Ancient Humans, Dubbed 'Denisovans', Interbred With Modern Humans

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#1
Ancient humans, dubbed 'Denisovans', interbred with us
http://www.bbc.co.uk/news/science-environment-12059564
By Pallab Ghosh Science correspondent, BBC News


Professor Chris Stringer: "It's nothing short of sensational - we didn't know know how ancient people in China related to these other humans"

Related stories

* DNA identifies new ancient human
* Neanderthal genes 'survive in us'
* 'Hobbit' island's deeper history

Scientists say an entirely separate type of human identified from bones in Siberia co-existed and interbred with our own species.

The ancient humans have been dubbed "Denisovans" after the caves in Siberia where their remains were found.

There is also evidence that this population was widespread in Eurasia.

A study in Nature journal shows that Denisovans co-existed with Neanderthals and interbred with our species - perhaps around 50,000 years ago.

An international group of researchers sequenced a complete genome from one of the ancient hominins (human-like creatures), based on nuclear DNA extracted from a finger bone.
'Sensational' find

According to the researchers, this provides confirmation there were at least four distinct types of human in existence when anatomically modern humans (Homo sapiens sapiens) first left their African homeland.
Denisovan tooth DNA from a tooth (pictured) and a finger bone show the Denisovans were a distinct group

Along with modern humans, scientists knew about the Neanderthals and a dwarf human species found on the Indonesian island of Flores nicknamed "The Hobbit". To this list, experts must now add the Denisovans.

The implications of the finding have been described by Professor Chris Stringer of the Natural History Museum in London as "nothing short of sensational".

Scientists were able to analyse DNA from a tooth and from a finger bone excavated in the Denisova cave in southern Siberia. The individuals belong to a genetically distinct group of humans that were distantly related to Neanderthals but even more distantly related to us.

The finding adds weight to the theory that a different kind of human could have existed in Eurasia at the same time as our species.
Infographic

Researchers have had enigmatic fossil evidence to support this view but now they have some firm evidence from the genetic study carried out by Professor Svante Paabo of the Max Planck Institute in Leipzig, Germany.

"A species of early human living in Europe evolved," according to Professor Paabo.

"There was a western form that was the Neanderthal and an eastern form, the Denisovans."

The study shows that Denisovans interbred with the ancestors of the present day people of the Melanesian region north and north-east of Australia. Melanesian DNA comprises between 4% and 6% Denisovan DNA.

David Reich from the Harvard Medical School, who worked with Svante Paabo on the study, says that the fact that Denisovan genes ended up so far south suggests they were widespread across Eurasia: "These populations must have been spread across thousands and thousands of miles," he told BBC News.

One mystery is why the Denisovan genes are unique in modern Melanesians and are not found in other Eurasian groups that have so far been sampled.
'Fleeting encounter'

Professor Stringer believes it is because there may have been only a fleeting encounter as modern humans migrated through South-East Asia and then on to Melanesia.
Denisova cave The remains were excavated at a cave site in southern Siberia

"It could be just 50 Denisovans interbreeding with a thousand modern humans. That would be enough to produce this 5% of those archaic genes being transferred," he said.

"So the impact is there but the number of interbreeding events might have been quite small and quite rare."

No one knows when or how these humans disappeared but, according to Professor Paabo, it is very likely something to do with modern people because all the "archaic" humans, like Denisovans and Neanderthals disappeared sometime after Homo sapiens sapiens appeared on the scene.

"It is fascinating to see direct evidence that these archaic species did exist (alongside us) and it's only for the last few tens of thousands of years that is unique in our history that we are alone on this planet and we have no close relatives with us anymore," he said.

The study follows a paper published earlier this year by by Professor Paabo and colleagues that showed there was interbreeding between modern humans and Neanderthals as they emerged from Africa 60,000 years ago.
 

GNC

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#2
Denisovans? Or could they be the long lost Ancient Astronauts and Von Daniken was right all along?
 

eburacum

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#3
My missus has been going on about this species (probably a sub-species, technically, I think) for a while now. She said it was called 'species X' up till now, apparently.

Note that they only seem to have interbred with the Melanesians. So we Europeans are fairly unlikely to have any 'Denisovan' blood in us.
 

rynner2

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#5
Siberians share DNA with extinct human species
Man's ancestors mated with Neanderthals and other related hominids during human evolution, according to a new study.
6:00AM GMT 01 Nov 2011

Researchers have found that people in East Asia share genetic material with Denisovans, who got the name from the cave in Siberia where they were first found.
The new study covers a larger part of the world than earlier research, and it is clear that it is not as simple as previously thought.

Professor Mattias Jakobsson, of Uppsala University in Sweden who conducted the study together with graduate student Pontus Skoglund, said hybridisation took place at several points in evolution and the genetic traces of this can be found in several places in the world.
He said: "We'll probably be uncovering more events like these.
"Previous studies have found two separate hybridisation events between so-called archaic humans - different from modern humans in both genetics and morphology - and the ancestors of modern humans after their emergence from Africa.

"There was hybridisation between Neanderthals and the ancestors of modern humans outside of Africa and hybridisation between Denisovans and the ancestors of indigenous Oceanians.
"The genetic difference between Neanderthals and Denisovans is roughly as great as the maximal level of variation among us modern humans."

The Uppsala scientists' study demonstrates that hybridisation also occurred on the East Asian mainland.
The connection was discovered by using genotype data in order to obtain a larger data set.
Complete genomes of modern humans are only available from some dozen individuals today, whereas genotype data is available from thousands of individuals.
These genetic data can be compared with genome sequences from Neanderthals and a Denisovan which have been determined from archeological material.
Only a pinky finger and a tooth have been described from the latter.

Genotype data stems from genetic research where hundreds of thousands of genetic variants from test panels are gathered on a chip.
However, this process leads to unusual variants not being included, which can lead to biases if the material is treated as if it consisted of complete genomes.

Prof Jakobsson and Skoglund used advanced computer simulations to determine what this source of error means for comparisons with archaic genes and have thereby been able to use genetic data from more than 1,500 modern humans from all over the world.
Prof Jakobsson said: "We found that individuals from mainly Southeast Asia have a higher proportion of Denisova-related genetic variants than people from other parts of the world, such as Europe, America, West and Central Asia, and Africa.
"The findings show that gene flow from archaic human groups also occurred on the Asian mainland."

Skoglund added: "While we can see that genetic material of archaic humans lives on to a greater extent than what was previously thought, we still know very little about the history of these groups and when their contacts with modern humans occurred."

Because they find Denisova-related gene variants in south east Asia and Oceania, but not in Europe and America, the researchers suggest that hybridisation with Denisova man took place about 20 million years ago :? , but could also have occurred earlier.
This is long after the branch that became modern humans split off from the branch that led to Neanderthals and Denisovans some 300,000 to 500,000 years ago.

Prof Jakobsson said: "With more complete genomes from modern humans and more analyses of fossil material, it will be possible to describe our prehistory with considerably greater accuracy and richer detail."
The findings were published in the online edition of the journal PNAS.

http://www.telegraph.co.uk/science/scie ... ecies.html
 
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#6
DNA scan sheds new light on mankind's mysterious cousins (Update)
August 30th, 2012 in Other Sciences / Archaeology & Fossils

Enlarge

Denisova molar, distal. Image courtesy of Max Planck Institute for Evolutionary Anthropology

Max Planck researchers describe Denisovan genome, illuminating the relationships between Denisovans and present-day humans.

The analyses of an international team of researchers led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, show that the genetic variation of Denisovans was extremely low, suggesting that although they were present in large parts of Asia, their population was never large for long periods of time. In addition, a comprehensive list documents the genetic changes that set apart modern humans from their archaic relatives. Some of these changes concern genes that are associated with brain function or nervous system development.

In 2010 Svante Pääbo and his colleagues sequenced DNA that they isolated from a finger bone fragment discovered in the Denisova Cave in southern Siberia. They found that it belonged to a young girl of a previously unknown group of archaic humans that they called "Denisovans". Thanks to a novel technique which splits the DNA double helix so that each of its two strands can be used for sequencing, the team was able to sequence every position in the Denisovan genome about 30 times over. The thus generated genome sequence shows a quality similar to genomes that have been determined from present-day humans.

Matthias Meyer at work in the clean lab. Credit: MPI for Evolutionary Anthropology

In a new study, which is published in this week's issue of the journal Science, Svante Pääbo and his colleagues compare the Denisovan genome with those of the Neandertals and eleven modern humans from around the world. Their findings confirm a previous study according to which modern populations from the islands of southeastern Asia share genes with the Denisovans. In addition, the genomes of people from East Asia, and South America include slightly more genes from Neandertals than those of people in Europe: "The excess archaic material in East Asia is more closely related to Neandertals than to Denisovans, so we estimate that the proportion of Neandertal ancestry in Europe is lower than in eastern Asia", the Leipzig researchers report.

Enlarge
This is a replica of the finger bone fragment of a Denisovan hominin on a human hand. Credit: MPI for Evolutionary Anthropology

"This is an extinct genome sequence of unprecedented accuracy", says Matthias Meyer, the lead author of the study. "For most of the genome we can even determine the differences between the two sets of chromosomes that the Denisovan girl inherited from her mother and father". From this the researchers can tell that genetic variation of the Denisovans was lower than in present-day humans. This is likely due to that an initially small Denisovan population that grew quickly while spreading over a wide geographic range. "If future research of the Neandertal genome shows that their population size changed over time in similar ways, it may well be that a single population expanding out of Africa gave rise to both the Denisovans and the Neandertals", says Svante Pääbo, who led the study.

The researchers furthermore generated a list of about 100,000 recent changes in the human genome that occurred after the split from the Denisovans. Some of these changes affect genes that are associated with brain function and nervous system development. Others possibly affect the skin, the eye and dental morphology. "This research will help determining how it was that modern human populations came to expand dramatically in size as well as cultural complexity while archaic humans eventually dwindled in numbers and became physically extinct", says Svante Pääbo.

Earlier this year, the Leipzig researchers had already made the entire Denisovan genome sequence available to the broader public by publishing it online.

More information: Matthias Meyer, Martin Kircher, Marie-Theres Gansauge, Heng Li, Fernando Racimo, Swapan Mallick, Joshua G. Schraiber, Flora Jay, Kay Prüfer, Cesare de Filippo, Peter H. Sudmant, Can Alkan, Qiaomei Fu, Ron Do, Nadin Rohland, Arti Tandon, Michael Siebauer, Richard E. Green, Katarzyna Bryc, Adrian W. Briggs, Udo Stenzel, JesseDabney, Jay Shendure, Jacob Kitzman, Michael F. Hammer, Michael V. Shunkov, Anatoli P. Derevianko, Nick Patterson, Aida M. Andrés, Evan E. Eichler, Montgomery Slatkin, David Reich, Janet Kelso, Svante Pääbo A high coverage genome sequence from an archaic Denisovan individual Science, August 30, 2012

Provided by Max Planck Society

"DNA scan sheds new light on mankind's mysterious cousins (Update)." August 30th, 2012. http://phys.org/news/2012-08-dna-scan-m ... usins.html
 
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#7
Extinct human cousin gave Tibetans advantage at high elevation

Tibetans were able to adapt to high altitudes thanks to a gene picked up when their ancestors mated with a species of human they helped push to extinction, according to a new report by University of California, Berkeley, scientists.

An unusual variant of a gene involved in regulating the body's production of hemoglobin – the molecule that carries oxygen in the blood – became widespread in Tibetans after they moved onto the high-altitude plateau several thousand years ago. This variant allowed them to survive despite low oxygen levels at elevations of 15,000 feet or more, whereas most people develop thick blood at high altitudes, leading to cardiovascular problems.

"We have very clear evidence that this version of the gene came from Denisovans," a mysterious human relative that went extinct 40,000-50,000 years ago, around the same time as the more well-known Neanderthals, under pressure from modern humans, said principal author Rasmus Nielsen, UC Berkeley professor of integrative biology. "This shows very clearly and directly that humans evolved and adapted to new environments by getting their genes from another species."

This is the first time a gene from another species of human has been shown unequivocally to have helped modern humans adapt to their environment, he said.

Nielsen and his colleagues at BGI-Shenzhen in China will report their findings online July 2 in advance of publication in the journal Nature.

The gene, called EPAS1, is activated when oxygen levels in the blood drop, triggering production of more hemoglobin. The gene has been referred to as the superathlete gene because at low elevations, some variants of it help athletes quickly boost hemoglobin and thus the oxygen-carrying capacity of their blood, upping endurance. At high altitude, however, the common variants of the gene boost hemoglobin and its carrier, red blood cells, too much, increasing the thickness of the blood and leading to hypertension and heart attacks as well as low-birth-weight babies and increased infant mortality. The variant or allele found in Tibetans raises hemoglobin and red blood cell levels only slightly at high elevation, avoiding the side-effects seen in most people who relocate to elevations above 13,000 feet.

"We found part of the EPAS1 gene in Tibetans is almost identical to the gene in Denisovans and very different from all other humans," Nielsen said. "We can do a statistical analysis to show that this must have come from Denisovans. There is no other way of explaining the data." ...

http://phys.org/print323519706.html
 

Cochise

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#8
Denis Ovens is a darts player. Maybe that should be under 'coincidences' :D
 

Iris

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That's interesting about the Denisovans. My cousin on my father's side did an advanced genetic reading with National Geographic.
Our people came over here from Ireland and Scotland and there are still distant relatives living there. It came up that there was 2% Neanderthal and 2% Denisovan.
 
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More about the DNA analysis on the spread of Denisovan genes through Asia.

The Other Neanderthal

Tantalisingly makes one wonder, with the extra Denisovan ancestral gene apparently giving the Tibetan population the ability to help withstand low oxygen and high altitude, could another rarer descendant of the Denisovan be the Yeti?
 

AgProv

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#11
And not Desdinovans?

(a rock band dealing with many Fortean-interest topics in their songs, the Blue Öyster Cult, were originally conceived as a means of translating a poetic Lovecraftian epic called "Inaginos" into a sort of rock opera. The Imaginos project faltered and failed, leaving behind a dozen or so songs of varying worth. Most of these were recorded on early BOC albums. One features an immortal soul called Desdinova, an agent of the Old High Ones, who has been among men and manipulating them over the millenia on behalf of his controllers... there, just explained the "gag" and made it even unfunnier...)
 

EnolaGaia

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#12
... And now we have genomic confirmation of Neanderthal / Denisovan interbreeding.

Cave girl was half Neanderthal, half Denisovan
Once upon a time, two early humans of different ancestry met at a cave in Russia.

Some 50,000 years later, scientists have confirmed that they had a daughter together.

DNA extracted from bone fragments found in the cave show the girl was the offspring of a Neanderthal mother and a Denisovan father.

The discovery, reported in Nature, gives a rare insight into the lives of our closest ancient human relatives.

Neanderthals and Denisovans were humans like us, but belonged to different species.

"We knew from previous studies that Neanderthals and Denisovans must have occasionally had children together," says Viviane Slon, researcher at the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) in Leipzig, Germany.

"But I never thought we would be so lucky as to find an actual offspring of the two groups." ...
FULL STORY: https://www.bbc.co.uk/news/science-environment-45271644
 

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#14

Jim

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I find this part fascinating, that neither actually became extinct but evolved as ingredients to add to homo sapiens:

"Neanderthals and Denisovans may have disappeared just because they were absorbed into modern human populations."
Seems to be the current viewpoint. They likely weren't the knuckle draggers were led to believe.
 

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#16
https://www.sciencemag.org/news/201...-mated-modern-humans-recently-15000-years-ago

The elusive Denisovans, the extinct cousins of Neanderthals, are known from only the scraps of bone they left in Siberia’s Denisova Cave in Russia and the genetic legacy they bequeathed to living people across Asia. A new study of that legacy in people from New Guinea now suggests that, far from being a single group, these mysterious humans were so diverse that their populations were as distantly related to each other as they were to Neanderthals.

In another startling suggestion, the study implies one of those groups may have survived and encountered modern humans as recently as 15,000 to 30,000 years ago, tens of thousands of years later than researchers had thought. “A late surviving lineage [of Denisovans] could have interbred with Homo sapiens” in Southeast Asia, paleoanthropologist Chris Stringer of the Natural History Museum in London, not a member of the team, said in a Skype interview during a session at the annual meeting of the American Association of Physical Anthropologists here. The new study was presented Thursday at the meeting.


 

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#17
Last week at this time, I was at a talk given by Dr. Adam Rutherford who said the messy human evolutionary tree was about to get more complex. I wonder if this was what he meant? Or, he knows that other studies are forthcoming that show more inter-breeding, etc. A "tree" isn't an apt description; neither is a "bush". We need some new analogy.
 

Monstrosa

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Last week at this time, I was at a talk given by Dr. Adam Rutherford who said the messy human evolutionary tree was about to get more complex. I wonder if this was what he meant? Or, he knows that other studies are forthcoming that show more inter-breeding, etc. A "tree" isn't an apt description; neither is a "bush". We need some new analogy.
Braided River perhaps?
 

Ogdred Weary

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#20
Last week at this time, I was at a talk given by Dr. Adam Rutherford who said the messy human evolutionary tree was about to get more complex. I wonder if this was what he meant? Or, he knows that other studies are forthcoming that show more inter-breeding, etc. A "tree" isn't an apt description; neither is a "bush". We need some new analogy.
geor.jpg
 

Razumov

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#21

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#22
Remains attributed to the Denisovans has now been found elsewhere (than the Denisova cave site). The altitude at which the new evidence was found helps to corroborate what was already known about Denisovans' connection to populations living at higher elevations.
First evidence of mysterious, ancient humans called Denisovans found outside of their cave

A 160,000-year-old Denisovan jawbone fossil has been found in a cave on the Tibetan plateau, according to a new study. This marks the first evidence of Denisovans found outside Denisova Cave in Siberia since the mysterious ancient human group was discovered in 2010.

Denisovans, who lived during a time that overlapped with Neanderthals, are known only from a few fossils discovered in a Siberian cave. But they also left a genetic legacy that lives on today in the DNA of some Asian, Australian and Melanesian humans. A Denisovan genome was sequenced in 2012 and compared with that of modern humans, revealing the trait.

Tibetans and Sherpas have a genetic variant that helps them live in low oxygen at high altitudes, which can be traced back to Denisovans.

But before the discovery of this jawbone, researchers wondered why this genetic variant existed. Tiny, fragmented remains of Denisovans had only ever been found in Denisova Cave, which sits at an altitude of 2,296 feet.

Baishiya Karst Cave on the Tibetan Plateau, where the jawbone was found, has an altitude of 10,761 feet. ...
FULL STORY: https://www.cnn.com/2019/05/01/world/denisovan-fossil-discovery-scn/index.html
 

Sharon Hill

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#23
Let the speculation run wild... https://www.nature.com/articles/d41586-019-01310-7

[I wonder if the Indian Army Mountaineers knew this was going to be published (though this was found in China, not Nepal)]

On hearing the news of a burly, robust hominin specialized for a cold, high-altitude life, one might just be forgiven for wondering whether the find is the first credible evidence of the yeti or Abominable Snowman (given that all other evidence has proved illusory: B. C. Sykes et al. Proc. R. Soc. B 281, 20140161; 2014). And last month, Nature published the discovery of a short-statured hominin species whose remains were found in a Philippine cave, reminiscent of the diminutive ‘Hobbit’ from Flores.
 

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#25
I recall both those papers and their findings. There's also a recently published discovery that there was at least one (apparently failed) "Out of Africa" migration wave earlier than the previously recognized (and once presumably sole) one. In addition there are increasingly solid indications that there were multiple paths of migration leading in different directions.

These sorts of findings make me think the dissemination of early hominins was a lot more complex and complicated than even the most recent interpretations would indicate. I don't find this surprising because the already convoluted storyline suggested by the available evidence is considerably different from the best interpretations of 40 - 50 years ago, when I was studying the subject at university.
 

lordmongrove

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I recall both those papers and their findings. There's also a recently published discovery that there was at least one (apparently failed) "Out of Africa" migration wave earlier than the previously recognized (and once presumably sole) one. In addition there are increasingly solid indications that there were multiple paths of migration leading in different directions.

These sorts of findings make me think the dissemination of early hominins was a lot more complex and complicated than even the most recent interpretations would indicate. I don't find this surprising because the already convoluted storyline suggested by the available evidence is considerably different from the best interpretations of 40 - 50 years ago, when I was studying the subject at university.
Totally agree and it seems Homo habills had a liniage outside of Africa to boot.
 
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#27
Arty Denisovans?

Lines engraved between 125,000 and 105,000 years ago on two animal bones found in northern China held some sort of meaning for their makers, researchers say.

These ancient markings provide the oldest evidence of symbolic activity by humans or our close evolutionary relatives in East Asia, says a team led by archaeologists Zhanyang Li and Luc Doyon, both of Shandong University in Jinan, China. A mysterious Stone Age population called Denisovans, which had close genetic ties to Neandertals, may have carved sets of parallel lines into the pair of bone fragments, the scientists suggest in the August Antiquity.

Denisovans inhabited East Asia at the same time that someone carved lines into bones at northern China’s Lingjing site (SN: 3/2/19, p. 11). But either Homo sapiens or Neandertals, who also left behind Stone Age creations with apparent symbolic meanings (SN: 3/17/18, p. 6), might instead have modified the Lingjing bones.

“Nonetheless, the two objects from Lingjing suggest that symbolic capacities were within the realm of cognitive abilities of [Homo] species that lived before and during the evolution of Homo sapiens in Africa,” Doyon says.

https://www.sciencenews.org/article/engraved-bones-reveal-symbolism-had-ancient-roots-east-asia
 
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