A new study, published in the journal Nature, shows that some Amazonian Native Americans descend partly from a Native American population that carried ancestry more closely related to the indigenous peoples of Australasia – Australians, New Guineans and Andaman Islanders – than to any present-day Native Americans or Eurasians.

“It’s incredibly surprising. There’s a strong working model in archaeology and genetics, of which I have been a proponent, that most Native Americans today extend from a single pulse of expansion south of the ice sheets – and that’s wrong. We missed something very important in the original data,” said study senior author Prof David Reich of Harvard Medical School.

Previous studies have shown that Native Americans from the Arctic to the southern tip of South America can trace their ancestry to a single population called the First Americans, who came across the Bering land bridge about 15,000 years ago. The new study indicates that there’s more to the story.

Prof Reich and his colleagues analyzed genetic information from 21 Native American populations from Central and South America.

The scientists also collected and analyzed DNA from nine additional populations in Brazil.

They then compared those genomes to the genomes of people from about 200 non-American populations.

The Tupí-speaking Suruí and Karitiana and the Ge-speaking Xavante of the Amazon had a genetic ancestor more closely related to indigenous Australasians than to any other present-day population.

This ancestor doesn’t appear to have left measurable traces 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 genetic markers from this ancestor don’t match any population known to have contributed ancestry to Native Americans, and the geographic pattern can’t be explained by post-Columbian European, African or Polynesian mixture with Native Americans,” Prof Reich and co-authors said.

“The ancestry is much older, perhaps as old as the First Americans. In the ensuing millennia, the ancestral group has disappeared,” said study first author Dr Pontus Skoglund of Harvard Medical School.

“We’ve done a lot of sampling in East Asia and nobody looks like this. It’s an unknown group that doesn’t exist anymore.”

The researchers named the mysterious ancestor Population Y, after the Tupí word ‘Ypykuéra’ (ancestor).

“Population Y and First Americans came down from the ice sheets to become the two founding populations of the Americas. We don’t know the order, the time separation or the geographical patterns,” Dr Skoglund said.

“About 2% of the ancestry of Amazonians today comes from this Australasian lineage that’s not present in the same way elsewhere in the Americas,” Prof Reich said.

“However, that doesn’t establish how much of their ancestry comes from Population Y.”

If Population Y were 100% Australasian, that would indeed mean they contributed 2% of the DNA of today’s Amazonians.

But if Population Y mixed with other groups such as the First Americans before they reached the Americas, the amount of DNA they contributed to today’s Amazonians could be much higher – up to 85 %.

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Pontus Skoglund et al. Genetic evidence for two founding populations of the Americas. Nature, published online July 21, 2015; doi: 10.1038/nature14895