Photograph by Maurício de Paiva
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Newly sequenced Native American genomes inform how humans first moved into and around the Americas. One of the new genomes comes from 9,600-year-old remains recovered from Lapa do Santo, an archaeological site in eastern Brazil seen here.

Photograph by Maurício de Paiva

Ancient DNA reveals complex migrations of the first Americans

Newly sequenced Native genomes showcase a wealth of surprises, from previously unknown populations to unique high-altitude adaptations.

“Where do I come from?” That's perhaps one of the most fundamental questions for humanity. Now, three studies of ancient and modern human DNA are offering some intriguing answers by providing a detailed new look at the complex peopling of the Americas.

Once modern humans left Africa about 60,000 years ago, they swiftly expanded across six continents. Researchers can chart this epic migration in the DNA of people both alive and long-dead, but they were missing genetic data from South America, the last major stop on this human journey. The trio of new papers—published today in the journals Science, Cell, and Science Advances—dramatically increases the number of sequenced whole genomes from South America's indigenous peoples, both living and ancient.

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“This basically provides the first picture of whole-genome data more than a thousand years old,” says Nathan Nakatsuka, a Ph.D. student at Harvard Medical School who coauthored the Cell study. Based on the results, researchers show evidence of several human migrations into South America, including two previously unknown to science. The data also help flesh out the story of how people settled and thrived in the highlands of the Andes.

“With the addition of these genomes and others published earlier this year, we’re starting to see the details of that history emerge,” Jennifer Raff, a geneticist at the University of Kansas who was not involved in the studies, says in an email.

What DNA can reveal

Forty years ago, researchers thought the peopling of the Americas was fairly straightforward. It was thought that humans arrived in a single southern wave of migration about 13,000 years ago, which corresponds to the spread across North America of distinctive stone tools attributed to a group called the Clovis culture.

But thanks to new archaeological discoveries and more precise dating techniques, we now know that the Clovis people wielding these tools weren't the first Americans. At several sites in North and South America, researchers have convincingly shown that pre-Clovis people arrived centuries before these tools appear. (Learn more about the first Americans.)

Studying ancient DNA adds extra detail to this picture, revealing the presence of genetically distinct groups who didn't leave behind unique physical traces. That said, it offers only a fuzzy, zoomed-out view. After all, early Native Americans didn't march across the land in one fell swoop. Instead, small groups of hunters and gatherers meandered through the region as they lived day to day collecting food, seeking shelter, making clothing and tools, and socializing with others.

“It’s easy to fall into the trap of oversimplifying what was probably an extremely complex process, depicting it as straight arrows southward,” Raff says.

Unexpected migrations

The studies published in Cell and Science tackle the broader tempo of humans' movement into South America. In large part, they agree on the big picture. About 25,000 years ago, Native Americans' ancestors split from the people living in Siberia. Later, they moved across a land bridge connecting Siberia and Alaska, making it into the Pacific Northwest between 17,000 and 14,000 years ago.

Once they got south of the ice sheets coating much of Canada, ancestral Native Americans split into two genetically distinct groups. One moved east, with some descendants settling in what's now southern Ontario. The other branch—sometimes called the Southern Native Americans—rapidly moved south about 14,000 years ago, becoming the main ancestors of today's indigenous Central and South Americans.

Both papers also show that there wasn't just one migration southward.

The researchers behind the Cell study, led by Max Planck Institute geneticist Cosimo Posth, found evidence for two previously unknown populations that also entered South America. Both are closely related to the main line of Southern Native Americans, but they're distinct enough to show up separately within ancient peoples' DNA.

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More than 10,000 years ago, Native peoples in Brazil started interring their dead at Lapa do Santo. In 2014, excavations revealed the remains of this adult man.

One of these groups is represented by Andean peoples who seem closely related to ancient Native Americans who lived in California's Channel Islands. The other connects ancient Native Americans who had arrived in Brazil and Chile by 9,000 years ago to Anzick-1, a baby boy who lived in Montana about 12,800 years ago. Anzick-1 is especially important because he's associated with the North American Clovis culture. While this is the first genetic hint of possible Clovis influence in South America, current evidence firmly rules against this group being the main ancestors of today's South Americans.

The Science paper, led by Natural History Museum of Denmark researcher J. Víctor Moreno-Mayar, shows another unexpected dispersal. While his team also saw migrations into South America 14,000 years ago, they found signs that a group living in Mexico or Central America spread out 8,700 years ago into South America and northward into what is now the U.S. Great Plains.

“When you try to include present-day South Americans into the picture, what you need is an extra population movement,” Moreno-Mayar says. “We have very little idea of which population represents that gene flow; the only thing we know is that it's on the Native American side.”

How to live the high life

The third new study, published in Science Advances, zooms in on the Andes, the mountainous spine of western South America. Archaeological evidence shows that people started living permanently in the Andean highlands about 9,000 years ago. But these aren't the easiest places to live, since it's cold and the air is thin, which makes it harder for human bodies to absorb oxygen. So how did Andean peoples move into this region, and how did they adapt to the harsh conditions?

To find out, researchers led by Emory University anthropologist John Lindo sequenced the whole genomes of seven Natives who lived in Peru's highlands between 1,600 and 6,100 years ago. The team also collected dozens of DNA sequences from two modern Native populations: the Aymara in Bolivia's highlands, and the Huilliche-Pehuenche, who live in Chile's coastal lowlands.

Comparing these DNA sequences revealed that the Andes' lowland and highland peoples split about 8,750 years ago, give or take a few centuries. The team also found signs of evolution acting on the highland Andeans' DNA, such as an uptick in gene variants linked to stronger hearts. If this is an adaptation to high altitudes, then the Aymara's bodies took a different approach than other high-altitude groups. Native Tibetans, for instance, more commonly have gene variants that affect blood's ability to carry oxygen.

“That was a bit of a surprise to me,” says study coauthor Mark Aldenderfer, an archaeologist at the University of California, Merced. “What we see is convergent evolution: Here's an environmental challenge that people are confronted with in their genomes, and there appear to be multiple ways to [solve] that.”

Andean DNA also bears the scars of diseases that Europeans brought to the region in the 1500s. When compared to pre-contact Andeans' DNA, modern Aymara genomes show shifts in two immune genes, one of which is linked to smallpox. Lowland populations don't show this change, which may help explain another grim result: how much each population collapsed after European contact. The authors estimate that the highland Aymara lost about 27 percent of its population post-contact, but lowland groups shrank by 95 percent.

“The fact that these populations adapted to such harsh environments, like the high-altitude environment of the Andes, may have provided some protection against either the European explorers themselves or protection from the pathogens [they] brought in,” says study coauthor Anna Di Rienzo, a human geneticist at the University of Chicago.

More data, more puzzles

While the three studies add new details, they also raise new questions. For one, there's still some tension between the archaeological and genetic records, particularly over the rapid move into South America around 14,000 years ago.

“The implication is that if you’re moving that far, that fast, there wasn’t anybody home ... and yet we know that we have people in the Americas prior to this time,” says Southern Methodist University archaeologist David Meltzer, one of the Science study's coauthors. “The next obvious question is, what is the relationship between the groups that we're mapping here, and the ones that we only have hints of genetically and archaeologically?”

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Researchers carefully exhume the remains of ancient Native Americans at Lapa do Santo.

Researchers also got conflicting results related to Population Y, a “ghost” population first proposed to explain why some indigenous South Americans seem to have more Australasian ancestry than other Native Americans. Moreno-Mayar's paper shows signs of Population Y in South America at least 10,000 years ago. But the researchers who suggested Population Y in the first place—the authors of the Cell study—found that they didn't need this extra group to explain their latest results.

To know more, scientists say that they'll need even more data. To do that, teams are working closely with Native groups both to collect DNA from today's populations and to sample the ancient remains of living Natives' likely ancestors.

The Science study, for instance, includes the DNA of the Spirit Cave mummy, the remains of a man who lived and died in Nevada about 10,700 years ago. In 2016, geneticists confirmed that he was Native American, paving the way for the nearby Fallon Paiute-Shoshone tribe to reclaim the remains. Len George, the tribal chairman of the Fallon Paiute-Shoshone, is a coauthor on the new study.

Decades ago, this level of community engagement and consent-seeking was hardly the norm. Now, researchers say it's an ethical bar they must, and should, clear.

“We are unfortunately taught many incorrect ideas about them both in history classes and also implicitly in the media: that indigenous Americans are all but extinct, that their great cultural achievements are only in the past, or should be attributed to anyone other than their ancestors,” Raff says.

“An understanding of the history of indigenous peoples, from both scientific and indigenous perspectives, is one way of seeing past these messages and recognizing the incredible resilience and achievements of the peoples of the Americas.”