DENISOVANS: NEW HUMAN SPECIES FROM ALTAI-SIBERIA

DENISOVANS

Research involving DNA seems to indicate there may have been an identified human ancestor living in Siberia and the Altai region — where Kazakhstan, Mongolia, China and Russia all come together — at the same time as early modern man and Neanderthals. DNA markers found by scientists in 30,000- to 50,000-year-old fossils that don't match those of modern humans or Neanderthal and appears to have belonged to species that split off from the branches leading to modern humans and Neanderthal a half million or so years ago. A lot questions about the finding remain and scientists that announced it have been cautious about making any bold claims about it. Researchers gave the new humans the informal name Denisovans, after the place the place the fossils were discovered.

Denisovans had very large and unusual teeth, unlike those of humans or Neanderthals. So far only some teeth and a piece of finger have been found so it is difficult to determine what the Denisovans looked like. Analysis of that 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 is Denisovan.

The existence of a new human relative 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. If the research does hold up it 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.

The genome, recovered from the finger bone showed that Denisovans are more closely related to Neanderthals than to modern humans. That indicates that both they and Neanderthals sprang from a common ancestor on a different branch of the evolutionary family tree than the one leading to modern humans. There's not enough evidence to determine whether Denisovans are a distinct species, the researchers said." [Source: Malcolm Ritter, AP, December 22, 2010 ***]

Scientists have no idea what Denisovans looked like, David Reich, a Harvard University researcher and an author of the paper, told AP. Apart from the genome, the researchers reported finding a Denisovan upper molar in the cave. Its large size and features differ from teeth of Neanderthals or early modern humans, both of which lived in the same area at about the same time as the Denisovans. 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. ***

Denisova Cave

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 \+\]

“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

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. \+\

DNA Says 'Denisovans' Roamed Widely In Asia

In 2010, AP reported, The Denisovan DNA code indicates they "roamed far from the cave that holds its only known remains. By comparing the DNA to that of modern populations, scientists found evidence that these "Denisovans" from more than 30,000 years ago ranged all across Asia. They apparently interbred with the ancestors of people now living in Melanesia, a group of islands northeast of Australia. There's no sign that Denisovans mingled with the ancestors of people now living in Eurasia, which made the connection between Siberia and distant Melanesia quite a shock."Source: Malcolm Ritter, AP, December 22, 2010 ***]

"Scientists found evidence that in the genomes of people now living in Melanesia, about 5 percent of their DNA can be traced to Denisovans, a sign of ancient interbreeding that took researchers by surprise. "We thought it was a mistake when we first saw it," Reich said. "But it's real." And that suggests Denisovans once ranged widely across Asia, he said. Somehow, they or their ancestors had to encounter anatomically modern humans who started leaving Africa some 55,000 years ago and reached New Guinea by some 45,000 years ago. It seems implausible that this journey took a detour through southern Siberia without leaving a genetic legacy in other Eurasian populations, Reich said. It makes more sense that this encounter happened much farther south, indicating Denisovans ranged throughout Asia, over thousands of miles and different climate zones, he said. ***

Todd Disotell of New York University told AP he and colleagues were "blown away" by the unexpected Melanesia finding, with its implication for where Denisovans lived. "Clearly they had to have been very widespread in Asia," and DNA sampling of isolated Asian populations might turn up more of their genetic legacy, he said. Rick Potts, director of the human origins program at the Smithsonian Institution, said the new work greatly strengthens the case that Denisovans differed from Neanderthals and modern humans. Still, they may not be a new species, because they might represent a creature already known from fossils but which didn't leave any DNA to compare, such as a late-surviving Homo heidelbergensis, he said. ***

Potts also said the Melanesia finding could mean that the Melanesians and the Denisovans didn't intermix, but simply happened to retain ancestral DNA sequences that had been lost in other populations sampled in the study. But he stressed he doesn't know if that's a better explanation than the one offered by the authors. "I am excited about this paper (because) it just throws so much out there for contemplation that is testable," Potts said. "And that's good science." ***

Denisovan Man, Modern Man and Hominid Migrations in Asia

Jamie Shreeve wrote in National Geographic: “Although the Denisovans’ genome showed that they were more closely related to the Neanderthals, they too had left their mark on us. But the geographic pattern of that legacy was odd. When the researchers compared the Denisovan genome with those of various modern human populations, they found no trace of it in Russia or nearby China, or anywhere else, for that matter—except in the genomes of New Guineans, other people from islands in Melanesia, and Australian Aborigines. On average their genomes are about 5 percent Denisovan. Negritos in the Philippines have as much as 2.5 percent. [Source: Jamie Shreeve, National Geographic, July 2013 \+\]

“Putting all the data together, Pääbo and his colleagues came up with a scenario to explain what might have occurred. Sometime before 500,000 years ago, probably in Africa, the ancestors of modern humans split off from the lineage that would give rise to Neanderthals and Denisovans. (The most likely progenitor of all three types was a species called Homo heidelbergensis.) While our ancestors stayed in Africa, the common ancestor of Neanderthals and Denisovans migrated out. Those two lineages later diverged, with the Neanderthals initially moving west into Europe and the Denisovans spreading east, perhaps eventually populating large parts of the Asian continent. \+\

“Later still, when modern humans ventured out of Africa themselves, they encountered Neanderthals in the Middle East and Central Asia, and to a limited extent interbred with them. According to evidence presented by David Reich at the Denisova symposium, this mixing most likely occurred between 67,000 and 46,000 years ago. One population of modern humans then continued east into Southeast Asia, where, sometime around 40,000 years ago, they encountered Denisovans. The moderns interbred with them as well and then moved into Australasia, carrying Denisovan DNA. \+\

“This scenario might explain why the only evidence so far that the Denisovans even existed is three fossils from a cave in Siberia and a 5 percent stake in the genomes of people living today thousands of miles to the southeast. But it left a lot of questions unanswered. If the Denisovans were so widespread, why was there no trace of them in the genomes of Han Chinese or of any other Asian people between Siberia and Melanesia? Why had they left no mark in the archaeological record—no distinctive tools, say? Who were they really? What did they look like? “Clearly we need much more work,” Pääbo acknowledged. \+\

“The best of all possible developments would be to find Denisovan DNA in a skull or other fossil with distinctive morphological features, one that could serve as a Rosetta stone for reexamining the whole fossil record of Asia. There are some intriguing candidates, most from China, and three skulls in particular, dated between 250,000 and 100,000 years ago. Pääbo is working closely with scientists at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing and has set up a DNA testing lab there. Unfortunately DNA does not preserve well in warmer climates. To date, no other fossil has been identified as Denisovan by the only way Denisovans can be known: their DNA.” \+\

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.” \+\

Latest Denisovan Findings: More Widespread in Asia

Denisovans show as much genetic diversity as Neanderthals, which suggests they ranged across a large area. New DNA evidence appears to indicate they likely ranged across much of Asia for tens of thousands of years and weren't just a small, isolated population, researchers wrote in a paper published in the journal Proceedings of the National Academy of Sciences. [Source: CBC News, November 16, 2015 *-*]

CBC News reported: Scientists have analyzed two molars found in Denisova cave and confirmed that they belong to two adult male Denisovans. On the teeth, University of Toronto researcher Bence Viola, a co-author of the paper, said, at first "I thought, 'Oh, that actually looks very human-like.” But when the rest of the tooth was found, he began to have doubts. "I thought, 'This is too big. This doesn't look human-like at all...In its size, it's comparable to hominins that lived two or three million years ago…but the age of it shows that it's very recent," While individuals have different tooth sizes, finding two teeth this large from two different, unrelated individuals suggests "the whole group probably had very large and weird teeth." They also likely had a very large and robust jaw to support such long tooth roots. But aside from that, we know nothing about what they looked like. *-*

“Differences in the DNA in the two teeth, along with the layers of the cave in which they were found, suggest that the two men lived about 60,000 years apart. The more recent would have lived around 50,000 to 70,000 years ago, while the earlier would have lived up to 130,000 years ago. The Denisovans also show as much genetic diversity as Neanderthals that lived as far away from one another as Spain and Siberia, said Paabo, another co-author of the paper."It just sort of in general would indicate they have a long history where they had substantial numbers of individuals in the population." *-*

“If that's the case, why have we never found any other Denisovan remains outside the Denisova cave? Viola suspects other Denisovan remains have already been uncovered in China – they just haven't been recognized as Denisovan yet. "I'm really convinced," he said. "The genetic data shows that these guys were spread over large parts of Asia, so we must have them." *-*

Image Sources:

Text Sources: New York Times, Washington Post, Los Angeles Times, Times of London, Lonely Planet Guides, Library of Congress, U.S. government, Compton’s Encyclopedia, The Guardian, National Geographic, Smithsonian magazine, The New Yorker, Time, Newsweek, Reuters, AP, AFP, Wall Street Journal, The Atlantic Monthly, The Economist, Foreign Policy, Wikipedia, BBC, CNN, and various books, websites and other publications.

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© 2008 Jeffrey Hays

Last updated May 2016

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