Denisovans: Characteristics, Discovery and DNA | Early European History And Religion

Home | Category: Neanderthals, Denisovans and Modern Humans / Neanderthals, Denisovans and Modern Human

DENISOVANS

Denisovan molar

Denisovans are an extinct group of hominins who coexisted with the Neanderthals and modern humans around 30,000 to 50,000 years ago and originated at least 200,000 years ago. Not much is known about them other than what can be gleaned from their DNA and a few rare fossils. Scientists first learned of their existence from an incomplete finger bone and two molars discovered in the Denisova Cave in the the Altai region — where Kazakhstan, Mongolia, China and Russia all come together. The finger bone and two have been dated by some to 80,000 years ago, but are generally placed in the 30,000 to 50,000 year old range.

The existence of Denisovans was unknown until the tip of a finger bone about 40,000 years old was found in 2010. Three molars have been found at that site. A partial Denisovan jawbone from about 160,000 years ago subsequently was discovered in a Tibetan cave. A Denisovan tooth was later found in Laos [Source: Will Dunham, Reuters, May 18, 2022]

Denisovans were discovered when DNA markers found by scientists in the finger and molar fossils didn't match those of modern humans or Neanderthal. Researchers gave the new humans the name Denisovans, after the place the place the fossils were discovered. Analysis of the Denisovan genome showed that Denisovans interbred with modern humans – about five per cent of the DNA of native Papua New Guineans and Australians and 0.2 per cent of the DNA of Asians and Native Americans are Denisovan.

Denisovans existence was first revealed in early 2010 from a sampling of DNA recovered from a finger bone discovered in the Denisova Cave in southern Siberia. The research, published online in the journal Nature in March 2010 by Johannes Krause and Svante Paabo of the Max Planck Institute for Evolutionary Anthropology, decoded the complete set of DNA from mitochondria. The research suggests a migration out of Africa around a half million years ago. Scientists are now looking for similarities between the DNA of the “Siberian ancestor” and that of Neanderthals, Homo erectus and homo heidelbergensis.

Websites and Resources on Hominins and Human Origins: Smithsonian Human Origins Program humanorigins.si.edu ; Institute of Human Origins iho.asu.edu ; Becoming Human University of Arizona site becominghuman.org ; Hall of Human Origins American Museum of Natural History amnh.org/exhibitions ; The Bradshaw Foundation bradshawfoundation.com ; Britannica Human Evolution britannica.com ; Human Evolution handprint.com ; University of California Museum of Anthropology ucmp.berkeley.edu; John Hawks' Anthropology Weblog johnhawks.net/ ; New Scientist: Human Evolution newscientist.com/article-topic/human-evolution

Limited Hard Evidence About Denisovans

Reconstruction of 13-year-old Denisovan by Hebrew University

Until the jawbone discovery in Tibet, the only Denisovan fossils scientists knew of were a tiny finger bone, three teeth, and fragments of a skull and jaw from Siberia. According to Business Insider: Yet DNA evidence suggests Denisovans were prolific across Asia, passing along their genetic makeup to Homo sapiens tens of thousands of years ago. “Denisovans are the only species of human that we know more about their DNA than what they actually look like," Westaway said. "How can we know so little about a key species of human that contributed to our DNA and was a major player in the story of human evolution?" The lack of Denisovan bones also makes it difficult to separate this ancestor from other ancient humans in the fossil record. [Source: Aylin Woodward, Business Insider, December 9, 2020]

“But as researchers discover more places that Denisovans once lived, identifying their fossils could get easier. “It could even be that Denisovan fossils are sitting in museums across the world," Mike Morley, a geoarchaeologist from Flinders University, told The Sydney Morning Herald. "We simply don't know what a Denisovan fossil looks like."

Associated Press reported: “ Neither the finger bone nor the tooth can be dated directly, but tests of animal bones found nearby show the Denisovan remains are at least 30,000 years old, and maybe more than 50,000 years old, Reich said. Yet, archaeologists have reported virtually no sign of the Denisovans, no tools or other indications of how they lived. Maybe that's because sites in Asia haven't been studied as systematically as Neanderthal sites in Europe, he said. [Source: Malcolm Ritter, AP, December 22, 2010]

Denisovan Specimens

The fossils of five distinct Denisovan individuals from Denisova Cave have been identified through their ancient DNA (aDNA): Denisova 2, 3, 4, 8, and 11. 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. [Source: Wikipedia]

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 in Tibet. 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.

In 2018, a team of Laotian, French, and American anthropologists, who had been excavating caves in the Laotian jungle of the Annamite Mountains since 2008, was directed by local children to the site Tam Ngu Hao 2 ("Cobra Cave") where they recovered a human tooth. The tooth (catalogue number TNH2-1) developmentally matches a 3.5 to 8.5 year old, and a lack of amelogenin (a protein on the Y chromosome) suggests it belonged to a girl barring extreme degradation of the protein over a long period of time.

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 Human. The Xiahe mandible shows morphological similarities to some later East Asian fossils such as Penghu 1,but also to Chinese Homo erectus.In 2021, Chinese palaeoanthropologist Qiang Ji suggested his newly erected species, Homo longi, may represent the Denisovans based on the similarity between the type specimen's molar and that of the Xiahe mandible.

Denisovan Characteristics

Denisovan bones from Denisova cave

Little is known of exact anatomical features of the Denisovans since the only physical remains discovered so far are a finger bone, four teeth, long bone fragments, a partial jawbone, and a parietal bone skull fragment. The finger bone is similar to that of female modern human but robust molars suggest a hominid more akin to a Neanderthal or archaic human. Geneticist Svante Paabo said. “What's fascinating about the Denisovans is we know next to nothing about how they looked. We have their genome and we have two teeth, and those teeth are huge. ... The only thing we can say is they must have been very big, or at least have big mouths.”

Denisovans had very large and unusual teeth, unlike those of humans or Neanderthals. Because only some teeth and a piece of finger have been found it is difficult to determine what the Denisovans looked like. The third molar is more like Homo habilis or even an australopithecines than a modern human or Neanderthal. The second molar is larger than those of modern humans and Neanderthals, and is more similar to those of Homo erectus and Homo habilis. [Source: Wikipedia]

Based on DNA clues scientists have determined there similarities between Denisovans and Neanderthals such as sloping forehead, long face and large pelvis. But Denisovans were also unique in that they had very wide skulls and large dental arch. Like Neanderthals, the mandible had a gap behind the molars, based on the Tibetan Denisovan jawbone, 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. [Source: Ari Rabinovitch, Reuters, September 20, 2019]

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; large nose; sloping forehead; protruding jaw; elongated and flattened skull; and wide chest and hips. The Denisovan tooth row was longer than that of Neanderthals and anatomically modern humans. See Denisovan Reconstruction Below

Denisova Cave and What Archaeologists Found There

Jamie Shreeve wrote in National Geographic: “In the Altay Mountains of southern Siberia, some 200 miles from where Russia touches Mongolia, China, and Kazakhstan, nestled under a rock face about 30 yards above a little river called the Anuy, there is a cave called Denisova. It has long attracted visitors. The name comes from that of a hermit, Denis, who is said to have lived there in the 18th century. Long before that, Neolithic and later Turkic pastoralists took shelter in the cave, gathering their herds around them to ride out the Siberian winters. [Source: Jamie Shreeve, National Geographic, July 2013 +]

Denisova Cave

“In the back of the cave is a small side chamber, and it was there that a young Russian archaeologist named Alexander Tsybankov was digging one day in July 2008, in deposits believed to be 30,000 to 50,000 years old, when he came upon a tiny piece of bone. It was hardly promising: a rough nubbin about the size and shape of a pebble you might shake out of your shoe...The bone preserved just enough anatomy for the paleontologist to identify it as a chip from a primate fingertip—specifically the part that faces the last joint in the pinkie. Since there is no evidence for primates other than humans in Siberia 30,000 to 50,000 years ago—no apes or monkeys—the fossil was presumably from some kind of human. Judging by the incompletely fused joint surface, the human in question had died young, perhaps as young as eight years old. +\

“Anatoly Derevianko, leader of the Altay excavations and director of the Institute of Archaeology and Ethnography in Novosibirsk, thought the bone might belong to a member of our own species, Homo sapiens. Sophisticated artifacts that could only be the work of modern humans, including a beautiful bracelet of polished green stone, had previously been found in the same deposits. But DNA from a fossil found earlier in a nearby cave had proved to be Neanderthal, so it was possible this bone was Neanderthal as well.” +\

“Derevianko decided to cut the bone in two. He sent one half to a genetics laboratory in California; so far he has not heard from that half again. He slipped the other half into an envelope and had it hand-delivered to Svante Pääbo, an evolutionary geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

In the summer of 2010 a human toe bone was found along with an enormous tooth, later linked with the fingertip, from “Layer 11,” in the cave, dated to 30,000 to 50,000 years ago. In Leipzig a graduate student named Susanna Sawyer analyzed its DNA. “To everyone’s shock, the toe bone had turned out to be Neanderthal, deepening the mystery of the place. The green stone bracelet found earlier in Layer 11 had almost surely been made by modern humans. The toe bone was Neanderthal. And the finger bone was something else entirely. One cave, three kinds of human being. “Denisova is magical,” said Pääbo. “It’s the one spot on Earth that we know of where Neanderthals, Denisovans, and modern humans all lived.”

Discovery of Denisovan Man

Elizabeth Kolbert wrote in The New Yorker: In 2009, “Pääbo “obtained a fragment of finger bone that had been unearthed in a cave in southern Siberia along with a weird, vaguely human-looking molar. The finger bone—about the size of a pencil eraser—was believed to be more than forty thousand years old. Pääbo assumed that it came either from a modern human or from a Neanderthal. If it proved to be the latter, then the site would be the farthest east that Neanderthal remains had been found. [Source: Elizabeth Kolbert, The New Yorker, August 15, 2011]

Denisovan phalanx distalis

Jamie Shreeve wrote in National Geographic: “Pääbo, a transplanted Swede, is arguably the world’s leading expert in ancient DNA, especially human DNA...When Pääbo received the package from Derevianko, his team was hard at work producing the first sequence of the entire Neanderthal genome... So it wasn’t until late 2009 that the little Russian finger bone drew the attention of Johannes Krause, at the time a senior member of Pääbo’s team. (He’s now at the University of Tübingen.) Like everyone else, Krause assumed the bone was from an early modern human. [Source: Jamie Shreeve, National Geographic, July 2013 +]

“Krause and his student Qiaomei Fu extracted the finger bone’s mitochondrial DNA (mtDNA), a small bit of the genome that living cells have hundreds of copies of and that is therefore easier to find in ancient bone. They compared the DNA sequence with those of living humans and Neanderthals. Then they repeated the analysis, because they couldn’t believe the results they’d gotten the first time around...Krause himself recalls that Friday as “scientifically the most exciting day of my life.” The tiny chip of a finger bone, it seemed, was not from a modern human at all. But it wasn’t from a Neanderthal either. It belonged to a new kind of human being, never before seen. +\

“In July 2011, three years after Tsybankov unearthed the bone chip, Anatoly Derevianko organized a scientific symposium at the archaeological camp a few hundred yards from Denisova cave...The year before, two other fossils had been found to contain DNA similar to that of the finger bone, both of them molars. The first tooth had turned up among the specimens from Denisova housed at Derevianko’s institute in Novosibirsk. It was bigger than either a modern human or a Neanderthal tooth, in size and shape resembling the teeth of much more primitive members of the genus Homo who lived in Africa millions of years ago. The second molar had been found in 2010 in the same cave chamber that had yielded the finger bone—indeed, near the bottom of the same 30,000-to-50,000-year-old deposits, called Layer 11. +\

“Remarkably, that tooth was even bigger than the first, with a chewing surface twice that of a typical human molar. It was so large that Max Planck paleoanthropologist Bence Viola mistook it for a cave bear tooth. Only when its DNA was tested was it confirmed to be human—specifically, Denisovan, as the scientists had taken to calling the new ancestors. “It shows you how weird these guys are,” Viola told me at the symposium. “At least their teeth are just very strange.” +\

“Pääbo’s team could extract only a tiny amount of DNA from the teeth—just enough to prove they came from the same population as the finger, though not from the same individual. But the finger bone had been spectacularly generous. DNA degrades over time, so usually very little remains in a bone tens of thousands of years old. Moreover, the DNA from the bone itself—called endogenous DNA—is typically just a tiny fraction of the total DNA in a specimen, most of which comes from soil bacteria and other contaminants. None of the Neanderthal fossils Pääbo and his colleagues had ever tested contained even 5 percent endogenous DNA, and most had less than one percent. To their amazement, the DNA in the finger bone was some 70 percent endogenous. Apparently, the cold cave had preserved it well. Given so much DNA, the scientists easily ascertained that there was no sign of a male Y chromosome in the specimen. The fingertip had belonged to a little girl who had died in or near Denisova cave tens of thousands of years before. +\

Impact of the Denisovan Discovery

Denisova cave location

Elizabeth Kolbert wrote in The New Yorker: “The finger fragment yielded astonishingly large amounts of DNA. When the analysis of the first bits was completed, Pääbo happened to be in the United States. He called his office, and one of his colleagues said to him, “Are you sitting down?” The DNA showed that the digit could not have belonged to a Neanderthal or to a modern human. Instead, its owner must have been part of some entirely different and previously unsuspected type of hominin. In a paper published in December, 2010, in Nature, Pääbo and his team dubbed this group the Denisovans, after the Denisova Cave, where the bone had been found. “GIVING ACCEPTED PREHISTORIC HISTORY THE FINGER,” ran the headline on the story in the Sydney Morning Herald. Amazingly—or perhaps, by now, predictably—modern humans must have interbred with Denisovans, too, because contemporary New Guineans carry up to six per cent Denisovan DNA. (Why this is true of New Guineans but not native Siberians or Asians is unclear, but presumably has to do with patterns of human migration.) [Source: Elizabeth Kolbert, The New Yorker, August 15, 2011]

“It has been understood for a long time that modern humans and Neanderthals were contemporaries. The discovery of the hobbits and now the Denisovans shows that humans shared the planet with at least two additional creatures like ourselves. And it seems likely that as DNA from more ancient remains is analyzed still other human relatives will be found; as Chris Stringer, a prominent British paleoanthropologist, told me, “I’m sure we’ve got more surprises to come.”

““If these other forms of humans had survived two thousand generations more, which is not so much, then how would that have influenced our view of the living world?” Pääbo said, once the excitement over the skullcap had passed and we were sitting over coffee. “We now make this very clear distinction between humans and animals. But it might not be as clear. That is sort of an interesting thing to philosophize about.” It’s also interesting to think about why we’re the ones who survived.”

History of Denisovans

Denisovan phalanx tertia shaft

According to Reuters: A common ancestor to Denisovans, Neanderthals, and Homo sapiens is thought to have lived in Africa 700,000 to 500,000 years ago, with a branch that led to Denisovans and Neanderthals splitting off 470,000 to 380,000 years ago. Homo sapiens first emerged in Africa roughly 300,000 years ago, then spread worldwide. By 200,000 years ago, four different archaic human species inhabited Asia including the Denisovans, Homo erectus, and diminutive island-dwelling peoples called Homo floresiensis and Homo luzonensis. Our species then joined the fray.

Denisovans and Neanderthals appear to have the same common ancestor, but both are genetically distinct from one another. Neanderthal and Denisovan are believed to have split apart between 400,000 to 500,000 years ago. Humans and Neanderthals divided into separate groups as far back as 765,000 years ago. Denisovans and Neanderthals ultimately disappeared – perhaps because their lineages were absorbed by modern humans.

Insights from Denisovan DNA

Jamie Shreeve wrote in National Geographic: “In 2012 Pääbo’s group published a new version of the finger bone’s genome—astonishingly, one that in accuracy and completeness rivals any living human’s genome that has been sequenced. The breakthrough came from a German postdoc in Pääbo’s lab named Matthias Meyer. DNA consists of two interlocking strands—the familiar double helix. Previous methods for retrieving DNA from fossil bone could read out sequences only when both strands were preserved. Meyer had developed a technique for recovering short, single-stranded fragments of DNA as well, greatly increasing the amount of raw material to work with. The method produced a version of the Denisovan girl’s genome so precise that the team could discriminate between genetic information inherited from her mother and that from her father. In effect, they now had two highly accurate Denisovan genomes, one from each parent. These in turn opened a window on the entire history of their population. [Source: Jamie Shreeve, National Geographic, July 2013 +]

“One immediate revelation was how little variation there was between the parents’ genomes—about a third as much as there is between any two living humans. The differences were sprinkled across the genomes, which ruled out inbreeding: If the girl’s parents had simply been closely related, they would have had huge chunks of exactly matched DNA. The pattern indicated instead that the Denisovan population represented by the fossil had never been large enough to have developed much genetic diversity. Worse, it seemed to have suffered a drastic decline sometime before 125,000 years ago—the little girl in the cave may have been among the last of her kind.” /+/

“The Denisovans also have something to say about our own kind. With virtually every letter of the Denisovan genetic code in hand, Pääbo and his colleagues were able to take aim at one of the profoundest mysteries: In our own genomes, what is it that makes us us? What defining changes in the genetic code took place after we separated from our most recent ancestor? Looking at the places where all living humans share a novel genetic signature but the Denisovan genome retains a primitive, more apelike pattern, the researchers came up with a surprisingly short list. Pääbo has called it the “genetic recipe for being a modern human.” The list includes just 25 changes that would alter the function of a particular protein. +\

“Intriguingly, five of these proteins are known to affect brain function and development of the nervous system. Among them are two genes where mutations have been implicated in autism and another that’s involved in language and speech. Just what those genes actually do to make us think, act, or talk differently than Denisovans, or any other creature that has walked the Earth, remains to be seen. The lasting contribution of studying Denisovan DNA, Pääbo says, “will be in finding what is exclusively human.”...But what of the little girl herself? The tiny bit of bone that is all we ever had of her—or at least the half that went to Leipzig—is gone now. In pulling DNA from it, Johannes Krause and Qiaomei Fu eventually used it all up. The little girl has been reduced to a “library” of DNA fragments that can be exactly copied again and again forever. In the scientific paper discussing the history of her population, Pääbo and his colleagues did mention, almost in passing, a few facts about her that they had gleaned from that library: She probably had dark hair, dark eyes, and dark skin.” +\

comparison of Denisovan and modern human skulls

200,000-Year-Old Denisovan Woman Studied

In 2021, scientists announced in an article in Nature Ecology & Evolution article that they had studied the physical remains of a Denisovan — female dated at 200,000 years old — for the first time. The bones are the oldest known remains of the Denisovans". “"This is the first time we have the physical remains of Denisovans that we can securely date to 200,000 years ago," Samantha Brown, a co-author of the study, said. "From here we can investigate their technology and behaviors and hopefully start to understand this population a little better." [Source: Taylor Avery,USA TODAY, December 1, 2021]

USA TODAY reported: Just six remains of the group have been found worldwide. One was discovered in China, and five were found in the Denisova Cave in Siberia, Russia. “It's from that Siberian cave that scientists recovered and later analyzed nearly 3,800 bone fragments which would reveal three Denisovan fossils dated to be 200,000 years old. The efforts, funded by the European Research Council and the Russian Academy of Sciences, began in 2017.

“Prior to this discovery, the oldest Denisovan remains were estimated to date between 122,000 to 194,000 years old. There were other exciting finds in the cave too. Scientists found stone tools and artifacts, the first to be discovered with Denisovan remains.

Denisovans, Modern Humans and Neanderthals

DNA Research has indicated that Denisovans, Neanderthals and modern humans interbred. Scientists believe that interbreeding with the Denisovans contributed to the development of the modern human immune system and possibly made humans living today susceptible to allergies.

According to DNA taken from a 50,000-year-old a fossilized Neanderthal toe bone found in a Siberian Cave: 2 percent of the DNA of modern people not of African descent came from Neanderthals and 0.5 percent of Denisovan DNA came from Neanderthals, and that an estimated 0.2 percent of the DNA of mainland Asians and Native Americans comes from Denisovans. [Source: Monte Morin, Los Angeles Times, December 18, 2013 \=]

Genetic analysis suggests the ancestors of modern humans interbred with Neanderthals and Denisovans. Neanderthal DNA makes up 1 to 4 percent of modern Eurasian genomes, Denisovans are most closely related to one group of living humans – the Melanesians of southeast Asia and their Australian neighbours. These groups carry Denisovan DNA from interbreeding event that must have happened as their ancestors passed through southern Asia over 40,000 years ago. and Denisovan DNA makes up 4 to 6 percent of modern New Guinean and Bougainville Islander genomes in the Melanesian islands.

comparison of Denisovan, Neanderthal and modern human anatomy

Reconstructing a Denisovan Based on DNA

Researchers at Hebrew University in Israel reconstructed a 13-year-old female Denisovan using DNA found in the pinky bone of Denisovan girl that age. Hebrew University genetics professor Liran Carmel told Reuters: It sounds like science fiction, but Carmel said that was enough to create a depiction of a full Denisovan skeleton. "This is the first time that we provide a detailed anatomical reconstruction showing us what these humans looked like," he said.[Source: Ari Rabinovitch, Reuters, September 20, 2019]

Reuters reported: His team developed a technology to decipher the ancient DNA and, more importantly, its gene activity. Gene activity, for example, differentiates between a frog and tadpole, even though their DNA is identical, Carmel said. DNA could indicate the Denisovan's dark skin, eyes and hair, Carmel said, but by mapping gene activity patterns, they could infer how the species stood out anatomically from modern humans or Neanderthals. They identified 56 traits, most in the skull, that differed.

“This helped them produce a rendering — claiming 85 percent accuracy — of a Denisovan skeleton that at first glance looks like it could be from a modern human, though differences are obvious on closer inspection. The skeletal reconstruction, along with an artist's rendering of the 13-year-old girl's head and face, were published in the journal Cell. The team repeated the process as a test with Neanderthals and chimpanzees, whose anatomies are known, and found the reconstruction to be 85 percent accurate. The discovery of more Denisovan DNA would further improve the rendering.

Image Sources: Wikimedia Commons, skull and anatomy charts and reconstruction from Hebrew University of Jerusalem

Text Sources: National Geographic, New York Times, Washington Post, Los Angeles Times, Smithsonian magazine, Nature, Scientific American. Live Science, Discover magazine, Discovery News, Natural History magazine, Archaeology magazine, The New Yorker, Time, Newsweek, BBC, The Guardian, Reuters, AP, AFP and various books and other publications.

Last updated April 2024