The Nature paper “Genetic evidence for two founding populations of the Americas” has a remarkable abstract.
Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia) Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
The Smithsonian goes into more detail.
Genetic studies have since connected both these ancient and modern humans to ancestral populations in Eurasia, adding to the case that a single migratory surge produced the first human settlers in the Americas. Aleutian Islanders are a notable exception. They descend from a smaller second influx of Eurasians 6,000 years ago that bear a stronger resemblance to modern populations, and some Canadian tribes have been linked to a third wave.
[David] Reich’s group had also previously found genetic evidence for a single founding migration. But while sifting through genomes from cultures in Central and South America, Pontus Skoglund, a researcher in Reich’s lab, noticed that the Suruí and Karitiana people of the Amazon had stronger ties to indigenous groups in Australasia—Australians, New Guineans and Andaman Islanders—than to Eurasians.
Other analyses haven’t looked at Amazonian populations in depth, and genetic samples are hard to come by. So the Harvard lab teamed up with researchers in Brazil to collect more samples from Amazonian groups to investigate the matter. Together they scrutinized the genomes of 30 Native American groups in Central and South America. Using four statistical strategies, they compared the genomes to each other and to those of 197 populations from around the world. The signal persisted. Three Amazonian groups—Suruí, Karitiana and Xavante—all had more in common with Australasians than any group in Siberia.
The DNA that links these groups had to come from somewhere. Because the groups have about as much in common with Australians as they do with New Guineans, the researchers think that they all share a common ancestor that lived tens of thousands of years ago in Asia but that doesn’t otherwise persist today. One branch of this family tree moved north to Siberia, while the other spread south to New Guinea and Australia. The northern branch likely migrated across the land bridge in a separate surge from the Eurasian founders. The researchers have dubbed this hypothetical second group “Population y” for ypykuéra, or “ancestor” in Tupi, a language spoken by the Suruí and Karitiana.
When exactly Population y arrived in the Americans remains unclear—before, after or simultaneously with the first wave of Eurasians are all possibilities. Reich and his colleagues suspect the line is fairly old, and at some point along the way, Population y probably mixed with the lineage of Eurasian settlers. Amazonian tribes remain isolated from many other South American groups, so that’s probably why the signal remains strong in their DNA.