DNA from extinct hominin may have helped ancient peoples survive in the Americas

(Press-News.org) Thousands of years ago, ancient humans undertook a treacherous journey, crossing hundreds of miles of ice over the Bering Strait to the unknown world of the Americas.

Now, a new study led by the University of Colorado Boulder suggests that these nomads carried something surprising with them—a chunk of DNA inherited from a now-extinct species of hominin, which may have helped humans adapt to the challenges of their new home.

The researchers will publish their results Aug. 21 in the journal Science.

“In terms of evolution, this is an incredible leap,” said Fernando Villanea, one of two lead authors of the study and an assistant professor in the Department of Anthropology at CU Boulder. “It shows an amount of adaptation and resilience within a population that is simply amazing.”

The research takes a new look at a species known as Denisovans. These ancient relatives of humans lived from what is today Russia south to Oceania and west to the Tibetan Plateau. The Denisovans likely went extinct tens of thousands of years ago. Their existence, however, remains poorly understood: Scientists identified the first known Denisovan just 15 years ago from the DNA in a fragment of bone found in a cave in Siberia. Like Neanderthals, Denisovans may have had prominent brows and no chins.

“We know more about their genomes and how their body chemistry behaves than we do about what they looked like,” Villanea said.

A growing body of research has shown that Denisovans interbred with both Neanderthals and humans, profoundly shaping the biology of people living today.

To explore those connections, Villanea and his colleagues including co-lead author David Peede from Brown University, examined the genomes of humans from across the globe. In particular, the team set its sights on a gene called MUC19, which plays an important role in the immune system.

The group discovered that humans with Indigenous American ancestry are more likely than other populations to carry a variant of this gene that came from Denisovans. In other words, this ancient genetic heritage may have helped humans survive in the completely new ecosystems of North and South America.

A little-known gene Villanea added that MUC19’s function in the human body is about as mysterious as Denisovans themselves. It’s one of 22 genes in mammals that produce mucins. These proteins make mucus, which, among other functions, can protect tissues from pathogens.

“It seems like MUC19 has a lot of functional consequences for health, but we’re only starting to understand these genes,” he said. 

Previous research has shown that Denisovans carried their own variant of the MUC19 gene, with a unique series of mutations, which they passed onto some humans. That kind of admixture was common in the ancient world: Most humans alive today carry some Neanderthal DNA, whereas Denisovan DNA makes up as much as 5% of the genomes of people from Papua New Guinea. 

In the current study, Villanea and colleagues wanted to learn more about how these genetic time capsules shape our evolution.

The group pored through already published data on the genomes of modern humans from Mexico, Peru, Puerto Rico and Colombia where Indigenous American ancestry and DNA is common. 

They discovered that one in three modern people of Mexican ancestry carry a copy of the Denisovan variant of MUC19—and particularly in portions of their genome that come from Indigenous American heritage. That’s in contrast to people of Central European ancestry, only 1% of whom carry this variant.

The researchers discovered something even more surprising: In humans, the Denisovan gene variant seems to be surrounded by DNA from Neanderthals. 

“This DNA is like an Oreo, with a Denisovan center and Neanderthal cookies,” Villanea said.

A new world Here’s what Villanea and his colleagues suspect happened: Before humans crossed the Bering Strait, Denisovans interbred with Neanderthals, passing the Denisovan MUC19 to their offspring. Then, in a game of genetic telephone, Neanderthals bred with humans, sharing some Denisovan DNA. It’s the first time scientists have identified of DNA jumping from Denisovans to Neanderthals and then humans. 

Later, humans migrated to the Americas where natural selection favored the spread of this borrowed MUC19.

Why the Denisovan variant became so common in North and South America but not in other parts of the world isn’t yet clear. Villanea noted that the first people who lived in the Americas likely encountered conditions unlike anything else in human history, including new kinds of food and diseases. Denisovan DNA may have given them additional tools to contend with challenges like these.

“All of a sudden, people had to find new ways to hunt, new ways to farm, and they developed really cool technology in response to those challenges,” he said. “But, over 20,000 years, their bodies were also adapting at a biological level.”

To build that picture, the anthropologist is planning to study how different MUC19 gene variants affect the health of humans living today. For now, Villanea said the study is a testament to the power of human evolution. 

“What Indigenous American populations did was really incredible,” Villanea said. “They went from a common ancestor living around the Bering Strait to adapting biologically and culturally to this new continent that has every single type of biome in the world.”

Other co-authors of the new study include researchers at Brown University; the University of Washington School of Medicine; Universidad Nacional Autónoma de México; University of Copenhagen; Clemson University; University of Padova; University of Turin; University of California, Berkeley; Université Paris- Saclay; and Trinity College Dublin.

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