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Ancient Tooth From Young Girl Discovered in Cave Unlocks Mystery of Denisovans, a Sister Species of Modern Humans

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A close-up of the tooth from a ‘birds-eye’ viewpoint. Credit: Fabrice Demeter (University of Copenhagen/CNRS Paris)

Denisovans, a sister species of modern humans, inhabited Laos from 164,000 to 131,000 years ago with important implications for populations out of Africa and Australia.

What connects a finger bone and some fossil teeth discovered in a cave in the remote Altai Mountains of Siberia to a single tooth found in a cave in the limestone landscapes of tropical Laos?

The answer to this question has been established by an international team of researchers from Laos, Europe, the United States, and Australia.

The human tooth was chanced upon during an archaeological survey in a remote area of Laos. Scientists have shown it originated from the same ancient human population first recognized in Denisova Cave (dubbed the Denisovans), in the Altai Mountains of Siberia (Russia).

Views of the TNH2-1 specimen. Credit: Nature Communications

The team of researchers made the major discovery during their 2018 excavation campaign in northern Laos. The new cave Tam Ngu Hao 2, also known as Cobra Cave, is located near the famous Tam Pà Ling Cave, where another important 70,000-year-old human (Homo sapiens) fossils had been previously found.

The international team of scientists are confident the two ancient sites are linked to Denisovans’ occupations despite being thousands of miles apart.

Their findings have been published in Nature Communications, led by The University of Copenhagen (Denmark), the CNRS (France), University of Illinois Urbanna-Champaign (USA), the Ministry of Information Culture and Tourism, Laos and supported by microarchaeological work undertaken at
What links a finger bone and some fossil teeth found in a cave in the remote Altai Mountains of Siberia to a single tooth found in a cave in the limestone landscapes of tropical Laos? The answer to this question has been established by an international team of researchers from Laos, Europe, the US, and Australia. Credit: Flinders University

Lead Author and Assistant Professor of Palaeoanthropology at the University of Copenhagen, Fabrice Demeter, says the cave sediments contained teeth of giant herbivores, ancient elephants, and rhinos that were known to live in woodland environments.

“After all this work following the many clues written on fossils from very different geographic areas our findings are significant,” Professor Demeter says.

“This fossil represents the first discovery of Denisovans in Southeast Asia and shows that Denisovans were in the south at least as far as Laos. This is in agreement with the genetic evidence found in modern-day Southeast Asian populations.”

A view from inside Denisova cave in the Altai Mountains of Russia. Note the very different vegetation and climate compared to Laos. Credit: Mike Morley, Flinders University

Following a very detailed analysis of the shape of this tooth, the research team identified many similarities to Denisovan teeth found on the Tibetan Plateau – the only other location that Denisovan fossils have ever been found.

This suggested it was most likely a Denisovan who lived between 164,000 and 131,000 years ago in the warm tropics of northern Laos.

Associate Professor Mike Morley from the Microarchaeology Laboratory at Flinders University says the cave site named Tam Ngu Hao 2 (Cobra cave), was found high up in the limestone mountains containing remnants of an old cemented cave sediment packed with fossils.

Inside Ngu Hao 2 cave showing the concreted remnant cave sediments adhering to the cave wall. The overlying whitish rock is a flowstone that caps the entire deposit. Credit: Fabrice Demeter (University of Copenhagen/CNRS Paris)

“We have essentially found the ’smoking gun’ – this Denisovan tooth shows they were once present this far south in the karst landscapes of Laos,” says Associate Professor Morley.

The complexity of the site created a challenge for dating and required two Australian teams.

The team from Macquarie University, led by Associate Professor Kira Westaway, provided dating of the cave sediments surrounding the fossils; and the team from Southern Cross University led by Associate Professor Renaud Joannes-Boyau conducted the direct dating of unearthed fossil remains.

“Establishing a sedimentary context for the fossils’ final resting place provides an internal check on the integrity of the find– if the sediments and fossils return a similar age, as seen in Tam Ngu Hao 2, then we know that the fossils were buried not long after the organism died,” says Associate Professor Kira Westaway.


A short video clip of Ngu Hao 2 (Cobra Cave) in northern Laos. The cave entrance is on the left. Credit: Fabrice Demeter (University of Copenhagen/CNRS Paris)

Dating directly the fossil remains is crucial if we want to understand the succession of events and species in the landscape.

“The good agreement of the different dating techniques, on both the sediment and fossils, attest to the quality of the chronology for the species in the region. And this has a lot of implications for population mobility in the landscape,” says A. Prof Renaud Joannes-Boyau from Southern Cross University

The fossils were likely scattered on the landscape when they were washed into the cave during a flooding event that deposited the sediments and fossils.

Unfortunately, unlike Denisova Cave, the humid conditions in Laos meant the ancient



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A tooth found in a cave in Laos is revealing more about the mysterious Denisovans

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Researchers believe the tooth belonged to a young female who lived at least 130,000 years ago and was likely a Denisovan — an enigmatic group of early humans first identified in 2010.

The lower molar is the first fossil evidence placing Denisovans in Southeast Asia and may help untangle a puzzle that had long vexed experts in human evolution.

The only definitive Denisovan fossils have been found in North Asia — in the eponymous Denisova cave in Siberia’s Altai Mountains in Russia. Genetic evidence, however, has tied the archaic humans most closely to places much further south — in what’s now the Philippines, Papua New Guinea and Australia.

“This demonstrates that the Denisovans were likely present also in southern Asia. And it supports the results of geneticists who say that modern humans and the Denisovans might have met in Southeast Asia,” said study author Clément Zanolli, a researcher in paleoanthropology at CNRS, the French National Center for Scientific Research and the University of Bordeaux.

Archaeologists uncovered the tooth in a place known as Cobra Cave, 160 miles (260 kilometers) north of Laos’ capital, Vientiane, where excavations began in 2018. The study, which published in the journal Nature Communications on Tuesday, estimated the molar was between 131,000 and 164,000 years old, based on analysis of cave sediment, the dating of three animal bones found in the same layer, and the age of rock overlying the fossil.

“Teeth are like the black box of an individual. They preserve a lot of information on their life and biology. They have been always used by paleoanthropologists, you know, to describe species or to distinguish between species. So for us paleoanthropologists (teeth) are very useful fossils,” Zanolli said.

Comparison with archaic human teeth

The researchers compared the ridges and dips on the tooth with other fossilized teeth belonging to archaic humans and found it didn’t resemble teeth belonging to Homo sapiens or Homo erectus — an archaic human that was the first to walk with an upright gait whose remains have been found across Asia. The cave find most closely resembled a tooth found in a Denisovan jawbone found on the Tibetan plateau in Xiahe county, in Gansu province, China. The authors said it was possible, though less likely, it could belong to a Neanderthal.

“Think about about it (the tooth) as if you are traveling into (a) valley between mountains. And the organization of these mountains and valleys is very typical of a species,” Zanolli explained.

Analysis of some protein in enamel from the tooth suggested that it belonged to a female.

Denisovan DNA lives on in some humans today because, once our Homo sapiens ancestors encountered the Denisovans, they had sex with them and gave birth to babies — something geneticists call admixture. This means we can look back into human history by analyzing current-day genetic data.

The “admixing” happened was thought to have happened more than 50,000 years ago, as modern humans moved out of Africa and likely crossed paths with both Neanderthals and Denisovans. But pinning down exactly where it happened has proven difficult — particularly in the case of Denisovans.

Definitively Denisovan?

Any addition to the meager hominin fossil record of Asia is exciting news, said Katerina Douka, an assistant professor of archaeological science at the department of evolutionary anthropology at the University of Vienna. She wasn’t involved in the research.

She said she would have liked to see “more and extensive evidence” that the tooth was definitively Denisovan.

“There is a chain of assumptions the authors accept in order to confirm that this is a Denisovan fossil,” she said.

“The reality is that we cannot know whether this single and badly preserved molar belonged indeed to a Denisovan, a hybrid or even an unknown hominin group. It might well be a Denisovan, and I would love it to be a Denisovan, because how cool would that be? But more confident evidence is needed,” she said.

In deeming the Laos tooth Denisovan, the researchers in this study relied heavily on a comparison with the Xiahe jawbone, Douka said. However, the jawbone, while thought by many to be Denisovan, was not an open-and-shut case. No DNA had been retrieved from the fossilized jawbone, only “thin” protein evidence, she added.

“Anyone working on this hominin group, where many major questions still remain, wants to add new dots on the map. The difficulty is in reliably identifying any fossils as that of a Denisovan,” she said. “This lack of robust biomolecular data, however, reduces significantly the impact of this new find and it is a reminder of how difficult it is to work in the tropics.”

The study authors said they planned to try and extract ancient DNA from the tooth, which, if possible, would provide a more definitive answer but the warm climate means that could be a long shot. The research team also plans to continue excavating the site after a pandemic-induced hiatus in the hope of more discoveries of ancient humans that lived in area.

“In this kind of environment, DNA doesn’t preserve well at all but we’ll do our best,” said study coauthor Fabrice Demeter, an assistant professor at the Lundbeck Foundation GeoGenetics Centre in Denmark.

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Remains of three Denisovans and one Neanderthal are uncovered in a Siberian cave 

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Remains of three Denisovans and one Neanderthal dating back 200,000 years have been uncovered in a Siberian cave, experts reveal.

The newly-found fossils were uncovered from the famous Denisova Cave in the Altai Mountains, southern Siberia, surrounded by archaeological remains such as stone tools and fossilised food waste.  

Neanderthals were a close human ancestor that lived in Europe and Western Asia from about 400,000 to 40,000 years ago.

Less is known about the Denisovans, another population of early humans who lived in Asia at least 80,000 years ago and were distantly related to Neanderthals.

Dating to 200,000 years ago, the new Denisovan bones are some of the oldest human fossils to have ever been genetically sequenced. 

The fact that the remains of both Neanderthals and Denisovans were found together raises questions about whether the two archaic human types lived there.  

Bone fragments taken from the cave that were used for molecular analysis. The analysis revealed three bone fragments as Denisovan and one as Neanderthal

NEANDERTHALS AND DENISOVANS 

Neanderthals were very early (archaic) humans who lived in Europe and Western Asia from about 400,000 years ago until they became extinct about 40,000 years ago. 

Denisovans are another population of early humans who lived in Asia and were distantly related to Neanderthals.

Much less is known about the Denisovans because scientists have uncovered fewer fossils of these ancient people.

The precise way that modern humans, Neanderthals, and Denisovans are related is still under study. 

However, research has shown that modern humans overlapped with Neanderthal and Denisovan populations for a period, and that they had children together (interbred). 

As a result, many people living today have a small amount of genetic material from these distant ancestors. 

Source: National Institutes of Health 

It’s already known that Denisovans diverged from Neanderthals. Both also bred with humans around 50,000 years ago, meaning the DNA of the early hominids survives today.

The new findings are detailed in Nature Ecology and Evolution by an international team, led by researchers from the Universities of Vienna and Tübingen, and the Max Planck Society in Munich, Germany.

In all, five hominin bones were found in the cave, including four that had enough DNA for mitochondrial analysis and identification – three as Denisovan and one as Neanderthal.

‘Finding one new human bone would have been cool, but five? This exceeded my wildest dreams,’ said study author Samantha Brown at the University of Tübingen. 

‘Denisovans are one of our most recent ancestors, and many people today still carry a small percentage of Denisovan DNA,’ Brown told USA Today, but she noted that there is still ‘very little information’ about this group. 

Denisovans are thought to have appeared at the site during an interglacial – a warm period during which the environment and temperatures were similar to today. 

It seems they had a ‘fully-fledged lithic tradition’, making use of raw material found in the alluvium of the nearby Anui River and hunting herbivores, such as bison, roe and red deer, gazelle and saiga antelope, and even woolly rhinoceros.  

Around 130,000 to 150,000 years ago, Neanderthals also appeared at the site, represented by the one newly-discovered Neanderthal fossil.

The remains were discovered at the Denisova Cave (entrance pictured here) in the Altai Mountains, southern Siberia

FILIPINO ETHNIC GROUP HAVE THE MOST DENISOVAN DNA, STUDY FINDS 

Modern-day people in the Philippines have the most Denisovan DNA in the world, a 2021 study found. 

Researchers in Sweden have found that the Philippine Negrito ethnic group known as the Ayta Magbukon have the highest level of Denisovan ancestry today.

The Ayta Magbukon people, who occupy the Philippines’ Bataan Peninsula, have more Denisovan DNA than the Papuan Highlanders, who were previously known as the present-day population with the highest level of Denisovan ancestry. 

Read more: Ayta Magbukon people have most Denisovan DNA in the world

Denisova Cave rose to fame 11 years ago, when genetic sequencing of a fossilised finger bone revealed a new, previously unknown human group – named ‘Denisovans’, in honour of the site.

But identifying further Denisovan remains at the cave has been challenging, as any human remains are fragmented and difficult to spot amongst hundreds of thousands of animal bones also present. 

Over the course of four years, a team led by anthropologist Katerina Douka at the University of Vienna worked to extract and analyse ancient proteins and DNA from nearly 4,000 bone fragments from Denisova Cave.   

The scientists used a biomolecular method known as peptide fingerprinting or ‘ZooMS’ – which uses collagen or other proteins preserved in archaeological artefacts to identify the species from which they derive.  

Such methods are the only means by which scientists could find human remains among the thousands of bones from the site, as more than 95 per cent were too fragmented for standard identification methods. 

The team focused on Denisova Cave’s oldest layers, which date to as early as 200,000 years ago. 

Brown analysed 3,800 bone fragments no larger than 1.5 inches in length that were previously deemed ‘taxonomically unidentifiable’.

However, she finally identified five bones whose collagen matched the peptide profile of humans. 

‘We were stunned to discover new human bone fragments preserving intact biomolecules from such ancient layers,’ said Douka.   

Research at Denisova Cave continues through fieldwork and targeted analyses of bones and sediments with a team of Russian archaeologists camped there for nearly six months each year.  

Excavations in the eastern chamber of Denisova Cave. The cave rose to fame 11 years ago, when genetic sequencing of a fossilised finger bone revealed a new, previously unknown human group – the Denisovans

Denisova Cave remains the only site so far discovered which contains evidence for the periodic presence of all three major hominin groups, Denisovans, Neanderthals and modern humans, in the last 200,000 years.              

Earlier this year, scientists reported that DNA discovered in Denisova Cave suggests early modern humans lived alongside Denisovans and Neanderthals at least 44,000 years ago. 

Last October, another team reported the discovery of Denisovan DNA in the Baishiya Karst Cave in Tibet.  

This discovery marked the first time Denisovan DNA has been recovered from a location that is outside Denisova Cave in Siberia, Russia.  

In August 2020, researchers revealed that DNA from an unknown ancient ancestor of humans that bred with Denisovans is still around today.  

THE DENISOVANS EXPLAINED

Who were they?

The Denisovans are an extinct species of human that appear to have lived in Siberia and even down as far as southeast Asia.

The individuals belonged to a genetically distinct group of humans that were distantly related to Neanderthals but even more distantly related to us. 

Although remains of these mysterious early humans have mostly been discovered at the Denisova Cave in the Altai Mountains in Siberia, DNA analysis has shown the ancient people were widespread across Asia. 

Scientists were able to analyse DNA from a tooth and from a finger bone excavated in the Denisova cave in southern Siberia.

The discovery was described as ‘nothing short of sensational.’ 

In 2020, scientists reported Denisovan DNA in the Baishiya Karst Cave in Tibet.

This discovery marked the first time Denisovan DNA had been recovered from a location that is outside Denisova Cave. 

How widespread were they?

Researchers are now beginning to find out just how big a part they played in our history. 

DNA from these early humans has been found in the genomes of modern humans over a wide area of Asia, suggesting they once covered a vast range.

They are thought to have been a sister species of the Neanderthals, who lived in western Asia and Europe at around the same time.

The two species appear to have separated from a common ancestor around 200,000 years ago, while they split from the modern human Homo sapien lineage around 600,000 years ago.

Last year researchers even claimed they could have been the first to reach Australia.

Aboriginal people in Australia contain both Neanderthal DNA, as do most humans, and Denisovan DNA.

This latter genetic trace is present in Aboriginal people at the present day in much greater quantities than any other people around the world.

 How advanced were they?

Bone and ivory beads found in the Denisova Cave were discovered in the same sediment layers as the Denisovan fossils, leading to suggestions they had sophisticated tools and jewellery.

Professor Chris Stringer, an anthropologist at the Natural History Museum in London, said: ‘Layer 11 in the cave contained a Denisovan girl’s fingerbone near the bottom but worked bone and ivory artefacts higher up, suggesting that the Denisovans could have made the kind of tools normally associated with modern humans.

‘However, direct dating work by the Oxford Radiocarbon Unit reported at the ESHE meeting suggests the Denisovan fossil is more than 50,000 years old, while the oldest ‘advanced’ artefacts are about 45,000 years old, a date which matches the appearance of modern humans elsewhere in Siberia.’

Did they breed with other species?

Yes. Today, around 5 per cent of the DNA of some Australasians – particularly people from Papua New Guinea – is Denisovans.

Now, researchers have found two distinct modern human genomes – one from Oceania and another from East Asia – both have distinct Denisovan ancestry.

The genomes are also completely different, suggesting there were at least two separate waves of prehistoric intermingling between 200,000 and 50,000 years ago.

Researchers already knew people living today on islands in the South Pacific have Denisovan ancestry.

But what they did not expect to find was individuals from East Asia carry a uniquely different type.

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One Living People Today Show More Traces of The Mysterious Denisovans Than Any Others

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The mysterious Denisovans were only formally identified about a decade ago, when a single finger bone unearthed from a cave in Siberia clued scientists in to the ancient existence of a kind of archaic hominin we’d never before seen.

 

But that’s only one side of the story. The truth is, modern humans had in fact already encountered Denisovans a long time before this. We crossed paths with them an eternity ago.

So far back, in fact, that we forgot about them entirely. Especially as they – and other archaic humans, such as the Neanderthals – faded into the unliving past, and Homo sapiens assumed sole human dominion over the world.

But even that’s kind of debatable.

All of these hominin varieties had a tendency to interbreed with one another when they co-existed, which is why, in a manner of speaking, ancient humans still live on in our modern human DNA.

Now, a new study reveals where the impression of this genetic fingerprint can most clearly be identified today.

According to the study, led by first author and human evolution geneticist Maximilian Larena from Uppsala University in Sweden, a Philippine Negrito ethnic group called the Ayta Magbukon has the highest level of Denisovan ancestry in the world today.

“Together with the recently described H. luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related,” the researchers explain in their study.

 

“Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.”

According to the results of the analysis – based on a comparison of around 2.3 million genotypes from 118 ethnic groups in the Philippines – the Ayta Magbukon’s level of Denisovan ancestry is approximately 30 to 40 percent greater than that of Papuans.

Photos of self-identified Negritos from across The Philippines. (Ophelia Persson)

This is so, even though Philippine Negritos later ‘diluted’ their gene pool’s amount of Denisovan genetics, with a more recent admixture of East Asian bloodlines, which carry lower amounts of Denisovan bloodlines.

If that dilution effect is accounted for, the Ayta Magbukon’s level of Denisovan ancestry extends as high as 46 percent greater than Australians and Papuans, the researchers suggest.

Even without that manipulation, however, the evidence suggests the Ayta Magbukon mixed less with later arrivals than other Philippine Negrito groups: preserving traces of very old bloodlines from an archaic source – one destined, for a very long time, to be forgotten.

 

The research team worked with volunteers and indigenous cultural communities who participated in this study, and the project was recognized by and implemented in partnership with the National Commission for Culture and the Arts (NCCA) of the Philippines.

“Some groups, such as Ayta Magbukon, interbred only a little with the people who later migrated to the islands,” says population geneticist Mattias Jakobsson, also from Uppsala University.

“That’s the reason why the Ayta Magbukon retained most of their Denisovan genes and therefore have the highest levels of those genes in the world.”

The findings are reported in Current Biology.

 

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