Biggest Denisovan fossil yet spills ancient human’s secrets

A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau

image-1-1440x697A Denisovan jawbone was discovered on Tibetan Plateau at an altitude of more than 3,000 metres.

Scientists have uncovered the most complete remains yet from the mysterious ancient-hominin group known as the Denisovans. The jawbone, discovered high on the Tibetan Plateau and dated to more than 160,000 years ago, is also the first Denisovan specimen found outside the Siberian cave in which the hominin was found a decade ago — confirming suspicions that Denisovans were more widespread than the fossil record currently suggests.

The research marks the first time an ancient human has been identified solely through the analysis of proteins. With no usable DNA, scientists examined proteins in the specimen’s teeth, raising hopes that more fossils could be identified even when DNA is not preserved.

“This is fantastic work,” says Katerina Douka, an archaeologist at the Max Planck Institute for the Science of Human History in Jena, Germany, who runs a separate project aiming to uncover Denisovan fossils in Asia. “It tells us that we are looking at the right area.”

Hunting for Denisovans

Until now, everything scientists have learnt about Denisovans has come from a handful of teeth and bone fragments from Denisova Cave in Russia’s Altai Mountains. DNA from these remains revealed that the Denisovans were a sister group to Neanderthals, both descending from a population that split away from modern humans about 550,00–765,000 years ago. And at Denisova Cave, the two groups seem to have met and interbred: a bone fragment described last year belonged an ancient-human hybrid individual who had a Denisovan father and Neanderthal mother.

But many expected that it was only a matter of time before researchers found evidence of Denisovans elsewhere. Some modern humans in Asia and Oceania carry traces of Denisovan DNA, raising the possibility that the hominin lived far away from Siberia. And some researchers think that unclassified hominin fossils from China could be Denisovan.

Screenshot_2019-05-01 Biggest Denisovan fossil yet spills ancient human’s secrets

The latest specimen, described in Nature, consists of half a lower jaw, with two complete teeth. A monk found it in Baishiya Karst Cave in China in 1980, and passed on to Lanzhou University. But it wasn’t until the 2010s that archaeologist Dongju Zhang and her colleagues began studying the bone.

The team faced a problem. The Denisova Cave remains had all been identified because they still contained some DNA, which could be compared with genetic sequences from other ancient humans. But there was no DNA left in the jawbone.

Instead, the scientists looked for ancient proteins, which tend to last longer than DNA. In dentine from the teeth, they found collagen proteins suitable for analysis. The team compared these with equivalent proteins in groups including Denisovans and Neanderthals, and found that they lined up closest with sequences from Denisovans.

The team were also able to piece together other snippets of information about the individual. One of the teeth was still erupting, for example, leading the authors to speculate that the jawbone belonged to an adolescent.

A virtual reconstruction of the jawbone.Credit: Jean-Jacques Hublin, MPI-EVA, Leipzig
Previous research2 identified Neanderthal remains using both proteins and DNA — but the success of the latest study could lead to a greater emphasis on getting ancient proteins out of fossils that haven’t yielded DNA, says Chris Stringer, a palaeoanthropologist at the Natural History Museum in London. The method could prove particularly useful for older samples or those from southeast Asia and other warm climates, where DNA degrades quickest.

But the field is still in its early stages, Stringer adds, and ancient-protein analysis currently has a smaller sample of early hominins for comparison than does DNA analysis. “Although it’s certainly very suggestive of a link with the Denisovans, I think I’d like to see bigger samples to really pin that down more,” he says.

Douka agrees: for now, ancient DNA analysis remains the “gold standard” for this kind of work, she says. Although there is no genetic material in the jawbone, Douka wonders whether researchers could still find DNA in the Tibetan cave — perhaps in sediment.

The Roof of the World

The altitude of the new Denisovan’s home — 3,280 metres above sea level — surprised researchers, and helps to solve a mystery about Denisovans’ genetic contribution to modern Tibetans. “It is astonishing that any ancient humans were at that altitude,” says Stringer.

Some Tibetans have a variant of a gene called EPAS1 that reduces the amount of the oxygen-carrying protein hemoglobin in their blood, enabling them to live at high altitudes with low oxygen levels. Researchers3 had thought that this adaptation came from Denisovans, but this was difficult to reconcile with Denisova Cave’s relatively low altitude of 700 metres. The latest study suggests that Denisovans evolved the adaptation on the Tibetan Plateau and passed it to Homo sapiens when the species arrived around 30,000–40,000 years ago, says co-author Frido Welker, a molecular anthropologist at the University of Copenhagen. If Denisovans in Asia were adapted to high altitudes, similar sites could harbor more of their remains.

He points to Sel’Ungur cave in Kyrgyzstan, about 2,000 metres above sea level, where a hominin child’s arm bone was found but did not yield any DNA. “Now I ask myself — maybe that specimen is also a Denisovan and not a Neanderthal, like we usually assume,” says Bence Viola, a palaeoanthropologist at the University of Toronto in Canada.

Re-evaluating fossils

And the fossil is likely to prompt scientists to reconsider the classification of other remains. “We can kind of work ourselves through the fossil record, and link up more and more specimens with the Denisovans,” says Viola.

One candidate is a jawbone known as Penghu 1, which was caught in a fishing net near Taiwan and has many similarities to the latest mandible. Welker and his colleagues hypothesize that this jaw could be Denisovan — but the ultimate proof will come from DNA or protein analysis, says Welker.

Sampling any remains for proteins or DNA is by its nature destructive, so there must good justification for doing so, he adds. “It’s not a light-hearted decision to make.”


A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau

Denisovans are members of a hominin group who are currently only known directly from fragmentary fossils, the genomes of which have been studied from a single site, Denisova Cave1,2,3 in Siberia. They are also known indirectly from their genetic legacy through gene flow into several low-altitude East Asian populations4,5 and high-altitude modern Tibetans6. The lack of morphologically informative Denisovan fossils hinders our ability to connect geographically and temporally dispersed fossil hominins from Asia and to understand in a coherent manner their relation to recent Asian populations. This includes understanding the genetic adaptation of humans to the high-altitude Tibetan Plateau7,8, which was inherited from the Denisovans. Here we report a Denisovan mandible, identified by ancient protein analysis9,10, found on the Tibetan Plateau in Baishiya Karst Cave, Xiahe, Gansu, China. We determine the mandible to be at least 160 thousand years old through U-series dating of an adhering carbonate matrix. The Xiahe specimen provides direct evidence of the Denisovans outside the Altai Mountains and its analysis unique insights into Denisovan mandibular and dental morphology. Our results indicate that archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

Mt. Gongpori and the Monkey Cave

There is a legend descended from Tibetan generations about their origin. Once upon a time, as the legend tells, Avalokitesvara*, a monkey and a Raksasi* were separately living on the three hills of a mountain. In deep loneliness, the Raksasi lured the monkey with all her attempts while the latter was meditating in one of the caves by the order of Avalokitesvara. Ambivalent but later enlightened by Avalokitesvara, the monkey eventually married the Raksasi and gave birth to six children, thus starting the history of Tibet.

*Raksasi: female form of Raksasa, a demon in Buddhism who eats humans. Raksasas are usually ugly and horrifying while Raksasis lure men by their beauty and then eat.


Denisovan Jawbone Discovered in a Cave in Tibet

In 1980, a Buddhist monk in Tibet entered a sacred cave to pray. On the floor, he found half of a human jawbone, studded with two teeth.

A team of scientists on Wednesday reported that the fossil belonged to a 160,000-year-old Denisovan, a member of a lineage of mysterious, Neanderthal-like humans that disappeared about 50,000 years ago.

The fossil is the first evidence of this species found outside the Denisova Cave in Siberia, buttressing the theory that these relatives of modern humans once lived across much of central and eastern Asia.

“I’m very excited — we have a Denisovan that’s somewhere else than Denisova,” said Bence Viola, a paleoanthropologist at the University of Toronto who was not involved in the new study. “We’d known about Denisovans for 10 years and hadn’t found them anywhere else.”
The new fossil demonstrates that Denisovans were remarkably hardy, able to endure harsh conditions on the Tibetan plateau, at an elevation of 10,700 feet, with only simple stone tools.

The find also suggests that these Denisovans may have evolved genetic adaptations to high altitudes, and that living Tibetans may have inherited those genes thanks to interbreeding between Denisovans and modern humans in prehistoric times.

In the 1970s, Russian researchers began excavating Denisova Cave in Siberia. Over the years, they found a wealth of bones. A few looked like they might have come from humans or an extinct human relative.
Hoping for clues, the archaeologists sent some of the bones to the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, whose experts excel at retrieving DNA from fossils.
Some of the bones contained Neanderthal DNA, it turned out. But in 2010, Max Planck researchers discovered that one finger bone held different genes from an unknown human lineage.

Over the past decade, scientists have discovered more Denisovan teeth and bone fragments, including a chunk of a skull. Denisovans appeared to have lived in the cave, off and on, from 287,000 years ago to about 50,000 years ago.

Judging from their DNA, Denisovans shared a common ancestor with Neanderthals about 400,000 years ago. They interbred with Neanderthals and with our own species. Today, people in East Asia, Australia, the Pacific islands and the Americas all carry some Denisovan DNA.

The spread of Denisovan DNA in living humans strongly suggested that they may have lived throughout East and Southeast Asia. And maybe not just there: Earlier this month, a team of researchers argued that a population of Denisovans reached New Guinea and interbred further with modern humans.

But year after year, no one could find a Denisovan fossil outside the Siberian cave.

In 2010, Dongju Zhang, an archaeologist at Lanzhou University in China, began studying the Tibetan jaw, which had been languishing in storage at her institution.

Right away, she could tell it was humanlike — but not human. “We all have chins, but this doesn’t have one,” Dr. Zhang said in an interview.

Eventually, she located the cave in Tibet where the jaw had been discovered. Monks at a nearby temple told her they regularly found human remains on their visits.

“They said they were half-bone and half-stone,” said Dr. Zhang.

When she and her colleagues made a small excavation in the cave, they found ancient tools, a sign of human occupation.

She emailed photos of the jaw to Jean-Jacques Hublin, a paleoanthropologist at the Max Planck Institute. Intrigued, he traveled to China to examine the fossil, and soon he and Dr. Zhang had begun a collaboration with other experts to learn more.

Chuan-Chou Shen and Tsai-Luen Yu of National Taiwan University handled the task of figuring out how old it was. The jaw still had bits of rock stuck to it, and these contained uranium. By measuring the uranium’s decay into thorium, Dr. Shen and Dr. Yu were able to estimate the bone’s age.

The jaw turned out to be at least 160,000 years old, by far the oldest evidence of humans on the Tibetan plateau. Its antiquity also supported the scientists’ hunch that it did not belong to our own species.

DNA could reveal its true identity. But Qiaomei Fu, a geneticist at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, found that no genetic material had survived.

Fortunately, other biological molecules can be found in fossils. At Max Planck, Frido Welker, a molecular anthropologist, discovered ancient proteins in the jawbone’s teeth.
The proteins were not from modern humans; instead, they were a match to Denisovan DNA from Siberia.

With the new discovery and other recent finds, a picture of the Denisovans has grown clearer. Everything about their heads seems to have been big, from their giant molars to their thick jaws to their massive brain cases. Dr. Viola speculated adults may have weighed well over 200 pounds.

“I’d assume they’d be very large and robust individuals,” he said. “These are like football players.”

The discovery of Denisovans living at high altitude is intriguing for another reason: Tibetans today share a special genetic link to Denisovans.

The cave in which the jawbone was found sits in a rugged valley.CreditDongju Zhang, Lanzhou University

When most people travel to high elevations, they respond to the low level of oxygen by making extra hemoglobin in their red blood cells.

“That’s bad, because it makes your blood thick,” said Emilia Huerta-Sanchez, a population geneticist at Brown University who was not involved in the new study.

But many Tibetans don’t make extra hemoglobin, thanks to an unusual version of a gene they carry called EPAS1. In 2014, Dr. Huerta-Sanchez and her colleagues discovered that this unusual gene came from Denisovans.

How did Denisovans end up with a gene that promotes health at high altitudes? And how did it end up becoming so common in Tibetans but so rare in other people?

Until scientists find DNA from Tibetan Denisovans, the history won’t be clear, Dr. Huerta-Sanchez said.

“We don’t know the order of events,” she said. “But Denisovans are such a mysterious group that anything we learn is exciting.”

In recent decades, Chinese paleontologists have found a number of puzzling bones that are almost human and are tens or hundreds of thousands of years old.

Researchers now may compare them to the Tibetan jaw, and search the fossils for ancient proteins.

“Denisovans are already somewhere in a museum drawer,” Dr. Welker predicted. “We just haven’t been able to link them together yet.”


Fossil Points to a Vanished Human Species in Himalayas

A fossil jaw found in the Himalayan highlands of Tibet belongs to a vanished human species called Denisovans, deepening the mystery of human evolution in Asia, scientists said Wednesday in a new study probing the roots of humankind.

Discovered by a local Buddhist monk, the fossil shows these archaic human relatives lived on the roof of the world in the rarefied air at almost 11,000 feet—an altitude that would leave many people today starved for oxygen. They settled at these frigid heights at least 160,000 years ago, more than 120,000 years before modern humankind arrived, said the scientists, who published their work on the fossil in the journal Nature.

Views of the virtual reconstruction of the fossil jawbone. The mandible is shown after digital removal of the adhering carbonate crust, and is so well preserved that it allows for a virtual reconstruction of the two sides. Photo: Jean-Jacques Hublin/MPI-EVA/Leipzig
While this early human species became extinct long ago, traces of their DNA survive in modern populations of Asia, the Pacific and Australia, several genome studies show. In fact, many people of Tibet today owe their unusual adaptation to such extreme high-altitude conditions, where there is 40% less oxygen in the air than at sea level, to a unique gene inherited from these primordial mountain dwellers.

“One of the most spectacular aspects of this discovery is the location,” said project co-leader Jean-Jacques Hublin, director of the department of human evolution at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “Nobody ever imagined that archaic humans would be able to dwell in such an environment.”

A team led by Dongju Zhang, top right, excavated in one of the two trenches in Baishiya Karst Cave in 2018. Photo: Dongju Zhang/Lanzhou University
The discovery is the most recent to highlight the early history of human development in Asia, which has been long overshadowed by human-fossil finds in Africa and Europe. “It became the sleeping beauty of paleoanthropology,” Dr. Hublin said. “We are now turning to Asia again.”

Until the new find, the Denisovans were known only through a fossil fingertip, three teeth and a toe bone found in 2008 far from Tibet in a cave in the Russian Altai Mountains of Siberia.

In 2010, scientists successfully exhumed DNA from that finger bone and discovered a special variation of a blood-cell gene called ESPA-1 that affects the body’s response to falling oxygen levels, key to survival at extreme altitudes. Inherited by many Tibetan people, it is considered by some researchers to be the strongest instance of natural selection ever documented in a human population.

No DNA was recovered from the latest find, the researchers said. But they speculate that Denisovans likely lived at this extreme altitude long enough to develop that special genetic adaptation and then passed it on to more modern humans with whom they interbred.

It took almost 40 years for the fossil jaw to go from the hands of the Buddhist monk who first picked it up to publication in a peer-reviewed scientific journal.

According to project co-leader Dongju Zhang at China’s Lanzhou University, the monk found the fossil in 1980 while visiting the Baishiya Karst Cave in Xiahe, Gansu, China. The deep cavern is a sacred site managed by a nearby temple. The steep approach to the cave entrance today is festooned with streamers of yellow, blue and red prayer flags.

“He grabbed something on the floor,” Dr. Zhang said. Recognizing something unusual about the primitive jawbone encrusted with mineral carbonate, “the monk gave it to the local living Buddha.” Known formally as the Sixth Gung-Thang Living Buddha, the religious leader in turn gave the jawbone to Lanzhou University.

Due to the unusual circumstances of the discovery, the researchers acknowledge they can’t prove that the jawbone came from the cave. But they were able to match the minerals on the jaw to deposits in the cave. Their recent excavation in the cave turned up stone tools and the bones of animals likely butchered for food dating to the same age as the fossil jaw.

“It blows my mind,” Dr. Hublin said.


ngm-1905-denisovan-jaw_ai2html-desktop-medium41586_2019_1139_Fig2_HTML41586_2019_1139_Fig9_ESMScreenshot_2019-05-01 Mysterious ancient human found in Tibet for first time15.-Virtual-reconstruction-of-the-Xiahe-mandible-upper-view-edited-Pixlrimage-6-1440x1080image-5-1440x96101-4.-Baishiya-Karst-Cave_compressed-1076x588image-1-1440x697image-9-1440x961image-8-1440x961Screenshot_2019-05-01 Ancient teeth hint at mysterious human relative






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