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Denisovans (Prehistoric Human Group)

Using novel DNA analysis to predict features from the scant fossil evidence discovered to date, researchers have produced the first tentative reconstruction of Denisovan comparative anatomy and an artistic conception of a juvenile female Denisovan's appearance.
This is what mysterious ancient humans might have looked like

We know that mysterious ancient humans called Denisovans once lived alongside Neanderthals, thanks to a few bones and teeth recovered from a cave in Siberia. Now, for the first time, researchers have shared what they might have looked like.

The previously recovered bone fragments include a pinky bone, teeth and a jawbone. Denisovans also left a genetic legacy that lives on today in the DNA of some Asians, Australians and Melanesians. A Denisovan genome was sequenced in 2012 and compared with that of modern humans, revealing the trait.

Denisovans not only interbred with Neanderthals, but with archaic Eurasian humans as well. Because their DNA lives on in some humans today, researchers have reason to believe that they once lived all throughout Asia. Yet, the fossil record is incredibly sparse.

Scientists may have been able to sequence their genome, but this small fossil record made it difficult to piece together their appearance -- until now.

In order to piece this puzzle together, researchers had to go a different route than normal reconstruction: DNA methylation data.

This process relies on extracting information from gene activity patterns, rather than DNA sequences. These patterns are chemical modifications that don't change the actual DNA sequence.

From these patterns, the researchers were able to predict Denisovan features. They began by comparing patterns between different human ancestor groups to find areas where they differed. They further analyzed the differences to determine how those might influence anatomical features. The researchers used current research on what we've learned about the different ways genes function to match those differences.

The study published Thursday in the journal Cell Press.

"We provide the first reconstruction of the skeletal anatomy of Denisovans," said Liran Carmel, study author at the Hebrew University of Jerusalem. "In many ways, Denisovans resembled Neanderthals, but in some traits, they resembled us, and in others they were unique."

The researchers tested their method on Neanderthals and chimpanzees since their anatomies are both understood. Their method was 85% accurate in predicting how their traits differed and why, resulting in reconstruction.

"By doing so, we can get a prediction as to what skeletal parts are affected by differential regulation of each gene and in what direction that skeletal part would change -- for example, a longer or shorter femur," said David Gokhman, study author and postdoctoral researcher at Stanford University.

When they applied this method to Denisovans, they found that 56 features were different from Neanderthals and modern humans. And 34 of those were in the skull alone, including a longer dental arch and a wider skull. ...
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FULL STORY: https://www.cnn.com/2019/09/19/world/denisovan-first-look-scn/index.html
 
Here are some images of the sculptural reconstruction of the young female Denisovan (based on the Denisova 3 fossil remains).

young-female-denisovan.jpg


young-female-denisovan-2.jpg
 
This other news article provides some reasonable cautionary comments from other researchers ...
From DNA, scientists create skull of Neanderthal cousin

Scientists say they’ve deciphered features of the skull and some other details of a mysterious, extinct cousin of Neanderthals by analyzing its DNA. ...

Experts not connected to the work were impressed.

While it’s impossible to know how accurately the study estimated Denisovan traits, its approach is “brilliant and original,” said Benedikt Hallgrimsson of the University of Calgary.

Once the appropriate fossils are found, the study’s specific predictions can be tested, said Hallgrimsson, who studies evolutionary aspects of how genes influence physical traits in mammals.

Bence Viola of the University of Toronto, who studies Denisovan fossils, called the work “a huge step forward ... This would have been called science fiction five years ago.”

The overall picture it gives of the anatomy is “invaluable,” although some details are probably incorrect, he said.

Viola said he was skeptical about an artist’s renderings that added skin, eyes and hair to the skull produced by the study. Scientists don’t know enough about Denisovans to ensure such renderings are accurate, he said.

Carmel, who commissioned the renderings, said they were as anatomically precise as possible but necessarily “also represent some artistic interpretations.”
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FULL STORY: https://www.apnews.com/c5434860797e4e53b99e3654f2392b83
 
Finally ... If you wish to dig into the details of the research, its comparative anatomy results, and the bases for the reconstruction here is the actual published report:

Reconstructing Denisovan Anatomy Using DNA Methylation Maps

David Gokhman, Nadav Mishol, Marc de Manuel, Tomas Marques-Bonet,Yoel Rak & Liran Carmel

DOI:https://doi.org/10.1016/j cell.2019.08.035

FULL ARTICLE (With Many Illustrations / Infographics):

https://www.cell.com/cell/fulltext/S0092-8674(19)30954-7
 
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New genomic research indicates modern humans, Denisovans, and Neanderthals were genetically similar enough to interbreed and produce offspring who were healthy and fertile. Such interbreeding has long been hypothesized. This study supports that hypothesis in terms of genomic similarities.
Neanderthals, Denisovans, humans genetically closer than polar bears, brown bears

Several genomic studies have previously shown that Neanderthals, Denisovans and anatomically modern humans interbred. Now, new research suggests the trio of populations were so genetically similar that they most certainly produced healthy, fertile hybrids.

In a new study, published Wednesday in the journal Proceedings of the Royal Society B, scientists quantified the genetic differences between early humans and their closest relatives, Neanderthals and Denisovans.

The analysis showed the genetic distance values separating the three human species were smaller than the differences between modern animal species -- like brown bears and polar bears -- known to produce healthy hybrid offspring. ...
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FULL STORY:
https://www.upi.com/Science_News/20...r-than-polar-bears-brown-bears/6821591204002/

PUBLISHED REPORT (Accessible at the link):
A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids
Richard Allen† , Hannah Ryan† , Brian W. Davis , Charlotte King , Laurent Frantz , Evan Irving-Pease , Ross Barnett , …
Proceedings of the Royal Society B
Published:03 June 2020
https://doi.org/10.1098/rspb.2020.0690
 
The first samples of Denisovan mitochondrial DNA found anywhere other than the Denisova Cave in Siberia indicates the little-understood Denisovans populated the Tibetan Plateau for a long time and may well have overlapped with modern humans in that area.
The first Denisovan DNA outside Siberia unveils a long stint on the roof of the world

Mysterious, now-extinct members of the human lineage called Denisovans lived at the roof of the world for possibly 100,000 years or more.

Denisovan mitochondrial DNA extracted from sediment layers in Baishiya Karst Cave on the Tibetan Plateau indicates that these humanlike folk inhabited the high-altitude site roughly 100,000 years ago and again around 60,000 years ago, say geoarchaeologist Dongju Zhang of Lanzhou University, China, and her colleagues. These are the first examples of Denisovan DNA found outside of Siberia’s Denisova Cave (SN: 12/16/19).

Cave sediment possibly dating from 50,000 to 30,000 years ago also yielded Denisovan mitochondrial DNA, the scientists report in the Oct. 30 Science. If further research confirms that age estimate, it raises the likelihood that Denisovans survived on the Tibetan Plateau long enough to encounter the first humans to reach those heights as early as 40,000 years ago.

In that case, ancient humans new to the region’s thin air may have acquired advantageous genetic traits for that environment by mating with resident Denisovans. Present-day Tibetans carry a Denisovan gene variant that aids high-altitude survival (SN: 7/2/14), although it’s not clear if interbreeding occurred on the Tibetan Plateau. ...
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FULL STORY: https://www.sciencenews.org/article/first-denisovan-dna-outside-siberia-found-tibetan-plateau-cave
 
Research into prehistoric human expansion into South East Asia confirms considerable genetic input from the mysterious Denisovan line, yet there remains a notable lack of Denisovan physical remains. Curiouser and curiouser ...
New DNA Evidence in Search for the Mysterious Denisovans

An international group of researchers including experts from the Natural History Museum and led by the University of Adelaide has conducted a comprehensive genetic analysis and found no evidence of interbreeding between modern humans and the ancient humans known from fossil records in Island Southeast Asia. The team found further DNA evidence of our mysterious ancient cousins, the Denisovans, which could mean there are major discoveries to come in the region.

In the study published in Nature Ecology and Evolution, the researchers examined the genomes of more than 400 modern humans to investigate the interbreeding events between ancient humans and modern human populations who arrived at Island Southeast Asia 50,000–60,000 years ago.

In particular, they focused on detecting signatures that suggest interbreeding from deeply divergent species known from the fossil record of the area.

The region contains one of the richest fossil records (from at least 1.6 million years) documenting human evolution in the world. Currently there are three distinct ancient humans recognized from the fossil record in the area: Homo erectus, Homo floresiensis (known as Flores Island hobbits) and Homo luzonensis.

These species are known to have survived until approximately 50,000–60,000 years ago in the cases of Homo floresiensis and Homo luzonensis, and approximately 108,000 years for Homo erectus, which means they may have overlapped with the arrival of modern human populations.

The results of the study showed no evidence of interbreeding. Nevertheless, the team was able to confirm previous results showing high levels of Denisovan ancestry in the region. ...

“We know from our own genetic records that the Denisovans mixed with modern humans who came out of Africa 50,000–60,000 years ago both in Asia, and as the modern humans moved through Island Southeast Asia on their way to Australia. The levels of Denisovan DNA in contemporary populations indicates that significant interbreeding happened in Island Southeast Asia. The mystery then remains, why haven’t we found their fossils alongside the other ancient humans in the region? Do we need to re-examine the existing fossil record to consider other possibilities?” ...
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FULL STORY: https://scitechdaily.com/new-dna-evidence-in-search-for-the-mysterious-denisovans/
 
Here are the bibliographic details and abstract for the newly-published research ...

Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture
João C. Teixeira, Guy S. Jacobs, Chris Stringer, Jonathan Tuke, Georgi Hudjashov, Gludhug A. Purnomo, Herawati Sudoyo, Murray P. Cox, Raymond Tobler, Chris S. M. Turney, Alan Cooper and Kristofer M. Helgen
22 March 2021, Nature Ecology & Evolution.
DOI: 10.1038/s41559-021-01408-0

Abstract
The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic ‘super-archaic’ species—Homo luzonensis and H. floresiensis—were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans—a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

SOURCE: https://www.nature.com/articles/s41559-021-01408-0
 
Popular representation, yes. I don't think there was any specific reason in regards to fossils or DNA to think they had fur.
 
And presumably the popular representations were in themselves based upon the legends of the little hairy guy?

But, -a person who lived in the mountains would have either been advanced enough to have clothing...or to have natural insulation.
 
They all lived happily together. I reckon there's a TV comedy show in this.

A decade ago, anthropologists shocked the world when they discovered a fossil pinkie bone from a then-unknown group of extinct humans in Siberia’s Denisova Cave. The group was named “Denisovans” in its honor. Now, an extensive analysis of DNA in the cave’s soils reveals it also hosted modern humans—who arrived early enough that they may have once lived there alongside Denisovans and Neanderthals.

The new study “gives [researchers] unprecedented insight into the past,” says Mikkel Winther Pedersen, a molecular paleoecologist at the University of Copenhagen who was not involved with the work. “It literally shows what [before] they have only been able hypothesize.”

Humans—including Neanderthals and Denisovans—are known to have occupied Denisova Cave for at least 300,000 years. Among the eight human fossils unearthed there are the pinkie, three bones from Neanderthals, and even one from a child with one Neanderthal and one Denisovan parent. The cave also contains sophisticated stone tools and jewelry at higher, later levels. But no modern human fossils have been found there. Those artifacts, extensive studies of DNA from these bones, and even one early study of DNA from soils have cemented the cave’s importance for piecing together human evolution.

But eight fossils are not much to go on, so Elena Zavala, a graduate student at the Max Planck Institute for Evolutionary Anthropology, and colleagues teamed up with Russian researchers to see what kind of DNA was present in the soils of the three-chamber cave (see video, below).

https://www.sciencemag.org/news/202...ls-denisovans-and-modern-humans-possibly-same
 
More on the Denisovan DNA print on Southeast Asian islands.

Denisovans are an elusive bunch, known mainly from ancient DNA samples and traces of that DNA that the ancient hominids shared when they interbred with Homo sapiens.

They left their biggest genetic imprint on people who now live in Southeast Asian islands, nearby Papua New Guinea and Australia. Genetic evidence now shows that a Philippine Negrito ethnic group has inherited the most Denisovan ancestry of all. Indigenous people known as the Ayta Magbukon get around 5 percent of their DNA from Denisovans, a new study finds.

This finding fits an evolutionary scenario in which two or more Stone Age Denisovan populations independently reached various Southeast Asian islands, including the Philippines and a landmass that consisted of what’s now Papua New Guinea, Australia and Tasmania. Exact arrival dates are unknown, but nearly 200,000-year-old stone tools found on the Indonesian island of Sulawesi may have been made by Denisovans (SN: 1/13/16). H. sapiens groups that started arriving around 50,000 years ago or more then interbred with resident Denisovans.

Evolutionary geneticists Maximilian Larena and Mattias Jakobsson, both at Uppsala University in Sweden, and their team describe the new evidence August 12 in Current Biology.

Even as the complexities of ancient interbreeding in Southeast Asia become clearer, Denisovans remain a mysterious crowd. “It’s unclear how the different Denisovan groups on the mainland and on Southeast Asian islands were related [to each other] and how genetically diverse they were,” Jakobsson says. ...

https://www.sciencenews.org/article/indigenous-people-philippines-denisovan-dna-genetics
 
Newly published research announces the confirmation of the oldest Denisovan fossil remains discovered to date - circa 200,000 years old, as well as the first stone artifacts unequivocally attributable to Denisovans.
Oldest Remains of Mysterious, Extinct Human Ancestors Unearthed in Siberian Cave

Scientists have unearthed the oldest fossils to date of the mysterious human lineage known as the Denisovans. With these 200,000-year-old bones, researchers have also for the first time discovered stone artifacts linked to these extinct relatives of modern humans, a new study finds. ...

Until now, scientists had only discovered half a dozen Denisovan fossils. Five were unearthed in Denisova Cave in Siberia, and one was found in a holy site in China, Live Science previously reported.

Now, researchers have discovered another three Denisovan fossils in Denisova Cave. Scientists estimated that they are about 200,000 years old, making them the oldest known Denisovans ever found. Previously, the earliest known Denisovan specimens were about 122,000 to 194,000 years old. ...

The researchers estimated the age of these Denisovan fossils based on the layer of earth in which they were uncovered. This layer also contained a slew of stone artifacts and animal remains, which may serve as vital archaeological clues on Denisovan life and behavior. ...

Previously, Denisovan fossils were only found in layers without such archaeological material, or in layers that might also have contained Neanderthal material.

"This is the first time we can be sure that Denisovans were the makers of the archaeological remains we found associated with their bone fragments ..."

The stone tools linked with these new fossils have no direct counterparts in north or central Asia. However, they do bear some resemblance to items found in Israel dating between 250,000 and 400,000 years ago – a period linked with major shifts in human technology, such as the routine use of fire, the researchers noted. ...

The scientists detailed their findings online Nov. 25 in the journal Nature Ecology & Evolution.
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FULL STORY: https://www.sciencealert.com/oldest...rious-denisovans-unearthed-in-a-siberian-cave
 
Here are the bibliographic details and abstract from the new research report.

Brown, S., Massilani, D., Kozlikin, M.B. et al.
The earliest Denisovans and their cultural adaptation.
Nat Ecol Evol (2021).
https://doi.org/10.1038/s41559-021-01581-2

Abstract
Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave’s sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205–192 ka at 68.2% or 217–187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.
 
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A molar discovered in Laos is believed to (probably) represent the first evidence of Denisovan habitation in southeast Asia.
Ancient tooth of mysterious Denisovan girl possibly found

The discovery of an ancient molar — a tooth that likely belonged to young girl who lived up to 164,000 years ago in a cave in what is now Laos — is new evidence that the mysterious human lineage dubbed the Denisovans, previously known only from caves in Siberia and China, also lived in Southeast Asia, a new study finds.

"This shows that Denisovans lived in a wide range of environments and latitude and were able to adapt to extreme conditions, from the cold mountains of the Altai [in Russia] and Tibet to the tropical forests of Southeast Asia," study co-author Clément Zanolli ... told Live Science. ...

"Genetic studies indicated that Denisovans were adapted to high altitude and cold climates, but now we also know that they were living in warmer and more humid climates and at low altitude," Zanolli added. ...

When the scientists compared this molar to teeth from other hominins ... they found its internal and external 3D structure resembled that of Neanderthals, but fell slightly outside their known range of variation. Moreover, the tooth also differed from that of modern humans and Homo erectus, the first known human species to use relatively sophisticated stone tools. Although the scientists could not exclude it as belonging to a Neanderthal, they suggested its close physical similarity to a Denisovan specimen from China indicated that the molar was likely Denisovan. ...
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FULL STORY: https://www.livescience.com/possible-denisovan-tooth-found-laos

PUBLISHED RESEARCH REPORT: https://www.nature.com/articles/s41467-022-29923-z
 
Another report on the tooth.

In 2018, a child living in the village of Long Gua Pa in northeastern Laos approached a team of archaeologists, eager to show them a cave full of bones.

The team began to chisel into the cave’s cementlike walls, exposing the remains of ancient rhinoceroses, tapirs, pigs, rodents—and a single, humanlike molar. Now, the researchers have identified the tooth as that of a Denisovan, mysterious cousins of Neanderthals and modern humans who likely died out about 30,000 years ago. The new find is the first fossil evidence of Denisovans in Southeast Asia—and it supports clues in the DNA in modern Indigenous populations that these ancient people once roamed the region.

“We have assumed that Denisovans were in Southeast Asia … but we just didn’t have the fossils for it,” says Bence Viola, a paleoanthropologist at the University of Toronto who has analyzed Denisovan teeth but was not involved in the new study. “This one is in the right place at the right time.”

Denisovans coexisted in Eurasia with Neanderthals beginning hundreds of thousands of years ago, and later with anatomically modern Homo sapiens as well. Although traces of their DNA live on in several modern populations—most notably in one group of Indigenous Filipinos who inherited about 5% of their genome from Denisovans—fossil evidence of their existence has been hard to come by. Researchers have uncovered a few teeth, a finger bone, and a piece of skull from Denisova Cave in Siberia, and a mandible with a pair of intact molars in Xiahe Cave on the Tibetan Plateau. Despite the genetic clues that Denisovans at one point dwelled in Southeast Asia, no fossils have turned up there.

The archaeologists who were led to the cave in 2018 had been excavating early modern human sites in Laos’s lush Annamite Mountains for 15 years. Now, in the depths of Cobra Cave, also known as Tam Ngu Hao 2, they dissolved rocky accretions around the mysterious tooth. The researchers pegged it as a permanent lower hominin molar. But from which species? ...

https://www.science.org/content/art...rst-fossil-evidence-denisovans-southeast-asia
 
Denisovan genes give immune advantage.

When modern humans first migrated from Africa to the tropical islands of the southwest Pacific, they encountered unfamiliar people and new pathogens.

But their immune systems may have picked up some survival tricks when they mated with the locals—the mysterious Denisovans who gave them immune gene variants that might have protected the newcomers’ offspring from local diseases. Some of these variants still persist in the genomes of people living in Papua New Guinea today, according to a new study.

Researchers have known for a decade that living people in Papua New Guinea and other parts of Melanesia, a subregion of the southwest Pacific Ocean, inherited up to 5% of their DNA from Denisovans, ancient humans closely related to Neanderthals who arrived in Asia about 200,000 years ago. Scientists assume those variants benefited people in the past—perhaps by helping the modern humans better ward off local diseases—but they have wondered how that DNA might still be altering how people look, act, and feel today. It’s been difficult to detect the function of Neanderthal and Denisovan DNA in Melanesians, however, because scientists have analyzed so little genetic data from living humans in Papua New Guinea and other parts of Melanesia.

The new study overcomes that problem by using genetic data from 56 individuals from Papua New Guinea that were recently analyzed for another paper, part of the Indonesian Genome Diversity Project. The researchers, mostly from Australia and New Guinea, compared those genomes with those of Denisovans from Denisova Cave in Siberia, as well as Neanderthals. They found the Papuans had inherited unusually high frequencies of 82,000 genetic variants known as single nucleotide polymorphisms, which arise from differences of a single base or letter in the genetic code—from Denisovans. ...

https://www.science.org/content/art...iven-people-papua-new-guinea-immune-advantage
 
More on the immune advantage.

Papua New Guineans, who have been genetically isolated for millennia, carry unique genes that helped them fight off infection — and some of those genes come from our extinct human cousins, the Denisovans.

The research also found that highlanders and lowlanders evolved different mutations to help them adapt to their wildly different environments.

"New Guineans are unique as they have been isolated since they settled in New Guinea more than 50,000 years ago," co-senior study author François-Xavier Ricaut, a biological anthropologist at the French National Center for Scientific Research (CNRS), told Live Science in an email.

Not only is the predominantly mountainous terrain of the island country particularly challenging, but infectious diseases are also responsible for more than 40% of deaths.

Locals therefore had to find a biological and cultural strategy to adapt, which means that the population of Papua New Guinea is a "fantastic cocktail" to study genetic adaptation, Ricaut said.

Modern humans first arrived in Papua New Guinea from Africa around 50,000 years ago. There, they interbred with Denisovans who'd been living in Asia for tens of thousands of years. As a result of this ancient interbreeding, Papua New Guineans carry up to 5% Denisovan DNA in their genomes. ...

https://www.livescience.com/health/...-that-help-their-immune-system-study-suggests
 
Denisovans lived on high altitude Tibetan plateau for 100,000 years

Researchers analyzed thousands of animal bone fragments unearthed at Baishiya Karst Cave, 3,280 meters above sea level near the city of Xiahe in China’s Gansu province — one of only three places the extinct humans were known to have lived. Their work revealed that Denisovans could hunt, butcher and process a range of different large and small animals, including woolly rhinos, blue sheep, wild yaks, marmots and birds.

The team of archaeologists working at the cave also uncovered a rib bone fragment in a layer of sediment that dates back between 48,000 and 32,000 years, making it the youngest of the handful of known Denisovan fossils — a clue that the species was around more recently than scientists previously thought.
Due to a dearth of fossil evidence, details on how these archaic human ancestors lived have been scarce. But the new study reveals Denisovans who lived in Baishiya Karst Cave were incredibly resilient, surviving in one of Earth’s most extreme environments during warmer and colder periods and maximizing the diverse animal resources available in the grassland landscape.

“We know that the Denisovans lived, occupied the cave and this Tibetan plateau for such a long time, we really want to know, how did they live there? How did they adapt to the environment?” said Dongju Zhang, an archaeologist and professor at Lanzhou University in China and co-lead author of the study published Wednesday in the journal Nature.

“They used all these animals available to them, so that means their behavior is flexible,” Zhang added.

The rib belonged to Denisovan who likely lived at a time when modern humans were dispersing across the Eurasian continent, said study coauthor Frido Welker, an associate professor at the Globe Institute’s Biomolecular Paleoanthropology Group at the University of Copenhagen. He said future research at the site and in the region could shed light on whether the two groups interacted there.
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