Tooth from mysterious human relative adds new wrinkles to their story

Discovered thousands of miles south of the only other known Denisovan fossils, the molar provides fresh evidence of the enigmatic humans’ spread across ancient Asia.

By Maya Wei-Haas, Michael Greshko
Published 18 May 2022, 19:52 BST
The newfound tooth hails from Laos’s Cobra Cave—a cramped hollow embedded in a lush escarpment, as shown here. Scientists required a system of ropes to access the cave.
Photograph by Fabrice Demeter

After scrambling up a steep rocky pitch in the Annamite Mountains of Laos, Laura Shackelford was initially underwhelmed. The palaeoanthropologist from the University of Illinois Urbana-Champaign stood in a cramped hollow known as Cobra Cave, looking for bones that a local Hmong boy had mentioned seeing. Flipping on her flashlight, she swept the beam of light from one seemingly barren wall to another.

Then she looked up.

“I saw almost nothing but bone,” says Shackelford, who is also a National Geographic Explorer. Embedded in the rubbly ceiling were fossils of animals long gone, scattered across the cave’s roof “almost like stars.”

For years Shackelford and her team had worked in Laos’s labyrinthine cave systems in search of ancient human remains, and she knew that this narrow passage was special. Shortly before her first trip into the cave, Shackelford’s colleague had found a particularly exciting fossil within the cave’s constellations of remains: a wrinkly partial molar more than 130,000 years old.

As Shackelford and her colleagues report in a new study partially funded by the National Geographic Society, the tooth is likely from a young girl who was part of a mysterious group of ancient humans known as the Denisovans. If confirmed, the find marks the southernmost fossil found to date of this enigmatic group.

The large molar’s overall shape and inner structures resemble previously identified Denisovan teeth in a jaw found at the edge of the Tibetan plateau. Fossils of this enigmatic group are rare, which makes it challenging to identify any newfound bones or teeth as Denisovan.
Photograph by Fabrice Demeter and Clément Zanolli

Denisovans split from their sister group, the Neanderthals, some 400,000 years ago as Neanderthals spread across Europe and Denisovans moved east into Asia. While scientists have uncovered many Neanderthals remains, Denisovan fossils have proven elusive. All of the previously confirmed Denisovan bones and teeth could easily fit in a sandwich-size plastic bag, and they all come from just two sites, one in Siberia and another in Tibet.

But scientists have long suspected Denisovans traipsed much farther south. Whenever the Denisovans crossed paths with early humans, they seem to have interbred, leaving their genetic fingerprints in most modern people of Asian descent.

The latest find in Laos, published this week in Nature Communications, reveals the stunningly varied range that Denisovans achieved, from frigid mountains and high plateaus to the steamy lowlands of Southeast Asia. “It kind of makes me think about how similar they are to us,” Shackelford says. “We’re incredibly flexible—that’s sort of the hallmark of modern humans.”

The likely Denisovan tooth is one of many new finds that hint at how much more is just waiting to be discovered in the region. “I do have to say, we’re so proud,” says study co-author Souliphane Boualaphane, an archaeologist with Laos’s Ministry of Information, Culture, and Tourism.

Unearthing an ancient menagerie

The tooth is the latest fossil find from the Annamite Mountains, which sprawl about 700 miles along the border between Laos and Vietnam. Over millennia, rivers have carved out the local limestone—the remnants of an ancient seafloor—into a system of caves that now snake through the range.

Though these craggy confines have proven fertile grounds for discovery, they’re not easy places to work. The area’s hot, humid climate causes bone to break down rapidly, and the rugged terrain means that whatever survives is hard to find. Despite these challenges, recent discoveries in Laos have documented tens of thousands of years of human activity in the region, including some of Southeast Asia’s oldest modern human remains.

Photograph by Fabrice Demeter and Clément Zanolli

Much of the modern research interest in Laos traces back to Thongsa Sayavongkhamdy, an influential Laotian archaeologist who painstakingly relocated sites that had been studied and abandoned in the 1930s, including the area that contains Cobra Cave. Sayavongkhamdy, a co-author on the new study, died in April; the study is dedicated to his memory. “It’s really thanks to him that our team has been able to work in Laos,” says Fabrice Demeter, the study’s co-lead author and a palaeoanthropologist at the Lundbeck Foundation GeoGenetics Centre in Copenhagen, Denmark.

Demeter and Shackelford have each spent more than a decade working in Laos, recently teaming up with cavers to navigate the steep escarpments. In 2018 they caught wind of Cobra Cave, whose entrance sits atop a rock face more than 110 feet above the surrounding plain. The cave is so cramped, a person of average height standing inside can touch both walls and the ceiling all at once.

Retrieving the cave’s fossils is also tricky since they’re embedded within breccia, a fruitcake-like type of rock that forms from jumbles of stony fragments. Chipping through it “is like trying to excavate out of concrete,” Shackelford says.

Yet Cobra Cave yielded amazing finds from the start. On December 3, 2018, geologist and caver Eric Suzzoni headed to the hollow on a reconnaissance trip ahead of Shackelford’s first visit inside, and he collected bits of rock and bone to show the team. He clambered down from the cave just before lunch to pass around his many fossil finds. “At some point Eric said, Oh, but I got something here,” Demeter says. From his front shirt pocket, Suzzoni pulled out the unusual molar.

“Almost immediately, we knew that it was hominin of some sort,” Shackelford says. “But it wasn't modern human.”

A black box of life

For nearly a decade, the only known remains of Denisovans were a few teeth, a pinky bone, and a fragment of skull uncovered at Denisova cave in southern Siberia. Then in 2019 a blockbuster announcement revealed a Denisovan jaw—known as the Xiahe mandible—in Baishiya Cave, on the edge of the Tibetan Plateau.

The newfound Laotian molar may just be one tooth, but it could still add a lot to scientists’ understanding of Denisovans. “Teeth are like a little black box of the life of the individual,” says Clément Zanolli, the study’s co-lead author and a palaeoanthropologist at France’s University of Bordeaux. In their shape, internal structure, chemistry, and wear patterns, teeth can preserve hints of an animal’s age, diet, and even the climate of their habitat.

Tooth shapes can also help scientists identify species among humans and their extinct cousins. The chewing surface of the Cobra Cave molar is much more wrinkled than that of modern human molars, and it has a crest that’s common within the teeth of Neanderthals. But the tooth’s overall shape and inner structure resemble the Denisovan teeth in the Xiahe mandible.

The Laotian tooth’s lack of roots or surface wear suggests that it belonged to a child who died before their adult teeth had fully formed, likely between 3.5 and 8.5 years of age. The molar probably washed into the cave alongside remains from other large animals, including ancient rhinos, pigs, macaques, and bovids. Based in part on the age of these animal remains, the molar is most likely between 131,000 and 164,000 years old.

After x-ray scanning the fossil to study its shape, the researchers sampled the tooth’s enamel in search of preserved proteins. Unlike delicate strands of DNA, proteins have a higher chance of surviving Laos’s hot, humid climate. The amino acid building blocks of these proteins can then give hints to the underlying genetic code, helping scientists untangle a specimen's identity.

This analysis revealed that the tooth belonged to an individual within the genus Homo, rather than an orangutan or other great ape. Proteins also show that the tooth belonged to a girl. Yet researchers didn’t find the proteins needed to place the tooth within a specific branch of the hominin family tree.

While the analysis cannot confirm Denisovan identity, “there’s nothing stopping us from looking for other proteins present in the enamel,” says study co-author Frido Welker, a palaeogeneticist at the University of Copenhagen’s Globe Institute. As methods for extracting and analysing DNA and associated proteins improve, Welker and his colleagues hope the tooth will yield more details.

And by minimising the amount of sample they took from the tooth, the study team has left the door open for future research that’s yet to be imagined. “People who are working on this field in 30, 40, 50 years with totally new technologies are going to appreciate that," says National Geographic Explorer Kendra Sirak, a Harvard Medical School research associate and ancient DNA expert who wasn’t involved with the new study.

The next mountain

For now the Cobra Cave tooth’s strongest Denisovan ties come from its location and its resemblance to the molar of the Xiahe mandible. While the Laotian molar is somewhat similar to those of Neanderthals, that species has never been found as far east as Laos, and genetic data show that Denisovans probably lived in Southeast Asia.

“Everything fits with what we would expect for a Denisovan lower molar,” says Bence Viola, a palaeoanthropologist at Canada’s University of Toronto who wasn’t involved with the study.

Piecing together the mysterious hominins’ anatomy has been a persistent challenge because, at least for now, Denisovan fossils are so scarce. The fact that the newfound tooth is a lower molar makes confirmation even more difficult, since only the Xiahe mandible contains lower molars firmly identified as Denisovan. Without support from DNA or additional proteins, “it’s very difficult to say anything conclusive,” says Aida Gomez-Robles, a palaeoanthropologist at University College London who wasn’t part of the study team.

Yet many more Denisovans might be hiding under scientists’ noses—or in cave ceilings above their heads. A dazzling array of hominin fossils have been found across Asia, many of which have been assigned to a vague catch-all group known as “archaic Homo.” In recent years, studies have suggested that some of these hominins could be Denisovans, or at least close relatives.

“Most likely we’ve been looking at Denisovans in museums and … fossil institutions for a very long time, but we haven't known what to call them,” Shackelford says.

Researchers also have more studies planned. According to Zanolli, the team is analysing the oxygen and carbon chemistry of the tooth’s enamel. Such studies could hint at the climate in which the Denisovan girl lived, as well as what she was eating as the molar formed.

For Shackelford, one of the study’s most exciting implications is the sheer number of discoveries that lie in wait among Laos’s cave-riddled peaks. “We’ve been working there for more than 10 years,” she says, “and we still haven’t made it off the first mountain.”


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