Tibetan Denisovan

Denisovans lived in Tibet 160,000 years ago

Alexander Markov, "Elements"

Until now, the Denisov man was known only from scanty finds from the Denisov cave in Altai: several teeth and bone fragments from which ancient DNA was extracted. A new method of identifying fossil bones from the remains of ancient proteins has allowed us to establish that the lower jaw, found in 1980 in Tibet at an altitude of 3280 meters, belonged to a Denisov man who lived here 160,000 years ago. The discovery showed that archaic Homo adapted to the harsh conditions of the highlands much earlier than thought. It also explained why the Denisovans had a variant of the EPAS1 gene, which helps to survive in the highlands and inherited by modern Tibetans. In addition, new data on the morphology of Denisovans forced a new look at some Middle Pleistocene anthropological finds made earlier in the East Asia: they may also turn out to belong to the Denisov man. Finally, the study showed that fossil bones in which DNA has not been preserved can be reliably identified by fragments of ancient protein molecules, which opens up new tempting prospects for paleoanthropologists.

We learned about the existence of Denisovans – a mysterious extinct species of people close to Neanderthals – about 10 years ago thanks to the achievements of an amazing new science of paleogenetics. Almost everything that was known about Denisovans until now was based on ancient DNA from a few teeth and small bones found in a single location - the Denisov cave in the Altai.

In addition, an important indirect source of information about Denisovans was the admixture of Denisov genes found in some Asian and Australian populations of modern humans. In particular, it was shown that Tibetans inherited from Denisovans a variant of the EPAS1 gene that helps to survive in hypoxia.

Many experts assumed that Denisovans were found not only in the vicinity of Denisova Cave, but were widespread. Otherwise, how to explain the significant admixture of Denisov genes in Papuans? Or the presence in the genomes of modern East Asians of traces of hybridization with at least two genetically distinct populations of Denisovans? And the presence of a genetic variant among Denisovans, indicating adaptation to the highlands, is not very consistent with the fact that Denisova Cave is located only 700 meters above sea level.

However, until now all the arguments in favor of the widespread distribution of Denisovans in different regions of Asia (including high-altitude areas) remained indirect, and the only point where the presence of Denisovans was proved was Denisova Cave.

An article authored by 19 paleoanthropologists and paleogeneticists from China, Germany, France, Great Britain, USA, Denmark and Austria, published in early May in the journal Nature (Chen et al., A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau), radically changed this situation. The article describes a fragment of the lower jaw from the karst cave of Baishiya (Baishiya Karst Cave), located in the county Xiahe Gannan is a Tibetan Autonomous Region, in the northeast of the Tibetan Plateau. The height of the cave above sea level is 3280 m (Fig. 1).

Fig. 1. The Baishiya Karst Cave in the northeastern part of the Tibetan Plateau. It is both a Buddhist sanctuary, a popular tourist attraction and the first location of the Denisov man outside of Altai. Photo by Dongju Zhang/Lanzhou University from the website sapiens.org .

The right half of the human jaw with two preserved molars, known as the "Xiahe jaw" (Xiahe mandible, Fig. 2), found in 1980 by a Buddhist monk. He presented the find to his teacher, the "living Buddha", and he subsequently handed it over to Lanzhou University.

Fig. 2. The jaw from Xiahe. All images, except c, are reconstructions made using computed tomography, in which the carbonate rock covering the bone is virtually "removed" (the missing left half of the jaw is also reconstructed in Figures a and b). An image from the discussed article in Nature.

In 2010, Chinese archaeologists began to study the surroundings of the cave. They managed to get permission to dig in the cave itself, which is a Buddhist sanctuary, only in 2016, and large-scale excavations began in 2018. So far, stone tools and animal bones with traces of processing have been found there. In addition, it became clear that the sites of ancient people were located not only in the cave, but also in its surroundings under the open sky. Apparently, prehistoric people lived in this high-altitude area for a long time and felt quite at ease there.

Scientists have not found out exactly where the jaw was found in the cave. But this did not prevent us from determining the age of the find. Uranium-thorium dating of three fragments of carbonate rock stuck to the jaw showed that the mineral crust on the bone was formed about 160,000 years ago – during the penultimate glaciation. The reliability of the dating is confirmed by the fact that the age of three samples taken from different parts of the jaw turned out to be almost the same (164.5 ± 6.2, 155 ± 15 and 163 ± 10 thousand years).

Thus, people settled in the Tibetan Plateau at least 120,000 years earlier than previously thought.

But who were these ancient mountaineers: Neanderthals, Denisovans, Sapiens, relic erectus, or representatives of some hitherto unknown branch of the human race? Ancient DNA could provide a reliable answer to this question. However, DNA has not been preserved in the jaw from Xiahe (at least in an amount sufficient for detection by modern methods). This is a common problem of paleoanthropological finds originating from areas with a warm climate. Nowadays in Tibet, even at an altitude of 3000 m, it is much warmer than in Altai at an altitude of 700 m, and this difference apparently persisted during periods of glaciation.

Fortunately, paleogeneticists have recently invented a new method of identifying fossil bones by amino acid sequences of collagens – very slowly breaking down proteins that can persist in bones much longer than DNA. Using this method, in 2016 it was shown that human bones from the Grotte du Renne associated with the Chatelperonian culture belonged to Neanderthals (F. Welker et al., 2016. Palaeoproteomic evidence identifies archaic hominins associated with the Chatelperronian at the Grotte du Renne). The scientists who developed this method from the Institute of Evolutionary Anthropology in Leipzig – Frido Welker, his supervisor Jean-Jacques Hublan and their colleagues - joined a team of Chinese archaeologists studying the jaw from Xiahe, which made possible the discovery in question.

Fragments of ancient collagen molecules were extracted from the dentin of the teeth (but not from the jawbone itself). More precisely, eight different collagens: COL1a1, COL1a2, COL2a1, COL3a1, COL5a1, COL5a2, COL9a1 and COL11a2. Ancient proteins were separated from modern contaminants in several ways, including by characteristic chemical changes occurring during protein degradation, such as deamidation of glutamine and asparagine and spontaneous hydrolysis leading to fragmentation of protein molecules.

As a result, it was possible to reliably reconstruct a significant part (from 2% to 61%) of the amino acid sequence of six of the eight ancient collagens. These data turned out to be enough to determine the place of the owner of the Xiahe jaw on the phylogenetic tree. The amino acid sequences of the corresponding collagens for other hominids (including fossils: Neanderthals and Denisovans) necessary for the construction of the tree were calculated on the basis of available genomic data (Fig. 3).

Fig. 3. A phylogenetic tree of hominids based on the amino acid sequence of six collagens. It can be seen that the ancient Tibetan (Xiahe) is closest to the Denisovans from the Denisova cave. The figure also shows that the available collagen fragments are sufficient for the correct reconstruction of hominid kinship relationships (because a tree constructed from fragments of six collagens has the correct topology, confirmed by genome-wide data). A drawing from the discussed article in Nature.

It turned out that the ancient inhabitant of Tibet forms a single branch on the tree with the Denisov man from the Altai cave. Simply put, the ancient Tibetan turned out to be a Denisovan!

This is the main result of the work, from which several important conclusions follow.

First, it became clear that populations of archaic Homo could adapt to the harsh conditions of the highlands already in the Middle Pleistocene. Until now, it was believed that only sapiens were capable of this.

Secondly, it finally became clear why the Denisovans had a variant of the EPAS1 gene, which helps to cope with hypoxia and much later "came in handy" to the sapiens who penetrated into Tibet: the Denisovans really lived high in the mountains, so this genetic variant was useful to them.

Thirdly, we received more information about the morphology of Denisovans overnight than during the previous years of studying the finds from the Denisova cave. Until now, we could say little about this beyond the fact that Denisovans had very large teeth (some conclusions, for example, about dark skin and dark eyes, were also made from genomic data. Now anthropologists have at their disposal a whole half of the lower jaw with two molars – a real storehouse of morphological information!

The jaw from Xiahe is massive and archaic in its shape, which is generally characteristic of the Middle Pleistocene Homo. In particular, it lacks a chin protrusion – a striking distinctive feature of Homo sapiens. According to some morphometric characteristics, it differs from the jaws of erectus and Neanderthals (Fig. 4). Exceptionally large molars with a complex occlusal surface confirm the proximity of the man from the Baishya cave to the Altai Denisovans.

Fig. 4. Comparison of the shape of the dental arch of a Denisovan from Xiahe (Xiahe, red asterisk) and other hominids using the principal component method. It can be seen that on this basis, the ancient Tibetan resembles some early Sapiens and Middle Pleistocene hominids (late Erectus or Heidelberg people, such as Tighenif 3). At the same time, it is very different from typical Erectus, Neanderthals and late Sapiens. A drawing from the discussed article in Nature.

Fourth, new data on the morphology of Denisovans allow us to rethink some of the findings made earlier. Of the age-comparable East Asian finds, the jaw from Xiahe is most similar to the Middle Pleistocene jaw Penghu 1 recently found in Taiwan (C.-H. Chang et al., 2015. The first archaic Homo from Taiwan). An important common feature of these two jaws is the complete absence of any hints of the third molar ("wisdom tooth"), for which there is simply no place in the jaw (Fig. 2). The two jaws are also similar in the structure of the roots of the teeth and some other signs. Naturally, the assumption suggests itself that the Taiwanese jaw also belongs to the Denisov man. This may also be true for other controversial Chinese finds, such as skull fragments from Suijiyao.

Anthropologists have long suspected that there is already a lot of material on Denisovans in the collections of Chinese archaeologists. But it was still impossible to prove this, because, as already mentioned, DNA is usually not preserved in finds from warm countries. But now, armed with a new method of identifying fossil bones by collagen residues, researchers will be able to quickly test these hypotheses. So in the near future we can count on new interesting discoveries that shed light on the history of the settlement of Asia by various types of people. This can be called the fifth important consequence of the work under discussion.

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