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Andrew Collins exclusively reveals the true face of a Siberian Denisovan.
What the Denisovans might have looked like has been one of the hottest debates in paleoanthropology since the discovery of this extinct human lineage back in 2010. Were they big or small? Did they look like their cousins, the Neanderthals, or were they more like anatomically modern humans in appearance? Lastly, were they the giants of legend as some are now speculating ?
Resolving these issues is difficult as just a handful of Denisovan fossil remains have been found. They include two enormous molars, two fragments of a parietal bone from a Denisovan skull, and a finger bone from a young female who lived 75,000 years ago - all found during excavations at the famous Denisova Cave in Siberia. There is also a 160,000-year-old mandible that was found in a cave on the edge of the Tibetan plateau in northwestern China and recently identified as being that of a Denisovan.
Despite this frustrating situation, in September 2019, it was announced that Professor Liran Carmel and Dr. David Gokhman of Hebrew University, Jerusalem, had used epigenetics to analyze gene regulation and cytosine degradation in order to determine the suspected physical make up of the Denisovan face. Their finished reconstruction shows the head and neck of a young female with a rounded head, wide mouth and jaw, minimal chin, brown skin, and striking brown eyes. So well received was their reconstruction that in December 2019 the team won the 2019 Science magazine’s People’s Choice for Breakthrough of the Year .
The Hebrew University team’s award-winning reconstruction of the Denisovan face. (Image: © Maayan-Harel)
Crucial in Carmel and Gokhman’s reconstruction of the Denisovan face was data gained from the lineage’s genome first sequenced in 2010 by the Max Planck Institute in Leipzig, Germany. This showed that a significant number of Denisovan genes have been inherited by modern human groups through interbreeding in the distant past. It is perhaps for this reason that Carmel and Gokhman’s Denisovan bears similarities to Papua New Guineans and also to certain Australian Originals, both of whom display anything up to 5 percent Denisovan DNA ancestry, the highest rate in any human groups. (See, for comparison, figure below which shows Koori Originals photographed around 1847 in Victoria, Australia. Their features, particularly the man in the middle, can easily be compared with Carmel and Gokhman’s Denisovan reconstruction).
Koori Originals photographed by Douglas T. Kilburn around 1847 in Victoria, Australia. Their features are comparable with those of Carmel and Gokhman’s Denisovan reconstruction. (Image: National Gallery of Victiria / )
So did all Denisovans look like Australian Originals, or indigenous Melanesians? The answer is almost certainly no. For example, studies of Denisovan genes inherited by modern populations in East Asia, Island Southeast Asia, and Papua New Guinea have revealed new information about the evolution of the Denisovan genome. This shows that soon after the Denisovans split from a common ancestor they shared with their cousins the Neanderthals (as much as 475,000-450,000 years ago) the population diverged into two separate types.
One Denisovan population came to inhabit a vast territory possibly extending from Central Asia, Siberia, and northern China in the north to Mongolia and Tibet in the south. Their descendants most likely moved through the Russian Far East before finally crossing the Beringia land bridge into North America; this occurring perhaps as early as 20,000 years ago. From the many discoveries being made in the Denisovan layer at the Denisova Cave it would seem that these Siberian Denisovans as they are known displayed a high level of advanced human behavior.
This included the creation of beautiful jewelry (see, for instance, the Denisovan bracelet below), the making of the earliest known musical instrument in the form of a whistle or flute, the earliest manufacture of bone needles, used most probably to create warm winter clothing, and the production of the earliest symbolic art. This takes the form of an exquisite carving of a mountain lion, possibly a child’s comfort toy, which has incised markings suggestive of a basic knowledge of cyclic time.
Denisovan bracelet found in the Denisova Cave, Siberia, and thought to be at least 50,000 years old. (Siberian Times)
It is also thought possible that the Siberian Denisovans developed a sophisticated blade tool technology that was afterwards adopted by the first modern humans to settle in Mongolia some 30,000-40,000 years ago.
The other population of Denisovans lived in southern and southeastern Eurasia, as well as in Island Southeast Asia, Melanesia and possibly even Australia. They displayed a more basic genome, suggesting that they were a more archaic lineage than their northern neighbors.
This second branch of Denisovans are known as Sunda Denisovans (occasionally Australo-Denisovans) after the former Sunda landmass that once linked the Malaysian Peninsula with Indonesia. They themselves would appear to have split into two distinct groups, the youngest of them, according to genetic evidence, perhaps lingering on in places like the Philippines and Papua New Guinea until around 15,000 years ago.
So far there is no hard evidence that the Sunda Denisovans developed the same advanced human behavior achieved by their northerly neighbors. Stone tools as much as 50,000 years old found on the Indonesian island of Sulawesi may have been made by Denisovans. If they were created by Denisovans then it would imply that their ancestors had not only crossed the Wallace Line, the deep water channel dividing most of the Indonesian archipelago from Sulawesi, but also that they had sea-going capabilities.
This said, the Sunda Denisovans are unlikely to have developed a sophisticated blade tool technology like their northerly counterparts, since only so-called flake tools existed in Island Southeast Asia during the prehistoric age.
If the portrait of the young female created by Carmel and Gokhman’s Hebrew University team is truly representative of a Denisovan, then it is the likeness of a Sunda Denisovan, not a Siberian Denisovan, whose evolutionary development was quite different to that of its southerly counterparts.
- Face of the Denisovans? Portrait of a Teen Revealed by Her DNA
- A Trove of New Denisovan Discoveries Revealed At A Recent Anthropological Conference
So the question remains: what did the Siberian Denisovans look like? How different would they have been to Carmel and Gokhman’s reconstruction? To answer this question the present writer asked independent researcher and writer Debbie Cartwright to help in the collation of everything available on the physical appearance of a Siberian Denisovan.
This included all obvious information obtained from the Denisovan genome, such as the fact that Denisovans had brown hair, brown eyes, and brown skin, along with any further information to be gleaned from the few fossil remains found to date. We also looked at the suspected effects on the lineage’s evolutionary development derived from knowledge that the Siberian Denisovans would appear to have thrived at very high altitudes and also in extremely cold conditions. This probably included the Altai Mountains of Siberia and Mongolia and the Tibetan plateau, one of the highest places on earth.
Such extreme environments might well have necessitated the development of specialized respiratory systems including highly adapted noses that were able both to absorb all available oxygen at altitudes where the air was particularly thin, while at the same time warming up the air sufficiently before it passed into the lungs. For instance, a study by Mark Shriver, a geneticist and anthropologist at Pennsylvania State University, found that the effects of climate upon the evolution of nose size and shape suggested that larger, narrower noses are more suited to higher and colder climates, while wider flatter noses are more suited to hot tropical climates.
The Neanderthal Connection
It is important also not to forget that Denisovans were related genetically to Neanderthals, meaning that they would have borne at least some physical characteristics in common with them. This probably included a heavy brow bridge, thickset features, and a receding chin - a fact confirmed with the discovery of the 160,000-year-old Denisovan mandible found in a cave on the Tibetan plateau in northwestern China. This is extremely wide and robust and lacks a well-defined chin.
The Xiahe mandible, only represented by its right half, was found in 1980 in Baishiya Karst Cave. ( Dongju Zhang, Lanzhou University )
Also, like the Neanderthals, the Denisovans probably had receding foreheads and extended occipital buns, meaning they perhaps had long heads, as opposed to the more rounded craniums displayed by some early modern human populations such as Australian Originals.
Modern Human Introgression
Having made the connection between Denisovans and Neanderthal physiology it is also likely that Denisovans had at least some traits in common with anatomically modern humans ( Homo sapiens ). When a previously misplaced fragment of the finger bone found in the Denisova Cave in 2008 was reunited with the second, more famous, fragment used by the Max Planck Institute to sequence the Denisovan genome, it was realized that the finger did not resemble that of a Neanderthal as had been widely expected. Although the finger bones of archaic humans such as Neanderthals and Homo erectus are extremely thick and quite stubby, the Denisovan finger bone is a lot slimmer, like that of an anatomically modern human.
This connection between anatomically modern humans and Denisovans is perhaps far deeper than anyone has so far suspected for, as the current writer has speculated elsewhere, there is a strong likelihood that the ancestors of the Siberian Denisovans, after leaving Africa, encountered pre-dispersal modern humans already occupying the Levant. Evidence for the existence of these early modern humans has come from the discovery at the Qesem Cave in Israel of eight teeth belonging to members of the Acheulo-Yabrudian Cultural Complex (AYCC), which thrived in the Levant corridor circa 420,000-250,000 years ago. These were found to be almost identical to those of anatomically modern humans.
Having interbred with these early modern humans, the Siberian Denisovans would then have continued their migration eastwards, entering Central Asia, Siberia, and finally, Mongolia and China. If correct, they would have been carrying physiological traits picked up from early modern humans living in the Levant. This is something that the Sunda Denisovans would seem to have missed out on since they most likely took a different route out of Africa, crossing the Arabian peninsula before entering southern Asia, southeastern Asia, and, finally, Island Southeast Asia.
The possibility that the Siberian Denisovans were carrying at least some early modern human genes might also help explain why the Siberian Denisovan genome is slightly different to that of the Sunda Denisovans, and why they would appear to have displayed advanced human behavior before their final disappearance around 45,000 years ago.
And so this brings us to an impression of the Siberian Densovan that appears as follows…
The face of a Siberian Denisovan by artist George Hernandez working in concert with writer-researcher Debbie Cartwright and the present author. Genetic information, Denisovan and Neanderthal fossils, and unique traits in anatomically modern humans were used to reconstruct this likeness. (Picture credit: © Hernandez/Cartwright/Collins)
For our reconstruction of the Siberian Denisovan we have included some physical traits seen in modern human populations that perhaps benefitted from introgression with this archaic human population. They include modern populations in North Asia, East Asia, and even North America - where First Peoples of the Great Lakes-St Lawrence River region such as the Ojibwa and Cree have been found to possess some Denisovan DNA. They, more than any other population, might well have retained Siberian Denisovan traits through the isolation of their ancestors prior to first contact with Europeans at the start of the historical period.
Debbie Cartwright and I then worked with talented Californian artist George Hernandez to achieve the best likeness of an archaic Siberian Denisovan, here revealed for the first time. It is shown also for comparison alongside Carmel and Gokhman’s own reconstruction.
The reconstructed face of a Siberian Denisovan (left) alongside the Hebrew University’s own representation of a Sunda Denisovan (right). (Picture credits: Left, © Hernandez/Cartwright/Collins; Right, © Maayan-Harel)
Many similarities can be noted between the two versions, including wide mouths, receding chins, heavy brow ridges, brown eyes, skin and hair, and also large noses, but there are also some differences as well. The face of the Siberian Denisovan is much longer, the brow ridge more prominent (like that of a Neanderthal), the forehead recedes more, while the cheekbone is much higher.
We have also chosen to give the Denisovan a narrow, aquiline nose with a prominent bridge, as opposed to the large, but much flatter nose, of the Carmel and Gokhman reconstruction. As we have seen, such distinctive noses helped in the absorption of oxygen in elevated environments where the air is particularly thin. Yet curiously, an aquiline nose (also known as the Roman or hooked nose) combined with a prominent bridge has often been compared with the head shape of a large bird, most obviously that of an eagle (the Latin word aquiline means “eagle-like).”
Bird shamanism would appear to have played a significant role in human development for as much as 400,000 years. If, as we suspect, the Siberians Denisovans did possess aquiline noses, then with their prominent bridges and heavy brow ridges there is every reason to suspect that their facial details could be said to resemble those of a bird, something noted in individuals with aquiline noses in more modern times.
Illustration comparing an individual with an aquiline nose, heavy brow and prominent nose arch with the head of an eagle by Charles Le Brun (Image: CC BY 4.0 ).
If correct, then this might have encouraged Siberian Denisovan groups to adopt the guise of birds to engage in early forms of animism and even shamanism, similar to that noted in connection with the AYCC inhabitants of the Qesem Cave in Israel as much as 400,000-250,000 years ago. In other words, Siberian Denisovans came to resemble birds both in physical appearance and in mannerisms, a connection emphasized and even celebrated through ritual practices.
Lastly, we chose to give our Denisovan thick, dreadlocked hair as opposed to the frizzy hair seen in Carmel and Gokhman’s reconstruction. Why did we do this? The answer is two-fold. First, it comes from the adoption of dreaded hair for socio-cultural and socio-religious purposes by various modern human populations such as the Himba people of Namibia, the Hindu Sadhus or holy men of India, and the Rastafarians of Jamaica.
Secondly, the deliberate management of long thick hair by dreading and the subsequent use of mud (as well as goat hair in the case of Himba women) to help coat it aids in the prevention of lice and other insect infestations. In addition to this, dreadlocks bunched up on the head would have accentuated the Denisovans’ suspected elongated heads, emphasizing their individual identity in a world that towards the end of their time circa 45,000-50,000 years ago, would have included Neanderthals, anatomically modern humans and, most likely, hybrids stemming from an admixture of all these various lineages of the homo genus.
- Genetic Study Suggests Denisovans Were the Mythological Rakshasas
- The Coming of the Thunder People: Denisovan Hybrids, Shamanism and the American Genesis
Clearly, such a unique feature is based on speculation of how the Siberian Denisovans managed long hair without cutting it and how it might have come to signify their ritual culture. This is an important point, for no matter what evidence is used to reconstruct the face of an archaic human, it will always involve some personal bias. This can be seen, for example, from the many different representations of Neanderthals. They range from virtual ape-men covered in thick body hair, to others where the individual becomes almost indistinguishable from any red-haired, freckled person you might encounter on the street today.
Thus, it has to be accepted that the Denisovan face imagined by artist George Hernandez under the directions of Cartwright and the author must by definition have its own personal bias. This said, we feel it is the closest representation to date of a Siberian Denisovan, as opposed to the face of the Sunda Denisovan developed by Carmel and Gokhman.
Further assessments on the shape of the Denisovan skull and the proportions of the face can only be achieved following the discovery of additional fossils; most urgently a complete cranium. Beyond this will be the eventual discovery of a Denisovan femur, which will help settle the debate over whether or not the Denisovans were of exceptional size and height.
This was first implied by the enormous size of the two Denisovan molars found in the Denisova Cave. Although the two fragments of the Denisovan skull found at the site in 2016 are also suggestive of a large body frame, not enough fossil remains have come to light to answer the question of height and girth with any degree of certainty. So, until such times we must be content with the two faces of a Denisovan presented to the public so far – that of Carmel and Gokhman’s team from the Hebrew University and that of our own. At least these provide some idea of what this extinct branch of the Homo genus might have looked like.
Complete Guide to the Denisovans, a Newer Hominid Species
The Denisovans are a recently identified hominin species, related to but different from the other two hominid species (early modern humans and Neanderthals) who shared our planet during the Middle and Upper Paleolithic periods. Archaeological evidence of the existence of Denisovans is so far limited, but genetic evidence suggests they were once widespread across Eurasia and interbred with both Neanderthals and modern humans.
Key Takeaways: Denisovans
- Denisovan is the name of a hominid distantly related to Neanderthals and anatomically modern humans.
- Discovered by genomic research in 2010 on bone fragments from Denisova Cave, Siberia
- Evidence is primarily genetic data from the bone and modern humans who carry the genes
- Positively associated with the gene which allows humans to live at high altitudes
- A right mandible was found in a cave in the Tibetan Plateau
The earliest remains were tiny fragments found in the Initial Upper Paleolithic layers of Denisova Cave, in the northwestern Altai Mountains some four miles (six kilometers) from the village of Chernyi Anui in Siberia, Russia. The fragments held DNA, and the sequencing of that genetic history and the discovery of remnants of those genes in modern human populations has important implications for the human habitation of our planet.
Scientific journal articles for further reading
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30. PubMed: 22936568 Free full-text article from PubMed Central: PMC3617501.
Pääbo S. The diverse origins of the human gene pool. Nat Rev Genet. 2015 Jun16(6):313-4. doi: 10.1038/nrg3954. PubMed: 25982166.
Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J, Pääbo S, Patterson N, Reich D. The genomic landscape of Neanderthal ancestry in present-day humans. Nature. 2014 Mar 20507(7492):354-7. doi: 10.1038/nature12961. Epub 2014 Jan 29. PubMed: 24476815. Free full-text article from PubMed Central: PMC4072735.
So, how do you reconstruct an extinct person's face when all you have to work with is some DNA on their fingertip? For this study, Gokhman and his colleagues looked for abnormalities in gene expression — or, how certain physical traits may be influenced by chemical inhibitors in a person's genetic code.
"There are various layers that compose our genome," Gokhman said. "We have the DNA sequence itself, where our genes are encoded. Then, on top of that, there are regulatory layers that control which genes are activated or deactivated, and in what tissue."
One of those layers is a process called DNA methylation. Methylation occurs when chemicals containing one carbon atom and three hydrogen atoms — also known as methyl groups — bind to certain DNA molecules. While this binding doesn't change the underlying DNA sequence, it can interfere with the way that specific genes are expressed. Certain patterns of methylation can indicate whether a cell has cancer, for example, and can lead to anatomical deformities.
So, the researchers looked at the available Denisovan DNA to compare the group's methylation patterns with those found in humans and Neanderthals to see where their gene expression overlapped, and where it diverged. Once the Denisovans' unique methylation profile was mapped, the researchers tried to figure out which physical traits were being altered by each methylated gene, based on known human disorders that result when those same genes are inhibited.
The team found a total of 56 traits in Denisovans that they predicted to be different from modern humans and Neanderthals, 32 of which resulted in clear anatomical differences. In addition to their wide skulls and jutting jaws, Denisovans had wider pelvises and rib cages than modern humans, and thinner, flatter faces than Neanderthals.
To test the accuracy of their anatomical predictions, the researchers also created similar methyl maps for Neanderthals and chimpanzees — two species with known anatomy — that they could use to check their predictions instantly. They found that about 85% of their predictions about which traits diverged and in what direction (say, whether a Neanderthal's skull was wider or thinner than a human's) were dead-on.
This gave the researchers hope that their reconstructed Denisovan was not far off from the ancient reality. A final test of their predictions came in May 2019, when a separate group of researchers reportedly identified a Denisovan jawbone for the first time. When Gokhman and his colleagues compared their predictions to the actual jawbone anatomy, they found that seven out of eight of their predictions matched.
"The only true test of our predictions is to find more Denisovan bones and match them," Gokhman said. His dream fossil, he added, would include part of a Denisovan face — "just faces are so divergent between different humans," he said.
Neanderthal genetics study reveals missing link in human history
Scientists sequenced Neanderthal Y chromosomes, opening a new chapter in the complex history of ancient peoples.
Ten years ago scientists published an analysis that changed our view of humanity.
The first whole-genome sequence of a Neanderthal revealed these ancient hominids were 99.7 percent identical to living humans — and that their DNA lives on as a result of interbreeding.
At the time, the team concluded that up to 2 percent of the DNA of modern people without African ancestry originated in Neanderthals. Today, we know that all living individuals' genes harbor this legacy.
The intervening years have revealed subsequent discoveries and caveats, but one essential element remained missing: the Y chromosomes of Neanderthals and Denisovans, another ancient hominid whose DNA is also carried by modern humans.
This was a problem largely borne out of chance. Many of the high-quality hominid fossils that DNA has been retrieved from have been female — and the Y chromosome is a paternal inheritance. There were bones and teeth of male Neanderthals and Denisovans with some DNA in them, but not enough for a comprehensive analysis of their Y chromosomes.
But on Thursday, researchers announced in the journal Science they were finally able to sequence Y chromosomes from two Denisovans and three Neanderthals. The results revise our understanding of humanity’s shared history and give insight into the children that resulted from these ancient humans interbreeding.
The hunt for Y chromosomes — Martin Petr, the paper’s first author and a postdoctoral candidate at the Max Planck Institute for Evolutionary Anthropology, and Janet Kelso, the paper’s senior author and professor at the Institute, tell Inverse they were “quite surprised” by the discovery.
The team knew from past studies that, when it came to familial relationships, Denisovans and Neanderthals were sister groups, while modern humans are their more distantly related “evolutionary cousins.” They expected the Y chromosomes to mirror that set-up.
But that's not what they found: Using an advanced method described as a targeted capture-based DNA sequencing approach, they were able to extract Y chromosome sequences from the ancient male specimens previously considered too poorly preserved to be of use. They discovered that the modern human and Neanderthal Y chromosomes were more related to each other, compared to the Denisovans' Y chromosomes.
“The fact that Neanderthal Y chromosomes are more similar to modern humans than Denisovans is very exciting as it provides us with a clear insight into their shared history,” Petr and Kelos explain.
Sequencing these chromosomes also gives a clearer timeline of ancient hominids' interactions with one another: The results suggest that, around 700,000 years ago, the Y chromosomes of Denisovans split from a lineage shared by Neanderthals and modern humans.
That result is consistent with the team’s hypothesis going into the study. What was a surprise was finding that the time when Neanderthals and modern human Y chromosomes shared a common ancestor was earlier than expected. They estimate the interbreeding with early modern humans that resulted in the replacement of the Neanderthal Y chromosome took place more than 100,000 years ago, and perhaps as much as 370,000 years ago.
“This led us to conclude that interbreeding between Neanderthals and very early modern humans resulted in replacement of the original Neanderthal Y chromosome with modern human Y chromosomes,” Kelso and Petr say.
This estimation is much older than what Kelos and Petr describe as the “already well-known interbreeding that contributed Neanderthal DNA to modern humans outside Africa, or that which contributed Denisovan DNA to people in Oceania.” Both took place considerably less than 100,000 years ago, they say.
In 2016, analysis of a Neanderthal woman's toe bone suggested modern humans and Neanderthals met and interbred around 100,000 years ago — an encounter that likely happened in the Middle East. Previously, the first interaction between the two species was thought to have been in Europe, between 50,000 and 65,000 years ago.
An August 2020 study suggests that intermixing between Neanderthals and modern humans could have happened between 200,000 and 300,000 years ago. And a study released in January — the one that found everyone's a little bit Neanderthal — also suggests that for hundreds of thousands of years, Homo sapiens migrated back-and-forth out of Africa and into Africa, bringing with them children who carried genes from other species of hominid.
Together, the research suggests there were different waves of “intermixing events” — the flow of migration and mating between Neanderthals and Homo sapiens more of a branching, steady stream than a dammed river.
Kelso and Petr say it’s plausible that they didn’t see the same Y chromosome replacement in Denisovans “simply because the Denisovans were geographically further away.” The current view is that Denisovans likely inhabited much of Asia, while Neanderthals were primarily located in Europe and Western Asia.
“We speculate that perhaps Denisovans were so far East that they did not encounter these very early modern human groups.”
Cultural consequences — In a companion commentary also published Thursday, Mikkel Heide Schierup, a professor at Aarhus University who studies evolutionary genetics, writes that this study “unequivocally shows that both male and female H. sapiens contributed to gene flow, suggesting that both H. sapiens and Neanderthal populations accepted children of mixed heritage.”
Kelso and Petr acknowledge this is a “fascinating” proposition, but are hesitant to say it is true. Understanding the cultural consequences of introgression is difficult to do with genetics alone, they note, and perhaps experts in archeology and human evolution are better-placed to give that type of insight.
Instead, the most tangible genetics takeaway is that “offspring of this interbreeding between Neanderthals and modern humans must have been viable and fertile," they say.
“This is an important point because there has been historically a lot of debate about whether or not Neanderthals and modern humans were ‘genetically incompatible,’” they explain. “Similarly, there has been some suggestion that archaic human Y chromosomes perhaps carried some mutations which made successful mixture with modern humans less likely.”
The study strongly suggests that’s not the case, because it’s evidence that early modern human-like Y chromosomes successfully spread through the Neanderthal population.
Next, the team wants to sequence hominid Y chromosomes that are even older – especially those belonging to more ancient Neanderthal specimens, and Neanderthals from a wider range of known habitat. The three specimens analyzed in this study were all from Western Eurasia, and we know that their range extended (at least) through southwestern and central Asia.
Ideally, they also want analyze Denisovan and Neanderthal Y chromosomes unaffected by any genetic mixing. Those samples could inform what factors might have driven the replacement observed here and allow the team to “go beyond the theoretical simulations in our current study,” Kelso and Petr say.
That may prove challenging. While human history is consistently being rewritten by new discoveries like this one, one thing appears to be constant: Ancient humans had a habit of not limiting themselves to their own species for sex.
A fascinating genome
To work out which of these options was more likely, the researchers examined sites in the genome where Neanderthal and Denisovan genetics differ. At each of these locations, they compared fragments of Denny's DNA to the genomes of the two ancient hominins. In more than 40% of cases, one of the DNA fragments matched the Neanderthal genome, whereas the other matched that of a Denisovan, suggesting that she had acquired one set of chromosomes from a Neanderthal and the other from a Denisovan. That made it clear that Denny was the direct offspring of two distinct humans, says Pääbo. “We’d almost caught these people in the act.”
Evidence mounts for interbreeding bonanza in ancient human species
The results convincingly demonstrate that the specimen is indeed a first-generation hybrid, says Kelley Harris, a population geneticist at the University of Washington in Seattle who has studied hybridization between early humans and Neanderthals. Skoglund agrees: “It’s a really clear-cut case,” he says. “I think it’s going to go into the textbooks right away.”
Harris says that sexual encounters between Neanderthals and Denisovans might have been quite common. “The number of pure Denisovan bones that have been found I can count on one hand,” she says — so the fact that a hybrid has already been discovered suggests that such offspring could have been widespread. This raises another interesting question: if Neanderthals and Denisovans mated frequently, why did the two hominin populations remain genetically distinct for several hundred-thousand years? Harris suggests that Neanderthal–Denisovan offspring could have been infertile or otherwise biologically unfit, preventing the two species from merging.
Neanderthal-Denisovan pairings could also have had some advantages, even if there were other costs, says Chris Stringer, a palaeoanthropologist at the Natural History Museum in London. Neanderthals and Denisovans were less genetically diverse than modern humans, and so interbreeding might have provided a way of “topping up” their genomes with a bit of extra genetic variation, he says. The study also raises questions over how matings between different human groups happened, says Stringer — for example, whether or not they were consensual. A more detailed account of the gene flow between Neanderthals and Denisovans in the future might offer hints into ancient human behaviour.
The Denisovans are the first ancient hominin species to be revealed by genes alone, not by fossil classification. While placed in the Homo genus, they have not yet been given a species classification as no physical description exists. They are named after the Denisova Cave in Russia where the first fossils were found.
Background of discovery
The age range of about 500,000 to 30,000 years ago given for this species is based on dating of the few fossils that exist and inferences made from genetic studies and sediment analysis.
Sediment analysis at Denisova cave indicates the Denisovans occupied the site from 300,000 to 50,000 years ago. Denisovan fossils have only been found in layer 11 but are too fragmentary to be dated. Animal bones in the same layer have radiocarbon dates of 50,000 years old but the youngest part of layer 11 dates to 16,000–30,000 years old. The micro-stratigraphy needs more work to determine accurate dates for this layer and the Denisovan remains.
Genes reveal Denisovans are cousins of Neanderthals and that the two split sometime around 400,000 to 500,000 years ago. Research on Denisovan DNA in modern Papua New Guineans suggests that the two populations interbred around 46,000 years ago. It is also suggested that another interbreeding event took place about 30,000 years ago and possibly as recently as 15,000 years ago. The evidence for the latter date is disputed, but it seems likely Denisovans were still around at least 30,000 years ago.
To date, the only fossil specimens come from Denisova Cave, a remote site in the Altai Mountains in Siberia, Russia, and the Baishiya Karst Cave on the Tibetan Plateau in China.
However, genetic studies indicate the Denisovan homeland once stretched from the Altai into eastern Asia. Denisovans contributed genes to present-day Melanesians and Indigenous Australians, so must have been present in an area where they could interact with the ancestors of these people as they migrated across southern Asia.
While placed in the genus Homo, the Denisovans still have no agreed taxonomic name. They are named after the Denisova Cave, Siberia, Russia, where the first fossils were found and identified.
Denisova Cave was, at various times, home to three species of humans – the Denisovans, Neanderthals (Homo neanderthalensis) and modern humans (Homo sapiens). A Neanderthal toe bone, identified by DNA, was found in the cave in 2010 (in layer 11.4 of the East Gallery) and was contemporary with the Denisovan finger bone. Neanderthals also left Mousterian stone points and scrapers in that cave and the region, mostly dated to 40,000 years. The cave also held sophisticated stone tools and bone artefacts that may have belonged to Homo sapiens. Exact dates for the layers that the artefacts and fossils were found in is problematic and it seems most likely that occupation was sequential, not contemporaneous.
Excavations at Denisova Cave have been ongoing since the 1970s, but it was more recent discoveries of human remains that made world headlines.
In 2008 a tiny finger bone (Denisova 3) was recovered from layer 11. As it was well preserved with a suitable date range (50,000 and 30,000 years old), it was sent for DNA analysis. The results of the mtDNA and nuclear DNA sequencing were published in 2010 – the bone belonged to a female from an unknown type of archaic human. While closely related to Neanderthals and modern humans, she was distinct enough to merit classification as a new species. Interestingly, the bone also had small amounts of Neanderthal DNA, indicating that the two groups had mixed previously. As the growth plate on her finger bone was not fused, the girl was aged between 5 and 7 years old when she died.
Other specimens from Denisova cave, all identified through their DNA, are:
- Denisova 2: a molar found in 1984, estimate to be 122,700–194,000 years old
- Denisova 4: a molar found in 2000
- Denisova 8: a molar found in 2010
- Denisova 11: a long bone fragment found in 2014 and determined to be from a hybrid (see below)
- Denisova 13: fragment of parietal bone from the back of skull found in 2016 and announced in 2019 after mtDNA analysis
The first and, as of 2020, only Denisovan fossil recovered from a different site was announced in May 2019. A mandible, found in 1980 by a Buddhist monk as he explored the Baishiya Karst Cave in Gansu, China, was taken from storage and reanalysed. It was identified using protein analysis, as DNA could not be extracted. It’s dated to at least 160,000 years old through U-series dating of rocky material attached to the bottom of the jaw. The altitude of this new Denisovan’s home — 3,280 metres above sea level on the Tibetan Plateau — while surprising, does explain the Denisovans’ genetic contribution to modern Tibetans (see below).
All the specimens recognised as being Denisovan were done so on the basis of protein or DNA analysis. No specimen has yet been described as Denisovan based on physical characteristics. It is highly likely, however, that some of the unclassified hominin fossils from Asia, such as Penghu 1, Dali and Xuchang 1 and 2 (skull fragments unearthed in Lingjing in 2017) are Denisovan. However, they are not suitable for DNA testing, so their relationship to the Denisovan fossils remains unknown.
Photograph of the 2 cm bone (Denisova 11)
Image: Buckley, Michael Derevianko, Anatoly Shunkov, Michael Procopio, Noemi Comeskey, Daniel Fiona Brock Douka, Katerina Meyer, Matthias et al.
© Scientific Reports
Relationships to other species
Evidence suggest that Neanderthals, Denisovans, and modern humans are all descended from or share a common ancestor with Homo heidelbergensis. DNA evidence suggests this common ancestor lived about 600,000 to 750,000 years ago. It seems likely, therefore, that around this time an ancestral group of H. heidelbergensis left Africa and then split shortly after. One branch ventured northwestward into West Asia and Europe and became the Neanderthals. The other branch moved east, becoming Denisovans. Those that stayed in Africa evolved into modern humans.
DNA evidence also makes it clear that these three closely related species later met and interbred, and that each species contributed genetic material to the others. For instance, living Europeans and Asians inherited about 1-4% of their DNA from Neanderthals, and Tibetans, Melanesians and Australian Aboriginals carry about 3-5 % of Denisovan DNA (this is explained by interbreeding of eastern Eurasian Denisovans with the modern human ancestors of these populations as they migrated towards Australian and PNG). Our species, Homo sapiens, may even have been interbreeding with Denisovans as recently as 15,000-30,000 years ago, according to a detailed analysis of the DNA of people living in Indonesia and Papua New Guinea published in 2019. If these dates are correct, the Denisovans are the most recently lived human species apart from our own.
Studies reveal that Denisovan DNA in modern humans can be advantageous. In 2014, researchers discovered that ethnic Sherpas likely inherited from Denisovans a ‘super athlete’ gene variant EPAS1 that helps them breathe easily at high altitudes.
One of the greatest discoveries relating to interbreeding between human species was that of a first-generation Neanderthal-Denisovan hybrid – or an individual whose parents belonged to two distinct species of humans. Denisovan 11 is a long bone fragment fossil found in Denisova Cave in 2012. It was stored in a collection of over 2000 unidentified bone fragments until 2016 when protein analysis on many of the fragments was performed to see whether they were human or animal.
Denisova 11 turned out to be human and was then sent for more detailed analysis. The fossil turned out to be from a girl – now nicknamed Denny – who was at least 13 years old and lived some 90,000 years ago. Her DNA analysis was published with great excitement in 2018 – Denny was a first generation hybrid with a Denisovan father and a Neanderthal mother. The genetic study was led by Svante Paabo and Viviane Slon from Max Planck Institute for Evolutionary Anthropology in Germany.
Since very few Denisovan fossils have been found, most of what we know about the extinct humans comes from their DNA. The species has not yet been described based on physical characteristics, but the following are apparent traits:
- large and lack the specialised features found in Neanderthal teeth
- have many unusual cusps and do not resemble modern human molars
- share no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.
While thousands of artefacts have been recovered from Denisova cave, none have so far been associated with the Denisovans. This makes it hard to form a detailed picture of cultural attributes specific to the Denisovans. However, it can be assumed that they were relatively advanced in terms of intelligence and lived a similar lifestyle to other humans at this time.
Reich, D. Richard, E. G. et al. (23 December 2010). "Genetic history of an archaic hominin group from Denisova Cave in Siberia". Nature. 468 (1012): 1053–60.
Rex Dalton (March 24, 2010). "Fossil finger points to new human species. DNA analysis reveals lost relative from 40,000 years ago". Nature. 464 (7288): 472–73.
Gibbons, Ann (August 2011). "Who Were the Denisovans?" (PDF). Science. 333 (6046): 1084–87.
Slon, Viviane Mafessoni, Fabrizio Vernot, Benjamin de Filippo, Cesare Grote, Steffi Viola, Bence Hajdinjak, Mateja Peyrégne, Stéphane Nagel, Sarah Brown, Samantha Douka, Katerina Higham, Tom Kozlikin, Maxim B. Shunkov, Michael V. Derevianko, Anatoly P. Kelso, Janet Meyer, Matthias Prüfer, Kay Pääbo, Svante (2018-08-22). "The genome of the offspring of a Neanderthal mother and a Denisovan father". Nature. 561 (7721): 113–116
Warren, Matthew (22 August 2018). "Mum's a Neanderthal, Dad's a Denisovan: First discovery of an ancient-human hybrid - Genetic analysis uncovers a direct descendant of two different groups of early humans". Nature. 560 (7719): 417–418.
Zhan-Yang Li et al, Late Pleistocene archaic human crania from Xuchang, China. Science 03 Mar 2017: Vol. 355, Issue 6328, pp. 969-972
Found: First Tibetan Evidence of Neanderthal Cousins, the Denisovans
For the first time, scientists have found fossils from an extinct ancient human lineage known as the Denisovans outside of Siberia.
Denisovans were an extinct group of hominins that were close relatives of Neanderthals. They are known primarily from a handful of fossil fragments found at Denisova Cave in Siberia, and from genetic clues that linger in the DNA of people across Asia.
But new fossil evidence reveals that these ancient human relatives also inhabited the Tibetan Plateau, the tallest and widest plateau on Earth, known as "the Roof of the World."
Protein analysis of a lower jawbone found in the plateau's Baishiya Karst Cave recently confirmed that the bone was Denisovan. Estimated by radioisotopic dating to be at least 160,000 years old, the jawbone section is the earliest sign of hominins in the region and predates evidence for modern humans on the Tibetan Plateau by about 30,000 to 40,000 years, scientists reported in a new study. [Denisovan Gallery: Tracing the Genetics of Human Ancestors]
Found in 1980 at an altitude of over 10,000 feet (3,000 meters), the jawbone portion contains two large molars, and was so well-preserved that scientists were able to model a virtual "mirror" of the existing half to create a complete lower jaw.
Their examination showed that the bone came from a population that was closely related to the Denisovans found in Siberia. Its location also addressed a long-standing mystery about Denisovans' genetic legacy.
The Siberian Denisovans' genetic makeup included adaptations for living at high altitudes &mdash but the altitude of the Siberian cave was only 2,297 feet (700 m). The discovery of the jawbone on the Tibetan Plateau shows that Denisovans were already living at extreme altitudes 160,000 years ago, and were adapted to low-oxygen environments, according to the study.
And they did so "long before the regional arrival of modern Homo sapiens," study co-author Dongju Zhang, an archaeologist with the Lanzhou University in China, said in a statement.
Though Denisovan fossils have been found in only two locations, some Denisovan DNA is retained in contemporary populations of Asian, Australian and Melanesian people, said Jean-Jacques Hublin, a study co-author and director of the Department of Human Evolution at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.
This hints that the ancient hominin group was likely more widespread than fossil evidence suggests, Hublin said in the statement.
It is debated whether Denisovans represent a distinct species of Homo or are an archaic subspecies of H. sapiens. DNA analyses showing Denisovans as a sister taxon of Neanderthals also concerns the classification of the latter as H. neanderthalensis or H. s. neanderthalensis. Proposed species names for Denisovans are H. denisova  or H. altaiensis. 
Denisova Cave is in south-central Siberia, Russia, in the Altai Mountains near the border with Kazakhstan, China and Mongolia. It is named after Denis (Dyonisiy), a Russian hermit who lived there in the 18th century. The cave was first inspected for fossils in the 1970s by Russian paleontologist Nikolai Ovodov, who was looking for remains of canids. 
In 2008, Michael Shunkov from the Russian Academy of Sciences and other Russian archaeologists from the Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences in Novosibirsk Akademgorodok investigated the cave and found the finger bone of a juvenile female hominin originally dated to 50–30,000 years ago.   The estimate has changed to 76,200–51,600 years ago.  The specimen was originally named X-woman because matrilineal mitochondrial DNA (mtDNA) extracted from the bone demonstrated it to belong to a novel ancient hominin, genetically distinct from both contemporary modern humans and from Neanderthals. 
In 2019, Greek archaeologist Katerina Douka and colleagues radiocarbon dated specimens from Denisova Cave, and estimated that Denisova 2 (the oldest specimen) lived 195,000-122,700 years ago.  Older Denisovan DNA collected from sediments in the East Chamber dates to 217,000 years ago. Based on artifacts also discovered in the cave, hominin occupation (most likely by Denisovans) began 287±41 or 203±14 ka. Neanderthals were also present 193±12 ka and 97±11 ka, possibly concurrently with Denisovans. 
The fossils of five distinct Denisovan individuals from Denisova Cave have been identified through their ancient DNA (aDNA): Denisova 2, Denisova 3, Denisova 4, Denisova 8, and Denisova 13. Denisova 11 was an F1 Denisovan-Neanderthal hybrid.  An mtDNA-based phylogenetic analysis of these individuals suggests that Denisova 2 is the oldest, followed by Denisova 8, while Denisova 3 and Denisova 4 were roughly contemporaneous.  During DNA sequencing, a low proportion of the Denisova 2, Denisova 4 and Denisova 8 genomes were found to have survived, but a high proportion of the Denisova 3 genome was intact.   Denisova 3 was cut into two, and the initial DNA sequencing of one fragment was later independently confirmed by sequencing the mtDNA from the second. 
These specimens remained the only known examples of Denisovans until 2019, when a research group led by Fahu Chen, Dongju Zhang and Jean-Jacques Hublin described a partial mandible discovered in 1980 by a Buddhist monk in the Baishiya Karst Cave on the Tibetan Plateau in China. The fossil became part of the collection of Lanzhou University, where it remained unstudied until 2010.  It was determined by ancient protein analysis to contain collagen that by sequence was found to have close affiliation to that of the Denisovans from Denisova Cave, while uranium decay dating of the carbonate crust enshrouding the specimen indicated it was more than 160,000 years old.  The identity of this population was later confirmed through study of environmental DNA, which found Denisovan mtDNA in sediment layers ranging in date from 100,000 to 60,000 years before present, and perhaps more recent. 
Some older findings may or may not belong to the Denisovan line, but Asia is not well mapped in regards to human evolution. Such findings include the Dali skull,  the Xujiayao hominin,  Maba Man, the Jinniushan hominin, and the Narmada hominin.  The Xiahe mandible shows morphological similarities to some later East Asian fossils such as Penghu 1,   but also to Chinese H. erectus. 
Divergence times Edit
Sequenced mitochondrial DNA (mtDNA), preserved by the cool climate of the cave (average temperature is at freezing point), was extracted from Denisova 3 by a team of scientists led by Johannes Krause and Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Denisova 3's mtDNA differs from that of modern humans by 385 bases (nucleotides) out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases. In comparison, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs. This suggested that Denisovan mtDNA diverged from that of modern humans and Neanderthals about 1,313,500–779,300 years ago whereas modern human and Neanderthal mtDNA diverged 618,000–321,200 years ago. Krause and colleagues then concluded that Denisovans were the descendants of an earlier migration of H. erectus out of Africa, completely distinct from modern humans and Neanderthals. 
However, according to the nuclear DNA (nDNA) of Denisova 3—which had an unusual degree of DNA preservation with only low-level contamination—Denisovans and Neanderthals were more closely related to each other than they were to modern humans. Using the percent distance from human–chimpanzee last common ancestor, Denisovans/Neanderthals split from modern humans about 804,000 years ago, and from each other 640,000 years ago.  Using a mutation rate of 1x10 −9 or 0.5x10 −9 per base pair (bp) per year, the Neanderthal/Denisovan split occurred around either 236–190,000 or 473–381,000 years ago respectively.  Using 1.1x10 −8 per generation with a new generation every 29 years, the time is 744,000 years ago. Using 5x10 −10 nucleotide site per year, it is 616,000 years ago. Using the latter dates, the split had likely already occurred by the time hominins spread out across Europe.  H. heidelbergensis is typically considered to have been the direct ancestor of Denisovans and Neanderthals, and sometimes also modern humans.  Due to the strong divergence in dental anatomy, they may have split before characteristic Neanderthal dentition evolved about 300,000 years ago. 
The more divergent Denisovan mtDNA has been interpreted as evidence of admixture between Denisovans and an unknown archaic human population,  possibly a relict H. erectus or H. erectus-like population about 53,000 years ago.  Alternatively, divergent mtDNA could have also resulted from the persistence of an ancient mtDNA lineage which only went extinct in modern humans and Neanderthals through genetic drift.  Modern humans contributed mtDNA to the Neanderthal lineage, but not to the Denisovan mitochondrial genomes yet sequenced.     The mtDNA sequence from the femur of a 400,000-year-old H. heidelbergensis from the Sima de los Huesos Cave in Spain was found to be related to those of Neanderthals and Denisovans, but closer to Denisovans,   and the authors posited that this mtDNA represents an archaic sequence which was subsequently lost in Neanderthals due to replacement by a modern-human-related sequence. 
Though their remains have been identified in only two locations, traces of Denisovan DNA in modern humans suggest they ranged across East Asia,   and potentially western Eurasia.  In 2019, geneticist Guy Jacobs identified three distinct populations of Denisovans in, respectively, Siberia and East Asia, New Guinea and nearby islands, and Oceania and to a lesser extent across Asia. Using coalescent modeling, the Denisova Cave Denisovans split from the second population about 283,000 years ago and from the third population about 363,000 years ago. This indicates that there was marked reproductive separation between Denisovan populations.  Based on the modern distribution of Denisovan DNA, Denisovans may have crossed the Wallace Line into Wallacea and also Sahul (New Guinea and Australia), with little back-migration to west of the line.  These Denisovans may have needed to cross large bodies of water. 
Using exponential distribution analysis on haplotype lengths, Jacobs calculated introgression into modern humans occurred about 29,900 years ago with the second population and 45,700 years ago in the third population. Such a late date for the second population could indicate survival as late as 14,500 years ago, which would make them the latest surviving archaic human species. New Guineans have introgression from these two latter populations. A third wave appears to have introgressed into East Asia, but there is not enough DNA evidence to pinpoint a solid timeframe. 
The mtDNA from Denisova 4 bore a high similarity to that of Denisova 3, indicating that they belonged to the same population.  The genetic diversity among the Denisovans from Denisova Cave is on the lower range of what is seen in modern humans, and is comparable to that of Neanderthals. However, it is possible that the inhabitants of Denisova Cave were more or less reproductively isolated from other Denisovans, and that, across their entire range, Denisovan genetic diversity may have been much higher. 
Denisova Cave, over time of inhabitance, continually swung from a fairly warm and moderately humid pine and birch forest to a tundra or forest–tundra landscape.  Conversely, Baishiya Karst Cave is situated at a high elevation, an area characterized by low temperature, low oxygen, and poor resource availability. Colonization of high-altitude regions, due to such harsh conditions, was previously assumed to have only been accomplished by modern humans.  Denisovans seem to have also inhabited the jungles of Southeast Asia. 
Little is known of the precise anatomical features of the Denisovans since the only physical remains discovered so far are a finger bone, three teeth, long bone fragments, a partial jawbone,  and a parietal bone skull fragment.  The finger bone is within the modern human range of variation for women,  which is in contrast to the large, robust molars which are more similar to those of Middle to Late Pleistocene archaic humans. The third molar is outside of the range of any Homo species except H. habilis and H. rudolfensis, and is more like those of australopithecines. The second molar is larger than those of modern humans and Neanderthals, and is more similar to those of H. erectus and H. habilis.  Like Neanderthals, the mandible had a gap behind the molars, and the front teeth were flattened but Denisovans lacked a high mandibular body, and the mandibular symphysis at the midline of the jaw was more receding.   The parietal is reminiscent of that of H. erectus. 
A facial reconstruction has been generated by comparing methylation at individual genetic loci associated with facial structure.  This analysis suggested that Denisovans, much like Neanderthals, had a long, broad, and projecting face larger nose sloping forehead protruding jaw elongated and flattened skull and wide chest and hips. However, the Denisovan tooth row was longer than that of Neanderthals and anatomically modern humans. 
Middle to Late Pleistocene East Asian archaic human skullcaps typically share features with Neanderthals. The skullcaps from Xuchang feature prominent brow ridges like Neanderthals, though the nuchal and angular tori near the base of the skull are either reduced or absent, and the back of the skull rounded off like in early modern humans. Xuchang 1 had a large brain volume of approximately 1800 cc, on the high end for Neanderthals and early modern humans, and well beyond the present-day human average. 
The Denisovan genome from Denisova Cave has variants of genes which, in modern humans, are associated with dark skin, brown hair, and brown eyes.  The Denisovan genome also contains a variant region around the EPAS1 gene that in Tibetans assists with adaptation to low oxygen levels at high elevation,   and in a region containing the WARS2 and TBX15 loci which affect body-fat distribution in the Inuit.  In Papuans, introgressed Neanderthal alleles are highest in frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissue. 
Early Middle Paleolithic stone tools from Denisova Cave were characterized by discoidal (disk-like) cores and Kombewa cores, but Levallois cores and flakes were also present. There were scrapers, denticulate tools, and notched tools, deposited about 287±41 thousand years ago in the Main Chamber of the cave and about 269±97 thousand years ago in the South Chamber up to 170±19 thousand and 187±14 thousand years ago in the Main and East Chambers, respectively. 
Middle Middle Paleolithic assemblages were dominated by flat, discoidal, and Levallois cores, and there were some isolated sub-prismatic cores. There were predominantly side scrapers (a scraper with only the sides used to scrape), but also notched-denticulate tools, end-scrapers (a scraper with only the ends used to scrape), burins, chisel-like tools, and truncated flakes. These dated to 156±15 thousand years ago in the Main Chamber, 58±6 thousand years ago in the East Chamber, and 136±26–47±8 thousand years ago in the South Chamber. 
Early Upper Paleolithic artifacts date to 44±5 thousand years ago in the Main Chamber, 63±6 thousand years ago in the East Chamber, and 47±8 thousand years ago in the South Chamber, though some layers of the East Chamber seem to have been disturbed. There was blade production and Levallois production, but scrapers were again predominant. A well-developed, Upper Paleolithic stone bladelet technology distinct from the previous scrapers began accumulating in the Main Chamber around 36±4 thousand years ago. 
In the Upper Paleolithic layers, there were also several bone tools and ornaments: a marble ring, an ivory ring, an ivory pendant, a red deer tooth pendant, an elk tooth pendant, a chloritolite bracelet, and a bone needle. However, Denisovans are only confirmed to have inhabited the cave until 55 ka the dating of Upper Paleolithic artifacts overlaps with modern human migration into Siberia (though there are no occurrences in the Altai region) and the DNA of the only specimen in the cave dating to the time interval (Denisova 14) is too degraded to confirm a species identity, so the attribution of these artifacts is unclear.  
Analyses of modern humans genomes show past interbreeding with at least two groups of archaic humans, Neanderthals  and Denisovans,   and that such interbreeding events occurred on multiple occasions. Comparisons of the Denisovan, Neanderthal, and modern human genomes has revealed evidence for a complex web of interbreeding among these lineages. 
Archaic humans Edit
As much as 17% of the Denisovan genome from Denisova Cave represents DNA from the local Neanderthal population.  The Denisovan genome shares more derived alleles with the Altai Neanderthal genome from Siberia than with the Vindija Cave Neanderthal genome from Croatia or the Mezmaiskaya cave Neanderthal genome from the Caucasus, suggesting that the gene flow came from a population that was more closely related to the Altai Neanderthal.  However, Denny's Denisovan father had the typical Altai Neanderthal introgression, while her Neanderthal mother represented a population more closely related to Vindija Neanderthals than to those of Altai. 
About 4% of the Denisovan genome derives from an unidentified archaic hominin,  perhaps the source of the anomalous ancient mtDNA, indicating this species diverged from Neanderthals and humans over a million years ago. The only identified Homo species of Late Pleistocene Asia are H. erectus and H. heidelbergensis.   It is unclear if Denisovan populations which introgressed into modern humans had this archaic hominin ancestry. 
Before splitting from Neanderthals, their ancestors ("Neandersovans") migrating out of Africa into Europe apparently interbred with an unidentified "superarchaic" human species who were already present there these superarchaics were the descendants of a very early migration out of Africa around 1.9 mya. 
Though Denisovans dispersed across Southeast Asia, a 2021 genomic study on modern Southeast Asians indicates that Denisovans (or at least the kin of the ones which introgressed into modern humans) never interbred with any endemic human species, including H. erectus soloensis, H. floresiensis, and H. luzonensis. It is also possible they did interbreed but produced no viable or fertile offspring, or the hybrid lineages have since died out. 
Modern humans Edit
A 2011 study found that Denisovan DNA is prevalent in Australian Aborigines, Near Oceanians, Polynesians, Fijians, Eastern Indonesians and Mamanwans (from the Philippines) but not in East Asians, western Indonesians, Jahai people (from Malaysia) or Onge (from the Andaman Islands). This means that Denisovan introgression occurred within the Pacific region rather than on the Asian mainland, and that ancestors of the latter groups were not present in Southeast Asia at the time, which in turn means that eastern Asia was settled by modern humans in two distinct migrations.  In the Melanesian genome, about 4–6%  or 1.9–3.4% derives from Denisovan introgression.  New Guineans and Australian Aborigines have the most introgressed DNA,  but Aborigines have less than New Guineans.  In Papuans, less Denisovan ancestry is seen in the X chromosome than autosomes, and some autosomes (such as chromosome 11) also have less Denisovan ancestry, which could indicate hybrid incompatibility. The former observation could also be explained by less female Denisovan introgression into modern humans, or more female modern human immigrants who diluted Denisovan X chromosome ancestry. 
In contrast, 0.2% derives from Denisovan ancestry in mainland Asians and Native Americans.  South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians.  The discovery of the 40,000-year-old Chinese modern human Tianyuan Man lacking Denisovan DNA significantly different from the levels in modern-day East Asians discounts the hypothesis that immigrating modern humans simply diluted Denisovan ancestry whereas Melanesians lived in reproductive isolation.   A 2018 study of Han Chinese, Japanese, and Dai genomes showed that modern East Asians have DNA from two different Denisovan populations: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from Denisova Cave. This could indicate two separate introgression events involving two different Denisovan populations. In South Asian genomes, DNA only came from the same single Denisovan introgression seen in Papuans.  A 2019 study found a third wave of Denisovans which introgressed into East Asians. Introgression, also, may not have immediately occurred when modern humans immigrated into the region. 
In other regions of the world, archaic introgression into humans stems from a group of Neanderthals related to those which inhabited Vindija Cave, Croatia, as opposed to archaics related to Siberian Neanderthals and Denisovans. However, about 13.1 and 3.3% of the archaic DNA in the modern Icelandic genome descends from these two latter groups, respectively, and such a high percentage could indicate a western Eurasian population of Denisovans which introgressed into either Vindija-related Neanderthals or immigrating modern humans. 
Denisovan genes may have helped early modern humans migrating out of Africa to acclimatize. Although not present in the sequenced Denisovan genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles (involved in the immune system's natural killer cell receptors) has led to the suggestion that it introgressed from Denisovans into modern humans in West Asia. In a 2011 study, half of the HLA alleles of modern Eurasians were shown to represent archaic HLA haplotypes, and were inferred to be of Denisovan or Neanderthal origin.  A haplotype of EPAS1, likely introgressed into Tibetans from Denisovans, allows them to live at high elevations in a low-oxygen environment.   Genes related to phospholipid transporters (which are involved in fat metabolism) and to trace amine-associated receptors (involved in smelling) are more active in people with more Denisovan ancestry. 
The riches within Denisovan DNA
Knowledge of the Denisovan people emerged from studies of ancient genomes, which began 20 years ago when scientists first developed techniques for extracting DNA from fossils and for creating copies of that genetic material which allowed them to study it.
Scientists at the Max Planck Institute in Leipzig were studying bones and teeth found in Denisova cave in the Altai Mountains in Siberia, where Neanderthal fossils had been found. One bone and one tooth, they discovered, belonged to a previously unknown species of ancient human.
These few fossils proved to be spectacularly rich in genetic material, allowing scientists to sequence entire genomes. It is this detailed information about the Denisovan genome that has demonstrated they interbred with modern humans.
Descendants of these unions, carrying small amounts of Denisovan DNA, went on to settle in Melanesia and Australia thousands of years ago.
In this way, we can see Denisovan DNA in that of modern humans, though we have no idea what the Denisovans looked like or where, exactly, they lived.