Lost Native American Ancestor Revealed in Ancient Child’s DNA

A baby girl who lived some 11,500 years ago survived for just six weeks in the harsh climate of central Alaska, but her brief life is providing a surprising and challenging wealth of information to modern researchers.

Her genome is the oldest-yet complete genetic profile of a New World human. But if that isn’t enough, her genes also reveal the existence of a previously unknown population of people who are related to—but older and genetically distinct from— modern Native Americans.

This new information helps sketch in more details about how, when, and where the ancestors of all Native Americans became a distinct group, and how they may have dispersed into and throughout the New World.

The baby’s DNA showed that she belonged to a population that was genetically separate from other native groups present elsewhere in the New World at the end of the Pleistocene. Ben Potter, the University of Alaska Fairbanks archaeologist who unearthed the remains at the Upward River Sun site in 2013 , named this new group “Ancient Beringians.”

The discovery of the baby’s bones, named Xach'itee'aanenh T'eede Gaay, or Sunrise Child-Girl in a local Athabascan language, was completely unexpected, as were the genetic results, Potter says.

Found in 2006 and accessible only by helicopter, the Upward River Sun site is located in the dense boreal forest of central Alaska’s Tanana River Valley. The encampment was buried under feet of sand and silt, an acidic environment that makes the survival of organic artifacts exceedingly rare. Potter previously excavated the cremated remains of a three-year-old child from a hearth pit in the encampment, and it was beneath this first burial that the six-week-old baby and a second, even younger infant were found.

A genomics team in Denmark, including University of Copenhagen geneticist Eske Willerslev, performed the sequencing work on the remains, comparing the child’s genome with the genes of 167 ancient and contemporary populations from around the world. The results appeared today in the journal Nature.

“We didn’t know this population even existed,” Potter says. “Now we know they were here for many thousands of years, and that they were really successful. How did they do it? How did they change? We now have examples of two genetic groups of people who were adapting to this very harsh landscape.”

The genetic analysis points towards a divergence of all ancient Native Americans from a single east Asian source population somewhere between 36,000 to 25,000 years ago—well before humans crossed into Beringia, an area that includes the land bridge connecting Siberia and Alaska at the end of the last ice age. That means that somewhere along the way, either in eastern Asia or in Beringia itself, a group of people became isolated from other east Asians for about 10,000 years, long enough to become a unique strain of humanity.

The girl’s genome also shows that the Beringians became genetically distinct from all other Native Americans around 20,000 years ago. But since humans in North America are not reliably documented before 14,600 years ago, how and where these two groups could have been separated long enough to become genetically distinct is still unclear.

The new study posits two new possibilities for how the separation could have happened.

The first is that the two groups became isolated while still in east Asia, and that they crossed the land bridge separately—perhaps at different times, or using different routes.

A second theory is that a single group moved out of Asia, then split into Beringians and ancient Native Americans once in Beringia. The Beringians lingered in the west and interior of Alaska, while the ancestors of modern Native Americans continued on south some time around 15,700 years ago.

“It’s less like a tree branching out and more like a delta of streams and rivers that intersect and then move apart,” says Miguel Vilar, lead scientist for National Geographic’s Genographic Project. “Twenty years ago, we thought the peopling of America seemed quite simple, but then it turns out to be more complicated than anyone thought.”

John Hoffecker, who studies the paleoecology of Beringia at the University of Colorado-Boulder, says there is still plenty of room for debate about the geographic locations of the ancestral splits. But the new study fits well with where the thinking has been heading for the last decade, he adds.

“We think there was a great deal more diversity in the original Native American populations than is apparent today, so this is consistent with a lot of other evidence,” Hoffecker says.

However, that same diversity—revealed through research on Native American cranial morphology and tooth structure—creates its own dilemma. How does a relatively small group of New World migrants, barricaded by a challenging climate with no access to fresh genetic material, evolve such a deep bank of differences from their east Asian ancestors? It certainly doesn’t happen over just 15,000 years, Hoffecker insists, referring to the estimated date of divergence of ancient Native Americans from Beringians.

“We’ve been getting these signals of early divergence for decades—the first mitochondrial work in the 1990s from Native Americans were coming up with estimates of 30, 35, even 40,000 years ago,” Hoffecker says. “They were being dismissed by everybody, myself included. Then people began to suspect there were two dates: one for divergence, and one for dispersal, and this study supports that.”

“Knowing about the Beringians really informs us as to how complex the process of human migration and adaptation was,” adds Potter. “It prompts the scientist in all of us to ask better questions, and to be in awe of our capacity as a species to come into such a harsh area and be very successful.”