Ancient Infant's DNA Reveals New Clues to How the Americas Were Peopled

Her 11,500-year-old remains suggest that all Native Americans can trace their ancestry to the same founding population.

Around 11,500 years ago, at a place that is now called the Upward Sun River, in the region that has since been named Alaska, two girls died. One was a late-term fetus; the other, probably her cousin, was six weeks old. They were both covered in red ochre and buried in a circular pit, along with hunting weapons made from bones and antlers. “There was intentionality in the burial ceremony,” says Ben Potter from the University of Alaska at Fairbanks, who uncovered their skeletons in 2013. “These were certainly children who were well-loved.”

Now, several millennia after their short lives ended, these infants have become important all over again. Within their DNA, Potter’s team has found clues about when and how the first peoples came to the Americas.

They did so from East Asia—that much is clear. Today, Russia and Alaska are separated by the waters of the Bering Strait. But tens of thousands of years ago, when sea levels were lower, that gap was bridged by continuous land, hundreds of miles wide and covered in woodlands and meadows. This was Beringia. It was a harsh world, but you could walk across it—and people did.

The Upward Sun River infants, who have been named Xach’itee’aanenh T’eede Gaay” (Sunrise Girl-Child) and “Yełkaanenh T’eede Gaay” (Dawn Twilight Girl-Child) by the local indigenous community, were found at a crucial point along this route. Few human remains have been found from such a northerly or westerly part of the Americas, or from such an ancient time. “It’s hard to impress upon you how rare they are,” says Potter. “The window into the past that these children provide is priceless.”

By analyzing the older infant’s genome, Potter and his colleagues, including José Víctor Moreno Mayar and Lasse Vinner, have shown that she belonged to a previously unknown group of ancient people, who are distinct from all known Native Americans, past and present. The team have dubbed them the Ancient Beringians.

“We’d always suspected that these early genomes would have important stories to tell us about the past, and they certainly didn’t disappoint,” says Jennifer Raff from the University of Kansas, who was not involved in the study.

By comparing Xach’itee’aanenh T’eede Gaay’s genome to those of other groups, the team showed that the Ancient Beringians and other Native Americans descend from a single founding population that started to split away from other East Asians around 36,000 years ago. They became fully separated between 22,000 and 18,000 years ago, and then split into two branches themselves. One gave rise to the Ancient Beringians. The other gave rise to all other Native Americans, who expanded into the rest of the Americas. Native Americans, then, diverged into two more major lineages—a northern and a southern one—between 14,600 and 17,500 years ago.

This story unequivocally supports the so-called Beringian standstill hypothesis, “which for a long time has been the dominant explanation for how people initially peopled the Americas,” says Raff. This scenario says that the ancestors of Native Americans diverged from other East Asians at a time when ice was smothering the Northern Hemisphere. That left them stranded and isolated for millennia somewhere outside the Americas, for their eastward movements were blocked by a giant ice sheet that covered much of North America. Only when that sheet started melting, around 15,000 years ago, could they start migrating down the west coast of the Americas.

Xach’itee’aanenh T’eede Gaay’s genome anchors this narrative in time, suggesting that the millennia-long pit stop took place between 14,000 and 22,000 years ago. It doesn’t, however, say where those early peoples stood still.

In one scenario, they paused in Beringia itself and split into two lineages there. One, the Ancient Beringians, stayed put. The other eventually made it further east and south and gave rise to the other Native Americans. If that’s right, “there was just a single migration of people from Asia who peopled the New World,” says Connie Mulligan from the University of Florida. She and others have found further evidence for that idea, but “this study provides the final piece needed to prove there was only a single migration,” she says.

But Potter prefers an alternative scenario in which the standstill took place further back in northeast Asia, and the Ancient Beringians split from other Native Americans there. Both groups then independently traveled into Beringia and subsequently into the Americas, perhaps by different routes or perhaps at different times.

Partly, this debate hinges on a controversial archeological site at the Bluefish Caves in Canada’s Yukon Territory. A recent study says that animal bones from the site, which seem to bear traces of human cut-marks, are 24,000 years old. Raff accepts the Bluefish evidence; Potter doesn’t. If the marks really were made by humans, and really are that old, people must have been in Beringia by that point, and likely paused there. If they’re not ... the find doesn’t really rule out either hypothesis.

Either way, both scenarios can now be tested with future data from either ancient DNA or archaeological finds. And both scenarios argue against an attention-grabbing study from last year which claimed that hominids were in North America 130,000 years ago, based on the bones of a mastodon that had supposedly been butchered with nearby stone tools. “I am super skeptical about that,” says Potter. “Early modern humans aren’t even out of Africa at that point, so you’d be talking about, I don’t know, a Denisovan? And there are no Denisovans within 10,000 miles of that site.”

It’s also unclear what became of the Ancient Beringians. They have no obvious direct descendants, and the people who currently live at the Upward Sun River—the Athabascans—are descended from one of the other groups of Native Americans. It’s possible that the Athabascans may carry traces of Ancient Beringian ancestry, but it’s hard to say without analyzing their genomes.

Such work has had a troubled history. As I’ve written before, in the 1990s, Arizona State University scientists collected samples from the Havasupai tribe to study the genetics of diabetes but, without their knowledge, also used those samples to study schizophrenia, inbreeding, and migration patterns. When the Havasupai found out, they successfully sued the university for $700,000 and banned its researchers from their land.

Another bitter controversy surrounded the Ancient One—an 8,500-year-old skeleton that was discovered in Washington State, and became known as Kennewick Man in non-native circles. For almost two decades, five tribes pushed for the bones to be reburied, fighting against parties who disputed his native ancestry. After an analysis of his genome confirmed that he was indeed Native American, Barack Obama signed an order in December 2016 finally allowing him to be reburied. The five tribes were all invited to take part in future studies, but only the Colville tribe accepted. “We were hesitant,” their representative James Boyd told The New York Times. “Science hasn’t been good to us.”

Some of the scientists involved in sequencing the Ancient One’s genome also worked on the Upward Sun River study. “They’ve made progress in doing more consultative and consensual research,” says Kim TallBear from the University of Alberta, who studies the intersection of race and genetics and is a member of the Sisseton-Wahpeton Oyate tribe. But she’s also disinterested in the questions they are asking. “This type of research is done largely for the benefit of nonindigenous peoples,” she says. They center a “settler-colonial narrative” about a “largely one-way migration story into the Americas and the idea that everyone is in some form an immigrant.”

Indigenous peoples, TallBear says, have more complex narratives about their relationship with their lands, and their webs of obligation with each other and other animals. “I am interested in indigenous worldviews conditioning more scientific inquiry. What different questions might indigenous peoples ask of genomics?”

Potter says that he takes these concerns very seriously, and worked hard to keep a positive relationship with indigenous communities. Unlike in the case of the Ancient One, he made sure to get the support of the Athabascans before any work was actually done and any DNA was sequenced.

“I’m also interested in what they’re interested in,” he says. “What can we include in our analysis that we can give back to them?” For example, after learning how important salmon fishing is to the Athabascans, his team found evidence of humans using salmon at the Upward Sun River site—the earliest such evidence in the Americas. “The longevity of resource use in the past is highly relevant to people now,” he says.

That's the kind of insight that TallBear is after: not into how people got there, but how they actually lived. And given the two dead infants, those lives were likely harsh. “We don’t know the overall population but we can reasonably infer that it was relatively low—maybe 20 to 40 people,” says Potter. “To have these children die over one or two summers, in the season with the most abundance of resources, tells us something about risky and delicate nature of life in the far north.”