Tooth of an Ancient Girl Fills Gap in Human Family Tree

A tooth found inside of a mountain cave in Laos has solved one of the biggest scientific mysteries of the Denisovans, a branch of ancient humans that disappeared roughly 50,000 years ago.

Since 2010, when Denisovan teeth and finger bones were first discovered, DNA testing has revealed that the enigmatic hominins were among the ancestors of people alive today in Australia and the Pacific.

But scientists didn’t understand how the Denisovans, whose scant remains had been found only in Siberia and Tibet, would have been able to interbreed with the group of humans who expanded east from Africa through Southeast Asia before reaching Australia, New Guinea and other islands in the Pacific.

Now, the discovery of a girl’s molar in Laos, published on Tuesday in the journal Nature Communications, puts Denisovans right in the path of modern humans who arrived in Southeast Asia tens of thousands of years later.

“We knew that Denisovans should be here,” said Laura Shackelford, a paleoanthropologist at the University of Illinois and a co-author of the new study. “It’s nice to have some tangible evidence of their existence in this area.”

Dr. Shackelford joined a team of French and Laotian colleagues on an expedition to the Annamite Mountains in northern Laos in 2008, and they have been digging up fossils ever since. In one of the many caves that riddle the mountains, they have unearthed human skull fragments dating back about 75,000 years, making them the oldest evidence of modern humans in Southeast Asia.

At the end of the researchers’ 2018 field season, children from a nearby village told Dr. Shackelford and her colleagues of another cave that contained bones. Her Laotian colleagues warned her that the cave was a favorite spot for cobras, but she decided a trip inside was worth the risk.

A team of caving experts scouted the site first, and then Dr. Shackelford made her way into a closet-sized cavity where the children claimed to have found bones. When she inspected the cave floor, she saw nothing.

“But then I turned my flashlight on, and I looked up,” she recalled. “All you could see were bones and teeth, embedded in the walls and in the ceiling of this cave. They were just sort of everywhere.”

Dr. Shackelford and her colleagues started working full-time in the new cave, which they dubbed Cobra Cave ( despite never encountering a snake). They chiseled rocks the size of soccer balls out of the walls and soaked them in a mild acid. The rock gradually disintegrated, leaving the harder fossils behind.

On close inspection, most of the fossils turned out to be bones from extinct mammals, such as pigs, deer and pygmy elephants. Gnaw marks on the bones revealed how they all ended up in a jumble in Cobra Cave: Porcupines likely carried them there and chewed on the bones to hone their teeth.

Sorting through the gnawed bones, the scientists found a surprise: a molar that resembled a human child’s tooth. But some features of the molar suggested it was not quite human. “We were so amazed and so excited,” Dr. Shackelford said.

They were even more delighted when geologists examined the cave wall to determine the age of the tooth. The tooth itself was too small to analyze, but the researchers found fossils and minerals nearby that contained radioactive elements that broke down at a regular pace. By measuring those elements, the researchers estimated the tooth was between 164,000 and 131,000 years old.

In other words, the Cobra Cave tooth is about twice as old as the oldest modern humans that Dr. Shackelford and her colleagues have found in the region. The tooth’s great age hinted that it belonged to an extinct relative of modern humans. But which one?

Humanity’s lineage split from the ancestors of chimpanzees about six million years ago in Africa. Over the next four million years, they evolved into upright, big-brained meat-eaters. At that point, some relatives began moving to Europe and Asia from Africa. One species, called Homo erectus, spread east as far as Indonesia.

Evidence from fossils and ancient DNA indicate that another wave of early humans traveled out of Africa even later. As the population spread across Europe and Asia, it split about half a million years ago. The western population became Neanderthals, and the eastern one became Denisovans.

Paleoanthropologists first discovered Neanderthal fossils in the mid-1800s in Germany and Belgium and have since found an abundance of bones marking the group’s range across Europe, the Middle East and Siberia. The fossils revealed Neanderthals as stocky, chinless humans. Tools and other remains offered glimpses into their minds: They were adept hunters who could stalk both rhinos and dolphins. They buried their dead and fashioned necklaces from eagle talons.

DNA in Neanderthal fossils also linked them to living humans. Soon after modern human ancestors moved out of Africa, they encountered Neanderthals in the Middle East and interbred with them — probably on several occasions.

Scientists have had a much harder time reconstructing the ancient migration of the Denisovans. For years, the only place where they fond these ancient humans was the Denisova Cave in Siberia. It was hard to see how people several thousand miles away, in Australia, New Guinea and nearby islands, could have ended up with Denisovan DNA.

The Denisovan samples from Siberia were limited to a few teeth and finger bones. Fortunately, scientists found an abundance of DNA in these specimens, and even extracted Denisovan DNA from dirt on the cave floor.

The evidence gathered so far indicates that Denisovans occupied the cave 300,000 years ago and inhabited the surrounding area off and on until about 50,000 years ago. They also appear to have left behind stone tools in the cave.

Given that Denisovans endured for hundreds of thousands of years, scientists were confident that they’d find Denisovan fossils elsewhere. In 2019, that proved to be the case. Chinese researchers announced the discovery of a 160,000-year-old jaw in a Tibetan cave with teeth matching those found at the Siberian site. That discovery in Tibet, more than 1,400 miles south of Siberia, drastically expanded the known range of Denisovans.

The jaw also provided a few more clues about the Denisovans themselves. For one thing, the proportions of the jaw and teeth implied they might have been tall and solidly built, like football players. To survive in the harsh environment of the Tibetan plateau, they would have had to withstand low oxygen in the air and cold weather.

Still, some 1,100 miles would have separated Denisovans in Tibet from modern human ancestors in Southeast Asia, leaving scientists to wonder how the two groups could have interbred.

Examining the tooth from the Cobra Cave in Laos, Dr. Shackelford and her colleagues did not know if it had come from Denisovans, Neanderthals, Homo erectus or some other unknown species of human. Over the past four years, they have been analyzing the tooth for clues.

Initially, they hoped that it would contain ancient DNA. But before destroying part of the tooth to find out, they had colleagues at the University of Copenhagen look at other mammal fossils found from the same sample of the Cobra Cave wall. Those specimens yielded no DNA, so they decided not to look for any in it.

But they had better luck when they searched for protein fragments in the molar’s enamel. The chemical makeup of the fragments has only been found in the teeth of modern humans, Neanderthals and Denisovans — but not those of other mammals.

Unfortunately, the protein composition is the same in all three groups of hominins, leaving the researchers unable to say which one the molar came from.

But the enamel of the juvenile tooth had one more piece of information to offer: It belonged to a girl. It lacked a specific enamel protein encoded by a gene on the Y chromosome, which is only carried by males.

The scientists made a high-resolution scan of the molar’s surface and interior, allowing them to compare its fine anatomical structure to more than 400 molars from living and extinct humans. Of those teeth, the Cobra Cave specimen most closely resembled a molar lodged in the Denisovan jaw from Tibet.

Shara Bailey, a paleoanthropologist at New York University who has studied the Tibetan jaw but was not involved in the new study, said this conclusion was sound. “I agree 100 percent with the analysis,” she said.

Dr. Bailey acknowledged that some people may wonder how a single tooth could reveal so much about its Paleolithic owner. But the cusps and ridges of teeth are complex landscapes, and the shape of those landscape is largely determined by genes, making teeth a rich trove of information about evolution.

“Teeth are the unsung heroes of paleoanthropology,” Dr. Bailey said.

The discovery of Denisovans in Laos shows that they were exactly where they needed to be to interbreed with modern humans who arrived in Southeast Asia thousands of years later.

Dr. Bailey and Dr. Shackelford agreed that more Denisovan fossils wait to be discovered elsewhere. Recent studies have found a small amount of Denisovan DNA in East Asians, for example, which their ancestors may have acquired through a separate interbreeding. And some ancient teeth that were already discovered in China and Taiwan seem now like they might have a Denisovan shape, warranting a fresh look.

But Bence Viola, a paleoanthropologist at the University of Toronto who was not involved in the study, said the Cobra Cave tooth itself provided some fresh clues about the Denisovans.

“These guys were able to deal with extensive snow cover and very low winter temperatures but at the same time with humid tropical environments,” he said. “Denisovans were very adaptable — likely more so than Neanderthals. They were most similar to modern humans in the end.”

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