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Ancient baby’s DNA reveals completely unknown branch of Native American family tree

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The genome of an infant buried 11,500 years ago reveals a newly discovered group of ancient people

The excavation at the Upward River Sun site in Alaska.
The excavation at the Upward River Sun site in Alaska.
Photo by Ben Potter

An Alaskan baby buried 11,500 years ago has clued scientists in to a forgotten branch of the Native American family tree. This child’s DNA is more genetically ancient than the ancestors of modern Native Americans — so it must have come from a previously unknown, even earlier population, the study says.

By analyzing the infant’s genome, researchers from the University of Alaska Fairbanks and the University of Copenhagen found that while all ancient Native Americans originated in East Asia, the family tree branched roughly 20,000 years ago. One group — the infant’s group, now named the Ancient Beringians — lived in the frozen north and eventually disappeared. The other moved south, splitting yet again roughly 15,000 years ago into two distinct populations that peopled North and South America.

We already knew the broad strokes of this story: ancient humans from Siberia probably crossed the Bering land bridge into Alaska sometime before 15,000 years ago. These ancient humans then spread, giving rise to most of the indigenous peoples of the Americas. Today’s study, published in the journal Nature, helps fill in more details about the genetic origins of Native Americans — and reveals a newly discovered group of ancient people.

“If you could ask for ancient DNA for Christmas, this is what you would ask for,” says Joshua Schraiber, a population geneticist at Temple University who did not take part in the study. “It gives you a much better window into population structure back then.”

In 2010, archaeologists led by Ben Potter at the University of Alaska Fairbanks unexpectedly discovered the ancient, cremated remains of a 3-year-old child at an archaeological site in central Alaska, called Upward Sun River. About a meter beneath the hearth, two infants were also buried in a circular pit filled with grave goods, including blades and hunting tools. Today’s study involves DNA extracted from one of the babies found in that pit in 2013.

The excavation of one of the ancient infants buried at the Upward River Sun site in Alaska.
The excavation of one of the ancient infants buried at the Upward River Sun site in Alaska.
Photo by Ben Potter

From their bones, the researchers estimated that one of the infants in the burial pit had been about six weeks old when it passed away, and the other was likely stillborn. Radiocarbon dating revealed that all three were roughly 11,500 years old. “We’re very lucky to have these preserved,” Potter says. “We’re treating them very respectfully and letting them provide a window into their prehistory, and past, and lifeways in ways that are unparallelled.”

Now, a team of scientists led by ancient DNA specialist Eske Willerslev at the University of Copenhagen has sequenced the complete genome of the 6-week-old infant — named “Xach’itee’aanenh T’eede Gaay” (sunrise girl-child) by the local indigenous community. The DNA of the other children had degraded too much for a full sequence, although there was enough to determine that the two babies buried together may have been cousins.

By comparing the ancient infant’s genome to those collected from other ancient and modern people, the team was able to reconstruct how it fit into the human family tree. They discovered that this infant was related to the founding population of Native Americans that originated in Siberia.

Adding this new clue to computer simulations of the peopling of North America helped the team flesh out the timeline — which they now suspect goes something like this: about 36,000 years ago in northeast Asia, the ancestors of modern Native Americans began splitting off from ancestral Asians. They continued to mingle and swap genes with other Asian populations until roughly 25,000 years ago, when they became genetically cut off from the rest of Asia.

Here’s where it gets a little murky: today’s study shows that around 20,000 years ago, the Ancient Beringians branched off from the ancestors of modern Native Americans. But the researchers don’t know where exactly that Ancient Beringian split happened: it might have been in Siberia. If so, then the two populations then migrated separately into the New World. It’s also possible, though, that a single founding population may have migrated into Beringia and lingered there long enough for the two lineages to branch apart. The Ancient Beringians then stayed in the icy north, and the ancestors of modern Native Americans moved south to eventually people North and South America.

The findings show that even one new genome can reshape our understanding of ancient human history, says Joshua Akey, a professor of evolutionary genomics at Princeton University who was not involved in the research. “It shows the power of ancient DNA — how much of our history is written in our DNA.”

These two hypotheses still need to be tested with archaeology, genetics, and new human remains — if they’re discovered. “This just opens up doors that hardly ever get opened, to understand in real, meaningful ways the ancient past,” Potter says. “It's all part and parcel with the human experience. But I have to say, I did not expect that it would be as rich and rewarding as it has been.”