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. 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 molars have been dated by some 80,000 years ago, but generally placed to in the 30,000 to 50,000 year old range.

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.

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.

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. 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.”

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]

Websites and Resources on Neanderthals: Wikipedia: Neanderthals Wikipedia ; Neanderthals Study Guide ; Neandertals on Trial, from PBS; The Neanderthal Museum ; The Neanderthal Flute, by Bob Fink Websites and Resources on Prehistoric Art: Chauvet Cave Paintings ; Cave of Lascaux; Trust for African Rock Art (TARA); Bradshaw Foundation; Australian and Asian Palaeoanthropology, by Peter Brown

Websites and Resources on Hominins and Human Origins: Smithsonian Human Origins Program ; Institute of Human Origins ; Becoming Human University of Arizona site ; Talk Origins Index ; Last updated 2006. Hall of Human Origins American Museum of Natural History ; Wikipedia article on Human Evolution Wikipedia ; Human Evolution Images; Hominin Species ; Paleoanthropology Links ; Britannica Human Evolution ; Human Evolution ; National Geographic Map of Human Migrations ; Humin Origins Washington State University ; University of California Museum of Anthropology; BBC The evolution of man"; "Bones, Stones and Genes: The Origin of Modern Humans" (Video lecture series). Howard Hughes Medical Institute.; Human Evolution Timeline ; Walking with Cavemen (BBC) ; PBS Evolution: Humans; PBS: Human Evolution Library; Human Evolution: you try it, from PBS; John Hawks' Anthropology Weblog ; New Scientist: Human Evolution; Fossil Sites and Organizations: The Paleoanthropology Society; Institute of Human Origins (Don Johanson's organization); The Leakey Foundation; The Stone Age Institute; The Bradshaw Foundation ; Turkana Basin Institute; Koobi Fora Research Project; Maropeng Cradle of Humankind, South Africa ; Blombus Cave Project; Journals: Journal of Human Evolution; American Journal of Physical Anthropology; Evolutionary Anthropology; Comptes Rendus Palevol ; PaleoAnthropology

Denisova Cave and What Archaeologists Found There

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

Denisovan phalanx distalis

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 <^^>]

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.” <^^>

Insights from Denisovan DNA

Denisovan phalanx tertia shaft

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.” \+\

DNA Says 'Denisovans' Roamed Across 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 ***]

Denisovan spread and evolution

"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." ***

Denisovans Roamed Across Large Swaths of 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 *-*]

secondary human expansion

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." *-*

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.

Marlowe Hood of AFP wrote: “Among their genetic legacy to some modern humans is a variant of the gene EPAS1 that makes it easier for the body to access oxygen by regulating the production of haemoglobin, according to a 2014 study. Nearly 90 percent of Tibetans have this precious variant, compared with only nine percent of Han Chinese, the dominant -- and predominantly lowland -- ethnic group in China.” [Source: Marlowe Hood, AFP, August 23, 2018 \=/]

Zach Zorich wrote in Archaeology: “A new technique for sequencing ancient DNA has allowed a multinational research team to reconstruct the genome of a person who lived in Siberia’s Denisova Cave between 30,000 and 82,000 years ago—with the same level of accuracy as genomes from modern people. This new DNA sequence gives researchers a clearer picture of how early hominins such as the Denisovans and Neanderthals were related to modern humans and to each other. [Source: Zach Zorich, Archaeology, December 17, 2012]

The analysis showed that Denisovans were much more closely related to Neanderthals than to Homo sapiens, and that in spite of coming from a small population, they managed to contribute genes to modern populations in Island Southeast Asia and Australia. According to David Reich, a geneticist at Harvard Medical School and a member of the research team, the new DNA sequence also shows that Native Americans and people from East Asia have more Neanderthal DNA, on average, than Europeans. Archaeologists have long thought that the largest population of Neanderthals lived in Europe, so the finding complicates the picture of the way modern people and Neanderthals are related. Either there was a separate event in which Neanderthals interbred with people in Asia, or the genetic contribution of Neanderthals in Europe was diluted by later migrations of Homo sapiens.

Denisovans, Modern Humans and Hominid Migrations in Asia

secondary human expansion

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.” \+\

“One possibility is that the bone belonged to a member of a group that was ancestral to both Neanderthals and Denisovans and that Neanderthals acquired different mitochondrial DNA after the two groups diverged.“Another alternative is that this ancestral group actually interbred with something much older, something like Homo erectus, and obtained its mitochondrial DNA from them,” Paabo said. [Source: Monte Morin, Los Angeles Times, December 6, 2013]

DNA from Neanderthal Toe Reveals Interbreeding with Humans and Denisovans

A 50,000-year-old toe bone from a Neanderthal, discovered in Denisova Cave in Siberia, gave up DNA indicating interbreeding between Neanderthals, modern humans and Denisovans scientists reported in the journal Nature. DNA from the Neanderthal toe fossil was compared to the genomes of 25 present-day human and a group of Denisovans. According to their analysis, Neanderthals contributed roughly 2 percent of their DNA to modern people outside Africa and half a percent to Denisovans, who contributed 0.2 percent of their DNA to Asian and Native American people.[Source: Monte Morin, Los Angeles Times, December 18, 2013 \=\]

Monte Morin wrote in the Los Angeles Time: “The biggest surprise, though, was the finding that a fourth hominin contributed roughly 6 percent of the DNA in the Denisovan genome. The identity of this DNA donor remains a mystery. “It is possible that this unknown hominin was what is known from the fossil record as Homo erectus,” said lead study author Kay Prufer, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “Further studies are necessary to support or reject this possibility.” \=\

“Geneticists and anthropologists said the inch-long bone and resulting analysis have greatly illuminated a period of time roughly 12,000 to 126,000 years ago. It does seem that Eurasia during the Late Pleistocene was an interesting place to be a hominin, with individuals of at least four quite diverged groups living, meeting and occasionally having sex,” biologist Ewan Birney of the European Bioinformatics Institute and Stanford geneticist Jonathan Pritchard wrote in a commentary that accompanied the study. \=\

“The toe bone was discovered in an ancient natural shelter called Denisova Cave, in Siberia’s Altai Mountains. It was in the same cave that archaeologists discovered evidence of the Denisovans, who were recognized as a distinct group in 2010. Based on DNA taken from the toe bone, researchers were able to determine that it belonged to a female Neanderthal. They could also tell that her parents were very closely related, and “were either half siblings who had a mother in common, double first cousins, an uncle and a niece, an aunt and a nephew, a grandfather and a granddaughter, or a grandmother and a grandson,” they wrote in the study.

“Such inbreeding might have been necessary because the Neanderthal population was very small, perhaps already well on the road toward extinction, the study authors suggested. “The data are consistent with the population being small enough that breeding among relatives was reasonably common,” said UC Berkeley biologist Montgomery Slatkin, a member of the research team. DNA analysis of additional Neanderthal remains would be needed to confirm that hunch, Slatkin said.

“The study authors estimated that the ancestors of Neanderthals and Denisovans split from the lineage that led to modern humans roughly 600,000 years ago, and then split between each other roughly 400,000 years ago. Based on the genomes of each group, researchers concluded that all of their populations were in decline at least 1 million years ago. Sometime after that, our ancestors began to grow in number while the Neanderthal and Denisovan populations continued to shrink. Researchers estimate that Homo sapiens became the planet’s sole surviving humans roughly 30,000 years ago.

While the study’s conclusions were sure to fire the imagination of the general public, at least one outside expert said the anthropological sleuthing had just begun. John Hawks, a paleoanthropologist at the University of Wisconsin, Madison, said it was very difficult to pin down the timing and number of groups involved in genetic mixing. We could really be looking at mixture from multiple different populations with different histories,” Hawks said.

Study authors hope that by mapping the Neanderthal genome they might gain insights into the evolution of modern humans. The list of DNA sequences that distinguish us from Neanderthals is relatively short, according to the study’s senior author, Svante Paabo, director of the Max Planck Institute’s department of genetics. It’s a catalog of the genetic features that sets all modern humans apart from all other organisms living or extinct,” Paabo wrote in a statement released by the institute. “I believe that in it hide some of the things that made the enormous expansion of human populations and human culture and technology in the last 100,000 years possible.”

Denisova cave artifacts

Humans Bred with Denisovans More than Once, Study Shows

A study published in the journal Cell in March 2018, shows modern humans appear to have mated with Denisovans in Siberia and a separate group of Denisovans as they traveled across South Asia “This is a breakthrough paper,” said David Reich, the Harvard University geneticist who was not involved with the study. “It’s a definite third interbreeding event,” one that adds to the previously known Denisovan and Neanderthal mixtures. [Source: Ben Guarino, Washington Post, March 16, 2018 ^||^]

Ben Guarino wrote in the Washington Post: “A team of scientists, led by University of Washington biostatistician Sharon Browning, took an approach that Reich called a “technical tour de force.” In the new study, Browning and her colleagues examined more than 5,500 genomes of modern humans from Europe, Asia and Oceania, looking for any possible archaic DNA. “We’re looking for segments of DNA in an individual that look quite different from the rest of the variation in the population,” Browning said. ^||^

“After the team fished out the DNA variations, the researchers matched the segments to Denisovan and Neanderthal sequences, known from samples in Siberia’s Altai Mountains. All groups studied, from British and Bengali people to Peruvians and Puerto Ricans, had a dense cluster that closely matched the Altai Neanderthals. Some populations also had a cluster that matched the Altai Denisovans, which was particularly pronounced in East Asians. The surprise was a third cluster – not like the Neanderthal DNA and only partially resembling the Altai Denisovans. ^||^

“This, the authors concluded, was a second and separate pulse of Denisovan genes into the DNA blender. “The geography is quite suggestive,” Browning said. The authors hypothesize that, as ancestral humans migrated eastward, they came across two different Denisovan populations. One pulse, to the north, shows up in people from China, Japan and Vietnam. The other Denisovan pulse appears to the south. “Maybe it was down in the southeast corner of Asia,” Browning said. “It could possibly have been on an island en route to Papua New Guinea, but we clearly don’t know.” ^||^

“Reich said he would not be surprised if methods similar to this one revealed additional mixtures. “I am sure there are others,” he said, considering the wide range of archaic groups across Eurasia. Browning plans to continue to hunt for additional mixtures, including among people of African descent who were excluded from this study because the warm continental climate makes finding archaic DNA a challenge. “We’re interested in other populations around the world, especially Africa,” she said.” |=|

Denny, the Neanderthal-Denisovan Love Child

Denny was an inter-species love child, with a Neanderthal mother and a Denisovan father, scientists reported in the journal Nature. Nicknamed by Oxford University scientists, Denisova 11 -- her official name -- was at least 13 when she died, for reasons unknown. "There was earlier evidence of interbreeding between different hominin, or early human, groups," said lead author Vivian Slon, a researcher at the Max Planck Institute for Evolutionary Anthropology. "But this is the first time that we have found a direct, first-generation offspring," she told AFP. [Source: Marlowe Hood, AFP, August 23, 2018 \=/]

Marlowe Hood of AFP wrote: “Denny's surprising pedigree was unlocked from a bone fragment unearthed in 2012 by Russian archeologists at the Denisova Cave in the Altai Mountains of Siberia. Analysis of the bone's DNA left no doubt: the chromosomes were a 50-50 mix of Neanderthal and Denisovan. "I initially thought that they must have screwed up in the lab," said senior author and Max Planck Institute professor Svante Paabo, who identified the first Denisovan a decade ago at the same site. Worldwide, fewer than two dozen early human genomes from before 40,000 years ago -- Neanderthal, Denisovan, Homo sapiens -- have been sequenced, and the chances of stumbling on a half-and-half hybrid seemed vanishingly small. \=/

“Or not. "The very fact that we found this individual of mixed Neanderthal and Denisovan origins suggests that they interbred much more often than we thought," said Slon. Paabo agreed: "They must have quite commonly had kids together, otherwise we wouldn't have been this lucky." A 40,000 year-old Homo sapiens with a Neanderthal ancestor a few generations back, recently found in Romania, also bolsters this notion. But the most compelling evidence that inter-species hanky-panky in Late Pleistocene Eurasia may not have been that rare lies in the genes of contemporary humans...Neanderthals and Denisovans might have intermingled even more but for the fact that the former settled mostly in Europe, and the latter in central and East Asia, the researchers speculated.” \=/

Oldest Known Human DNA Linked to Denisovans

homo sapien lineage

The oldest known human DNA — from the bone of a hominin living in what is now the Sima de los Huesos in Northern Spain, dated to approximately 400,000 years ago — appears to have belong to an unknown hominin, presumably a common ancestor of Denisovans and Neanderthals but with closer links to Denisovans than Neanderthals. Scientists detailed their findings on this in the December 5, 2013 issue of the journal Nature. [Source: Charles Q. Choi, Live Science, December 4, 2013 \=\]

Charles Q. Choi of Live Science wrote: “To discover more about human origins, researchers investigated a human thighbone unearthed in the Sima de los Huesos, or "Pit of Bones," an underground cave in the Atapuerca Mountains in northern Spain. The bone is apparently 400,000 years old. "This is the oldest human genetic material that has been sequenced so far," said study lead author Matthias Meyer, a molecular biologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. "This is really a breakthrough — we'd never have thought it possible two years ago that we could study the genetics of human fossils of this age." Until now, the previous oldest human DNA known came from a 100,000-year-old Neanderthal from a cave in Belgium. \=\

“The Sima de los Huesos is about 100 feet (30 meters) below the surface at the bottom of a 42-foot (13-meter) vertical shaft. Archaeologists suggest the bones may have been washed down it by rain or floods, or that the bones were even intentionally buried there. This Pit of Bones has yielded fossils of at least 28 individuals, the world's largest collection of human fossils dating from the Middle Pleistocene, about 125,000 to 780,000 years ago. "This is a very interesting time range," Meyer told LiveScience. "We think the ancestors of modern humans and Neanderthals diverged maybe some 500,000 years ago." The oldest fossils of modern humans found yet date back to about 200,000 years ago.\=\

”The researchers reconstructed a nearly complete genome of this fossil's mitochondria — the powerhouses of the cell, which possess their own DNA and get passed down from the mother. The fossils unearthed at the site resembled Neanderthals, so researchers expected this mitochondrial DNA to be Neanderthal. Surprisingly, the mitochondrial DNA reveals this fossil shared a common ancestor not with Neanderthals, but with Denisovans, splitting from them about 700,000 years ago. This is odd, since research currently suggests the Denisovans lived in eastern Asia, not in western Europe, where this fossil was uncovered. The only known Denisovan fossils so far are a finger bone and a molar found in Siberia. "This opens up completely new possibilities in our understanding of the evolution of modern humans, Neanderthals and Denisovans," Meyer said.” \=\

Why is 400,000-Year-Old DNA from Spain is Linked to 50,000-Year-Old Asia-Based Denisovans?

Charles Q. Choi of Live Science wrote: “The researchers suggest a number of possible explanations for these findings. First, this specimen may have been closely related to the ancestors of Denisovans. However, this seems unlikely, since the presence of Denisovans in western Europe would suggest an extensive overlap of territory with Neanderthal ancestors, raising the question of how both groups could diverge genetically while overlapping in range. Moreover, the one known Denisovan tooth is significantly different from teeth seen at the Pit of Bones. [Source: Charles Q. Choi, Live Science, December 4, 2013 \=\]

“Second, the Sima de los Huesos humans may be related to the ancestors of both Neanderthals and Denisovans. The researchers consider this plausible given the fossil's age, but they would then have to explain how two very different mitochondrial DNA lineages stemmed from one group, one leading to Denisovans, the other to Neanderthals. \=\

“Third, the humans found at the Sima de los Huesos may be a lineage distinct from both Neanderthals and Denisovans that later perhaps contributed mitochondrial DNA to Denisovans. However, this suggests this group was somehow both distinct from Neanderthals but also independently evolved several Neanderthal-like skeletal features. \=\

“Fourth, the investigators suggest a currently unknown human lineage brought Denisovan-like mitochondrial DNA into the Pit of Bones region, and possibly also to the Denisovans in Asia. "The story of human evolution is not as simple as we would have liked to think," Meyer said. "This result is a big question mark. In some sense, we know less about the origins of Neanderthals and Denisovans than we knew before."” \=\

Neanderthals and Denisovans Strengthened Our Immune System?

Research from Stanford, the Max Planck Institute for Evolutionary Anthropology and the Institute Pasteur have suggested interbreeding with the Neanderthals strengthened the immune system of modern humans. Linda Marsa wrote in Discover: “When our ancestors mated with Neanderthals and Denisovans, a recently discovered archaic human group, they picked up some of their genes. Now researchers say that DNA inherited from these extinct hominins may have fortified the modern immune system. A team at Stanford University focused on human leukocyte antigen (HLA) class 1 genes, which play a vital role in rallying the immune system to fight off bacteria and viruses. Because diseases can be endemic to specific regions of the world, these genes exist in thousands of versions, known as alleles. [Source: Linda Marsa, Discover, December 22, 2011 ><

“To analyze the origin of these alleles, the scientists looked at bone marrow registries containing the HLA genes of millions of people from all parts of the globe. By comparing DNA from modern populations with the reconstructed genomes of Neanderthals and Denisovans, they discovered that several HLA variants from the archaic groups are still around. For example, the ancient gene for HLA-A, which helps the body resist viruses like Epstein-Barr, is present in half of all modern Europeans, more than 70 percent of Asians, and up to 95 percent of people in Papua New Guinea. Other ancient alleles are involved in the regulation of natural killer cells, essential for immune defense. ><

“Our ancestors’ liaisons with Neanderthals and Denisovans may have made them less susceptible to local infections, proposes Stanford immunologist Laurent Abi-Rached, giving them a survival advantage as they migrated out of Africa to Europe and Asia. “Breeding with our evolutionary cousins may have facilitated the spread of modern humans by preventing them from getting sick.”“ ><

Human-Neanderthal-Denisovan Interbreeding: the Cause of Modern Allergies


Three genes inherited from Neanderthal may have given modern humans overly-sensitive immune systems, making them susceptible to allergies Ian Sample wrote in The Guardian: “Passionate encounters between ancient humans and their burly cousins, the Neanderthals, may have left modern people more prone to sneezes, itches and other allergies, researchers say. The curious legacy comes from three genes that crossed into modern humans after their distant ancestors had sex with Neanderthals, or their close relatives the Denisovans, more than 40,000 years ago. [Source: Ian Sample, The Guardian January 7, 2016]

“The three genes are among the most common strands of Neanderthal and Denisovan-like DNA found in modern humans, suggesting they conferred an evolutionary advantage. They probably boosted the immune system, since the genes are involved in the body’s first line of defence against pathogens such as bacteria and fungi. But people who carry the three genes seem to pay a price in the form of an overly-sensitive immune system. One study by the US genetics company 23andme found that carriers of the genes were more likely to have asthma, hay fever and other allergies. |=|

“The genes are thought to have spread through modern humans when small groups of pioneers who left Africa met and had sex with Neanderthals already long at home in Eurasia. Unlike the new arrivals, the Neanderthals had spent 200,000 years adapting to life in the region, and their immune systems had become tuned to the new infections they faced. “A small group of modern humans leaving Africa would not carry much genetic variation,” said Janet Kelso, who led the research at the Max Planck Institute for evolutionary Anthropology in Leipzig. “You can adapt through mutations, but if you interbreed with the local population who are already there, you can get some of these adaptations for free.” |=|

“Kelso’s team scanned the genomes of modern day humans for evidence of Neanderthal or Denisovan genes and then looked at how common they were in people from around the world. Among the three immune system genes that stood out, two closely matched Neanderthal DNA. The most common was found in all non-Africans, the other only in Asians. The third gene was more similar to Denisovan DNA and much rarer, found in only a handful of people from Asia who took part in the study.

“The findings suggest that modern humans inherited Neanderthal and Denisovan genes in three waves depending on where and when the groups met. The genes proved so beneficial that they remain in our genomes to this day. The study is reported in the American Journal of Human Genetics.The work is backed up by separate research published in the same journal by scientists at the Pasteur Institute in Paris. Geneticist Lluis Quintana-Murci analysed DNA from participants in the 1000 Genomes Project and compared their DNA with ancient human genomes. He focused specifically on 1500 immune genes and found that most adaptations occurred in the past 6,000 to 13,000 years, when humans shifted from a hunter-gatherer lifestyle to farming. |=|

“But Quintana-Murci said the most striking discovery was of the same three genes that Kelso found. In his study, the trio of genes were among the most common Neanderthal or Denisovan DNA found in modern people. “Interbreeding with archaic humans does indeed have functional implications for modern humans,” Kelso said. “The most obvious consequences have been in shaping our adaptation to our environment - improving how we resist pathogens and metabolise novel foods.” “For all the benefits they bring, the downsides of Neanderthal genes might not be so bad. “They might have increased our susceptibility,” said Kelso. “But I wouldn’t go so far as to say Neanderthals gave us allergies.” |=|

Unknown Hominin

Research Denisovan DNA revealed evidence it interbred with an unknown hominin species. Charles Q. Choi wrote in Live Science: “Scientists discovered that apparently Denisovans interbred with an unknown human lineage, getting as much as 2.7 to 5.8 percent of their genomes from it. This mystery relative apparently split from the ancestors of all modern humans, Neanderthals and Denisovans between 900,000 years and 4 million years ago, before these latter groups started diverging from each other. [Source: Charles Q. Choi, Live Science, December 18, 2013]

Kay Prüfer, a computational geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, said enigmatic lineage could even potentially be Homo erectus, the earliest undisputed predecessor of modern humans. There are no signs this unknown group interbred with modern humans or Neanderthals. "Some unknown archaic DNA might have caught a ride through time by living on in Denisovans until we dug the individual up and sequenced it," Prüfer told LiveScience. "It opens up the prospect to study the sequence of an archaic (human lineage) that might be out of reach for DNA sequencing."

Image Sources: Wikimedia Commons

Text Sources: National Geographic, New York Times, Washington Post, Los Angeles Times, Smithsonian magazine, Nature, Scientific American. Live Science, Discover magazine, Discovery News, Ancient Foods ; Times of London, Natural History magazine, Archaeology magazine, The New Yorker, Time, Newsweek, BBC, The Guardian, Reuters, AP, AFP, Lonely Planet Guides, World Religions edited by Geoffrey Parrinder (Facts on File Publications, New York); History of Warfare by John Keegan (Vintage Books); History of Art by H.W. Janson (Prentice Hall, Englewood Cliffs, N.J.), Compton’s Encyclopedia and various books and other publications.

Last updated September 2018

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