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South America was the last continent to be settled, and many scientists once assumed it was a rather straightforward affair. Ancient people descending from a mostly homogenous population were thought to have expanded into the continent about 15,000 years ago—relatively recently in the span of human history—learned to live in diverse environments including the deep jungle and windswept altiplano, and then more or less stayed put.

But a study published today in Nature reveals these migrations were anything but simple. Examining ancient and modern genomes collected from across South America and beyond, the team found that genetically diverse groups populated the continent in at least three separate pulses. And some people or communities carried with them possibly advantageous genes acquired from long-ago Australasian ancestors.

“The genetic diversity present before colonialism is largely lost,” making it harder for scientists to appreciate South America’s complicated population history, says Cosimo Posth, an archaeogeneticist at the University of Tübingen who wasn’t involved with the Nature paper. So working to resurface even pieces of that diversity “is an extremely important effort.” His team published a complementary study today in Current Biology, finding evidence of unexpected genetic diversity and otherwise invisible migrations in 52 ancient genomes from Argentina and Uruguay.

In the Nature study, Tábita Hünemeier, a geneticist at the University of São Paulo and the Institute of Evolutionary Biology, collaborated with researchers and Indigenous communities across Latin America to sequence 128 whole genomes from living people from north Mexico to southern Argentina. The team then analyzed them alongside existing databases and previously published ancient genomes.

Previous work had identified the first two waves of settlement in South America, the earliest of which included people related to the Anzik child, who was buried in Montana 12,700 years ago. A second dispersal followed about 9000 years ago and ultimately contributed more to the genomes of most ancient and modern South Americas, including those Posth studied.

Hünemeier and her team found evidence of a third dispersal, whose genetic signature first appears in their data about 1300 years ago and then spreads widely across the continent and even into the Caribbean. The newcomers show hints of being related to Mesoamericans from Mexico and Central America, but so far, researchers don’t know exactly where they came from or who were their closest relatives. “Without the source population and more direct evidence [of a third pulse] from ancient DNA, it’s hard to really wrap our heads around” how and when a third migration might have happened, Posth says.

The study also digs deeper into a mystery that has bedeviled the genetic history of the Americas for over a decade: How did traces of Australasian ancestry end up in some ancient and modern South American genomes? Genetic variants from this lineage make up only about 2% of ancestry in the people who carry it, but that proportion has stayed remarkably consistent over the past 10,000 years. “This signal is found again and again and again,” Posth says. “It must mean something.”

Hünemeier suspects people carrying this ancestry were among several distinct populations that lived for thousands of years in Beringia, the now-drowned landmass that connected eastern Siberia to Alaska, and that it eventually spread southward into the Americas from there. (This Australasian ancestry, sometimes known as Population Y or the Ypykuéra signal after the Tupi word for “ancestor,” is different from the genetic sequences some Polynesian populations share with South American ones. Scientists continue to debate how that more recent gene flow happened—for example, whether Polynesian voyagers may have reached western South America about 800 years ago—but the findings from the Nature paper have no bearing on that mystery.)

Hünemeier’s team is also the first to look at whether the genes inherited from ancient Australasian ancestors would have conveyed any benefits. The researchers found at least some of these genes relate to fertility and immune response and appear to have undergone natural selection. That suggests they might have provided an evolutionary advantage in certain circumstances. If so, it could explain why people retained these genes over such a long period of time, Hünemeier says, but she emphasizes that hypothesis needs more testing.

“This adds a step forward,” Posth says, even if “it’s not the end of the story.”

Lizzie Wade is a contributing correspondent for Science based in Mexico City. She covers archaeology and anthropology, with a focus on the Americas. Her work for Science has won awards from the Society for American Archaeology and the American Geophysical Union, and her reporting has been supported by the Pulitzer Center. Lizzie is the author of the book Apocalypse: How Catastrophe Transformed Our World and Can Forge New Futures (Harper, 2025). Her work has also appeared in Archaeology, Slate, Smithsonian, The New York Times, and Wired, among others.

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