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Ancient genomics is recasting the story of the Americas’ first residents

Trove of DNA from prehistoric inhabitants reveals that the continents’ early settlers moved far and fast.

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An ancient arrowhead that belonged to people associated with the Clovis culture, an early group of settlers in the Americas.

An ancient arrowhead that belonged to people associated with the Clovis culture, an early group of settlers in the Americas.Credit: Carolina Biological Supply Co/Visuals Unlimited/SPL

Ancient genomics is finally beginning to tell the history of the Americas — and it’s looking messy.

An analysis of genomes from dozens of ancient inhabitants of North and South America, who lived as long ago as 11,000 years — one of the largest troves of ancient DNA from the region studied so far — suggest that the populations moved fast and frequently. The findings were published on 8 November in Cell1 and Science2.

The studies suggest that North America was widely populated over a few hundred years, and South America within one or two thousand years by related groups. Later migrations on and between the continents connected populations living as distantly as California and the Andes.

“These early populations are really blasting across the continent,” says David Meltzer, an archaeologist at Southern Methodist University in Dallas, Texas, who co-led the Science study.

The studies also suggest that prehistory of the Americas — the last major land mass to be settled — was just as convoluted as that of other parts of the world.

“I think this series of papers will be remembered as the first glimpse of the real complexity of these multiple peopling events,” says Ben Potter, an archaeologist at the University of Alaska Fairbanks. “It’s awesome.”

Archaeological guesswork

For decades, the peopling of the Americas was painted in broad brushstrokes, using data from archaeological finds and DNA from modern humans.

Scientists discerned that groups crossed the Bering land bridge from Siberia into present-day Alaska and then moved steadily south as the last Ice Age ended. Humans carrying artefacts from a culture known as Clovis, including sophisticated projectile points, began to populate the interior of North America around 13,000 years ago. For decades, researchers thought that people associated with this culture were the continents’ first inhabitants.

But the discovery of ‘pre-Clovis’ settlements — including a nearly 15,000-year-old site at the southern tip of Chile — pointed to an even earlier wave of migration to the Americas, presumably also over the Bering land bridge.

The first ancient-DNA studies from the region, the first of which were published in 2014, began to add detail to this picture. The genome of a baby boy buried roughly 12,700 years ago in Montana alongside Clovis artefacts3, and genomes from other ancient individuals4, hinted at two early populations of Native Americans.

The Montana baby, known as the Anzick boy, belonged to a population known as the Southern Native Americans, who are most closely related to present-day Indigenous populations from South America. They split from Northern Native Americans, who are genetically closer to many contemporary groups in eastern North America, around 14,600–17,500 years ago. The common ancestor of these two groups split from East Asians some 25,000 years ago, scientists established this year by sequencing the genome of 11,500-year-old human remains from Alaska5.

But this timeline was based on a small number of ancient genomes from the Americas, and scientists expected that further data would paint a much more detailed and complex picture of the continents’ early history, as well as reveal later migrations in the region.

Excavators at Jiskairumoko

Excavators at a burial place in Jiskairumoko, an archaeological site in Peru.Credit: Mark Aldenderfer

Same genes, far apart

The two latest studies include genome data from 64 ancient Americans, including more than a dozen specimens older than 9,000 years.

They also provide the first detailed look at the ancient inhabitants of Central and South America and their early movements into the region.

To chart these migrations, Meltzer and his colleague Eske Willerslev, a palaeogeneticist at the University of Copenhagen and the University of Cambridge, UK, compared genetic data from the 12,700-year-old Anzick boy with genome sequences from 10,700-year-old remains from a Nevada cave and 10,400-year-old remains from southeastern Brazil.

The genomes were remarkably similar, despite the great distance between them, Willerslev says, pointing to a rapid population expansion from Alaska. “As soon as they get south of the continental ice caps, they’re exploding and occupying the land,” he says.

An independent team led by David Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts, also found evidence1 for a rapid expansion into South America, through analysing 49 ancient genomes from Central and South Americans. These included a 9,300-year-old individual from Belize, a 9,600-year-old from southeastern Brazil and 10,900-year-old remains from Chile.

Both teams documented multiple later human migrations into South America. For instance, Reich’s team found that the genetic signal of the earliest inhabitants, closely related to the Anzick boy, had largely vanished from later South Americans, suggesting that different groups had by then moved in from the north.

Reich and his colleagues also found a perplexing connection between a 4,200-year-old human in the Central Andes and ancient inhabitants of the Channel Islands off the coast of California. The team does not think that humans migrated directly between these two regions — but instead that they are linked by migrations by a population that was once more widespread.

Gaps down under

Potter says that the main conclusions of the two papers are broadly consistent, painting a nuanced picture that will become clearer with more data. “Complex and realistic are the two adjectives I would use,” he says.

Even with dozens more newly discovered ancient genomes from the Americas, researchers are still probably missing important aspects of the region’s population history, says Reich. “There are many dots that are not filled in,” he says. “I think as these studies scratch the surface, they make things more, rather than less, complicated.”

For instance, the earliest migrations deduced by the researchers seem to have involved people associated with the Clovis culture, but Meltzer wonders what became of humans associated with pre-Clovis sites. “If you’re moving that far that fast across space, there probably wasn’t anybody else in the way.”

Another lingering mystery surrounds a 2015 discovery, made independently by both Reich’s6 and Willerslev’s7 teams, that some modern inhabitants of the Amazon seem to share genetic ancestry with Australasian groups that include both the Papua New Guineans and Aboriginal Australians. Reich posited that this commonality points to a hitherto unknown migration to the Americas that vanished from all but the most isolated groups in the Amazon.

But Reich is now questioning that hypothesis because his team did not find significant evidence of Australasian ancestry in any of the ancient South and Central American genomes it analysed.

Willerslev, however, did link the genome of the 10,400-year-old individual from southeastern Brazil to an Australasian lineage. The finding has him wondering if there were migrations to the Americas that predated even those behind the pre-Clovis sites. “I think we are in for major surprises,” he says.

Jennifer Raff, an anthropological geneticist at the University of Kansas in Lawrence, says that the emerging picture of the Americas is less a revision of the earlier models, and more of an elaboration. “It’s not that everything we know is getting overturned. We’re just filling in details,” she says. “We’re now moving to a much more detailed, much more accurate and richer history. That’s where the field was always going, and it’s nice to be there now.”

Nature 563, 303-304 (2018)

doi: 10.1038/d41586-018-07374-1
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Updates & Corrections

  • Correction 09 November 2018: The lead image in this story has been replaced; the original image was incorrectly labelled as an arrow point from the Clovis culture.

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