Native Americans who live between the Artic and the southern tip of Chile are thought to have descended from Siberians who crossed the Bering land bridge from the Asian continent some 15,000 years ago. They are the so-called First Americans. But was there just one migration wave or were there multiple founding populations? Two major papers published this week take completely different views, though they’re now working together to see if their data and interpretations can be reconciled.

Both studies uncovered a genetic link between Native Americans living in the Amazon today and indigenous groups in Australasia, which includes Australia, New Guinea, and nearby islands in the Pacific. However, according to the Science study, which examined ancient and modern genomes, there was a single wave into the Americas, and the genetic link with Australasia was due to more recent gene flow events. Meanwhile, the Nature study, which compares the DNA of modern populations worldwide, found a second, previously unknown wave of migration from Australasia by the mysterious Population Y, which vanished in the ensuing millennia. 

^{Origins and population history of Native Americans based on Raghavan et al. Science 2015.}

The team led by University of Copenhagen and University of California at Berkeley researchers sequenced and compared the genomes of present-day Native Americans, Siberians, and tropical Pacific islanders with ancient American genomes spanning 200 to 6,000 years in age.

They estimate that ancestral Native Americans migrated from Siberia to the Americas no earlier than 23,000 years ago. Though, they may have spent as long as 8,000 years in isolation in the Bering Strait area before arriving. Then, around 13,000 years ago, this ancestral group split into two branches: Their descendants are the Athabascans of North America and the Amerindians who are dispersed across both continents. This diversification coincided with melting glaciers and the creation of pathways into the interior. 

Since they found no evidence for multiple waves of entry, the team thinks that the genetic differences that we see among Native American populations today are the result of events after this initial wave. This subsequent gene flow may explain why some Native Americans share ancestry with present-day East Asians (including Siberians) and Australasians.

"It's a surprising finding and it implies that New World populations were not completely isolated from the Old World after their initial migration," University of Copenhagen’s Eske Willerslev says in a statement. "We cannot say exactly how and when this gene flow happened, but one possibility is that it came through the Aleutian Islanders living off the coast of Alaska."

^{Deep genetic affinities between Amazonian populations in South America and Australasians. Warmer colors indicate stronger affinities. Pontus Skoglund/Harvard Medical School.}

Meanwhile, a group led by Harvard Medical School researchers analyzed publicly available genetic data from Native American populations in Central and South America today, and then compared these with the genomes of people from nearly 200 populations outside of the Americas.

Amazonians, they found, bear an unexpected genetic connection to indigenous people in Australasia. In particular, the ancestor of the Tupí-speaking Suruí and Karitiana and the Ge-speaking Xavante of the Amazon was more closely related to indigenous Australasians than to any other population today: About two percent of their ancestry comes from this Australasian lineage.

This ancestor didn’t seem to leave a trace in other Native American groups in South, Central, or North America, and no match was found in any population that’s known to have contributed to Native American ancestry. The team named the mysterious ancestral group Population Y, after "Ypykuéra," which means ancestor in Tupí. After they crossed the Bering land bridge, Population Y disappeared in the millennia that followed.

"We’ve done a lot of sampling in East Asia and nobody looks like this," Harvard’s Pontus Skoglund says in a statement. "It’s an unknown group that doesn’t exist anymore." The team thinks that this ancestry may be as old as the First Americans. They both headed south from the ice sheets to become the two founding populations of the Americas.