image title

New Denisovan DNA expands diversity, history of species

October 29, 2020

Discovery extends the time of occupation of the Tibetan Plateau by hominins, suggests intermixing with early modern humans

While the continents of Africa and Europe have been obvious and fruitful treasure troves for exploration and discovery of our modern human origins, Asia has been somewhat overlooked. Scientists have thought that modern humans left Africa about 60,000 years ago and, as they colonized Western Eurasia, found a world empty of any other archaic hominin species. This assumption stemmed in part from the fact that the prehistory of Asia is poorly known compared with that of Africa and Europe.

But research published this week in the journal Science adds more evidence to the record that Denisovans, a group of extinct hominins that diverged from Neanderthals about 400,000 years ago, may have more widely inhabited northeast central Asia.

Ancient Denisovan mitochondrial DNA has been recovered in sediments from Baishiya Karst Cave, a limestone cave at the northeast margin of the Tibetan Plateau, 3,280 meters above sea level. Samples of sediments were analyzed by an international team including Arizona State University researcher Charles Perreault. Denisovan mitochondrial DNA was recovered that has been dated from around 100,000 to 60,000 years ago, and also possibly as recently as 45,000. If true, this last date may overlap with the presence of modern humans in northeast central Asia.

Perreault is a research affiliate with the Institute of Human Origins and an associate professor with the School of Human Evolution and Social Change.

“When we started developing this project about 10 years ago,” said Perreault, “none of us expected Baishya Cave to be such a rich site. We’ve barely scratched the surface — three small excavation units have yielded hundreds of stone tools, fauna and ancient DNA. There’s a lot that remains to be done.”

A mandible fossil (the “Xiahe mandible”) from the same cave and dated to 160,000 had been previously identified, tenuously, as Denisovan, based on a single amino acid position. This current study dispels any doubt left that the Denisovans occupied the cave.

This discovery in Baishiya Karst Cave is the first time Denisovan DNA has been recovered from a location that is outside Denisova Cave in Siberia, Russia — previously the single location in the world where a handful of DNA-bearing Denisovan fossil bones had been discovered. In 2010, a finger bone belonging to a previously unknown hominin species was found buried in Denisova Cave, in the Russian Altai Mountains. Evidence of this new species forced anthropologists to revise their model of human evolution outside of Africa.

Finding Denisovan DNA on the Tibetan Plateau itself is surprising. Evidence of archaic hominins 2,000 meters above sea level is unusual. Life this high on the plateau is harsh for many reasons, including its thin air, and humans can develop altitude sickness anywhere above 2,500 meters above sea level. This suggests that the Denisovans may have evolved adaptations to high altitude, much like modern Tibetans. The dates of the sediments with mitochondrial DNA, along with the older 160,000-year-old Xiahe mandible, suggest that the Denisovans were on the plateau perhaps continuously for tens of thousands of years — more than enough for genetic adaptations to emerge. 

Getting DNA samples from geographic locations outside of Siberia is also important to understand the genetic diversity and the population structure and history of the Denisovan group as a whole. Researchers suspected that Denisovans were widespread in Asia, based on the extensive Denisovan genomic signal among present-day Asians.

The Denisovan fossil and the DNA it contained indicate that early modern humans coexisted in Asia with other archaic hominin species, but, unexpectedly, that they interbred with them. Like Neanderthals, Denisovan population intermixed with modern humans as they dispersed into Asia. In fact, there’s evidence that the genetic adaptations to high altitude in present-day Tibetans come from Denisovans. If confirmed, this is a great example of how intermixing with local archaic populations has shaped, and helped, the spread of modern humans around the world. In this case, it allowed humans to colonize the Tibetan Plateau perhaps faster than they would otherwise have been able to.

“Baishiya Cave is an extraordinary site that holds tremendous potential to understand human origins in Asia,” Perreault said. “Future work in Baishiya Cave may give us a truly unique access to Denisovan behavior and solidifies the picture that is emerging, which is that Denisovans, like Neanderthals, were not mere offshoots of the human family tree — they were part of a web of now-extinct populations that contributed to the current human gene pool and shaped the evolution of our species in ways that we are only beginning to understand.”

Research article: "Denisovan DNA in Late Pleistocene sediments from Baishiya Kartst Cave on the Tibetan Plateau," Science. Dongju Zhang et al.

Top photo: Tibet cave site. Photo by by Charles Perreault/ASU

Julie Russ

Assistant director , Institute of Human Origins


image title

ASU archaeologist goes 'Jeep' into Mongolia

December 13, 2016

Research in the relatively unstudied region could have a big impact on our knowledge of human origins

When archaeologist Charles Perreault traveled to Mongolia for some investigative fieldwork, he didn’t bring the typical tool set of shovels and spades. Instead, he brought two all-terrain Jeeps, beginning a new project that will improve our knowledge of the early hominin groups that occupied northeast Asia, including ancient Homo sapiens, Neanderthals and a newly discovered species called Denisovans.

As an assistant professor at Arizona State University’s School of Human Evolution and Social Change, Perreault studies cultural evolution, or the way that people share cultural information like technology through social interaction. He is also an evolutionary anthropologist, meaning he looks at archaeological evidence to research the ancestors of modern humans.

Perreault did his master’s thesis on basketry technology in Peru, but as he worked to finish his graduate program, he often found himself being driven by questions about human evolution. Finding the answers to those questions soon required him to start looking beyond more recent archeological sites in the Americas to older, more foundational sites in Eurasia.

In graduate school, Perreault worked on the riddle of why humans first decided to live in the high-altitude environment of Tibet. But it was Mongolia that truly began to draw Perreault’s interest, particularly after archaeologists found millennia-old hominin bone fragments in a cave near the country’s shared border with Russia in 2008.

A little revolution

The Russian cave finding that inspired Perreault was significant for several reasons — first, because some bone fragments within were identified as belonging to Neanderthals. Before then, Perreault explained, scientists believed that Neanderthals were mostly limited to Western Europe. Suddenly, their range had doubled.

Second, analysis of part of a pinky bone from the cave revealed the existence of an entirely new hominin species, dubbed Denisovans after the cave where scientists found the fragment. These Denisovans — cousins of Neanderthals and modern humans — were the first species to ever be identified on ancient DNA alone.

Lastly, further analysis of other ancient bones from the site suggested that Neanderthals had interbred with Denisovans at some point in history. And by comparing the Neanderthal and Denisovan DNA samples to modern human DNA samples, scientists found that people today have genes from both groups in their DNA. This means that Neanderthals and Denisovans also interbred with ancient Homo sapiens — a finding that sheds new light on the interactions between hominin groups thousands of years ago.

photo of a cave surveyed by Dr. Perreault in northern Mongolia

One of the rock shelters surveyed by ASU assistant professor Charles Perreault in northern Mongolia. Photo by Perreault


“It led to a little revolution in our understanding of human evolution outside of Africa,” Perreault said. ­“As modern humans expanded their territories, they weren’t just colonizing some empty world. They were entering and colonizing areas populated with other hominin species … maybe with different language, clothing and culture. That’s crazy when you think about it.”

It was just crazy enough, in fact, to inspire Perreault to begin his own journey across the globe to Mongolia. Part of the appeal, of course, was the chance to do archaeology in the region of the groundbreaking Denisovan find — but the undertaking was not without its challenges.

“We have to build everything from the foundation,” Perreault said. “We know little about that part of the world, so the effort is just to get a basic understanding of [questions like], ‘When did people arrive in that region?’”

Research, risks and rocky roads

By summer 2016, Perreault found himself in the Darkhad Valley of northern Mongolia, but before he could even think about excavating, he had to first find potential archaeological sites. He and his team of two drivers, two archaeologists from the Mongolian Institute of Archaeology and two American archaeologists formed an off-road caravan. Every day, they drove for eight to 10 hours, crossing miles of mountains and rivers — hence the all-terrain Jeeps.

“The goal of the trip was to find prospective sites to go back to and do excavation. So this time around, it was just traveling, trying to find caves or rock shelters,” Perreault said. “We looked at the caves to see if there were any cultural artifacts on the surface, but we didn’t dig a single hole.”

photo of Dr. Perreault exploring a rockshelter in the southern part of the Darkhad Valley.

Perreault explores a rock shelter in the southern part of the Darkhad Valley. Photo by David B. Madsen

With a daunting amount of ground to cover and limited time to cover it, the team knew they couldn’t afford to just throw darts at a map. Instead, Perreault tried to gather as much information as possible in advance. By looking at geological maps, for example, he was able to note the locations of limestone outcrops, an ideal rock type for cave formation. He also reviewed reports and papers from other archaeology projects near Mongolia to see what others had found. He even tracked down and talked to another archaeologist who had once driven through the region 10 years prior and reported seeing a few rock shelters.

“The good type of rock is there, people have seen rock shelters, Mongolia has a deep archaeological record, and very important sites have been found in similar geological settings in Russia,” Perreault said. “Taken together, all these things suggest to us that this is an area that has some potential.”

Of course, no amount of advance research guarantees success in the field.

“It’s possible we could have gone there and found nothing,” he said. “But it went very well; it went better than I expected.”

In fact, by the end of the three weeks, Perreault’s team had found about a dozen rock shelters.

Now that the first step is done, he plans to do some test excavations next summer in the three or four more promising caves. If all goes well, a bigger team of workers and researchers will come in to do a full excavation — and with the possibility of rock-hard permafrost to dig through, that looks to be no small feat.

Photo of Dr. Perreault collecting data in front of a rock shelter in Mongolia

Perreault is shown collecting data in front of a rock shelter in Mongolia. Photo by David B Madsen

Perreault explained that in the initial stages of an archaeological project, much of the energy is devoted to excavation, with a preliminary analysis of artifacts sometimes conducted in the field. For example, students often help by cleaning and cataloging artifacts on site.

Once the team has excavated a greater portion of the site, which could be years later, the primary investigator will do a deeper analysis of the uncovered artifacts.

Perreault plans to be involved both in the excavation and the artifact analysis in later stages of the project. He is excited for the new discoveries the sites might yield. Though these archaeological ventures tend to be long affairs, he welcomes the challenge.

“Hopefully, there’s enough stuff there to keep me busy for the next 10 years or so,” he said.

Mikala Kass

Communications Specialist , ASU Knowledge Enterprise