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

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

An ancient arrowhead that belongs 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.

An analysis of the genetics from the ancient inhabitants of North and South America. 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 archeologist at Southern Methodist University in Dallas, Texas, who co-led the Science study.

The studies also suggest the prehistory of the Americas – the last major mass of the world.

"I believe this series of papers will be remembered as the first glimpse of the real complexity of these multiple peopling events," says Ben Potter, an archeologist at the University of Alaska Fairbanks. "It's awesome."

Archaeological guesswork

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

Scientists discerned that groups the Bering land bridge from Siberia into present-day Alaska and then moved steadily south as the last Ice Age ended. Humans carrying artfacts 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 the pre-Clovis' settlements – including a nearly 15,000-year-old site at the southern tip of Chile, presumably also over the Bering land bridge.

The first ancient DNA from the region, the first of which were published in 2014, started to add detail to this picture. 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, belongs to the Southern Native Americans, which are closely related to present-day. 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 the East of the 25,000 years ago, scientists established this year by sequencing the genome of 11,500-year-old human remains from Alaska5.

But this timeline is a small number of the most recent and the most recent.

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 look at the ancient inhabitants of Central 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 in 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. They're exploding and occupying the land, "he says.

An independent team led by David Reich, a 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 the genetic signal of the earliest inhabitants, closely related to the Anzick boy, had largely vanished from the later South Americans.

Reich and his colleagues also found a perplexing connection between a 4,200-year-old human in the Central andes 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.

Gaps down under

This picture will be clearer with more data. "I would use," he says.

Even with the oldest genomes from the Americas, says Reich. "There are many dots that are not filled in," he says. "I think these 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 been associated with the Clovis culture, but Meltzer wonders what became of humans associated with pre-Clovis sites. "If you're moving that fast across the space, there was probably no otherbody else in the way."

Another lingering mystery surrounds at 2015 discovery, made independently by both Reich's6 and Willerslev's7 Amazon, that seems to be a genetic ancestry with Australasian groups that includes both the Papua New Guineans and Aboriginal Australians. Reich posited this commonality to 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 been 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 the emerging picture of the Americas is 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 are now moving to a much more detailed and richer history. "That's where the field was always going".

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