle the altitude on to the present-day inhabitants of the Tibetan Plateau.

Nature, 2024. DOI: 10.1038/s41586-024-07612-9  (About DOIs).