Genetics Rewrites the History of Early America—And, Maybe, the Field of Archaeology

The genome of an infant from Upward Sun River, Alaska offers tantalizing insight into the story of human migration

A scientific illustration of the Upward Sun River camp in what is now Interior Alaska. Illustration by Eric S. Carlson in collaboration with Ben A. Potter

The story of how Homo sapiens spread from Africa to the rest of the world is a tangled epic, full of false starts and dead ends. Yet perhaps nowhere is the puzzle more difficult than in the Americas, two landmasses divided from the rest of the world by two huge oceans. Zoom out, though, and you’ll see that isolation has only been imposed for the last 11,000 years; before then, a narrow land bridge called Beringia stretched between Siberia and Alaska, providing an icy highway for travelers.

This week, scientists reported explosive new findings on the genetic story of one of those ancient travelers: an infant girl named Xach’itee’aanenh T’eede Gaay by the local indigenous people, who lived for a brief time 11,500 years ago in an Alaskan community now called Upward Sun River. The infant’s genome has the power to rewrite what we know about the human journey into North America—and in doing so, points to the larger genetic revolution that is reshaping the field of archaeology.

For decades, archaeologists have hypothesized that humans entered the Americas from Asia using Beringia (the first man to suggest the existence of a land bridge was actually a 16th-century Spanish missionary named Fray Jose de Acosta). But even as more sites of occupation were discovered in Siberia and Alaska, pointing to human occupation and the movement from west to east, questions remained. When exactly did the migration happen, and how did it happen? In one wave, or many?

In January 2017, researchers at the Canadian Museum of History concluded that a horse jawbone found in the Bluefish Caves of the Yukon bore human markings from 24,000 years ago, meaning that early Americans had settled here by 22,000 BC. That would push back the date of human occupation in North America by 10,000 years. But those findings—like so many in this field—proved controversial, and haven’t been universally accepted by the archaeology community.

The new report on Xach’itee’aanenh T’eede Gaay complicates this narrative further. While she may be “just” 11,500 years old, she provides incontrovertible evidence for the timing of human migration.

Within her genome is the story of a newly discovered population of early Americans whose ultimate fate remains a mystery, as their genes are no longer visible in modern populations. “This individual represents a previously unknown population, which is also the earliest known population of Native Americans,” says Eske Willerslev, an evolutionary geneticist and one of the authors of the new study. “We can address fundamental questions such as when people came into North America because this population is related to everyone else.”

The Upward Sun River girl, buried next to an even younger infant in a ceremonial grave with red ochre on both of them, is a member of what researchers are calling the Ancient Beringians. Prior to sequencing her genome, scientists had identified two main groups of Native Americans: Northern Native Americans and Southern Native Americans, who split off sometime after entering the continent. This infant child belongs to neither of those two groups. That means that, somewhere along the way, another split must have occurred to create this unique Ancient Beringian group.

Using demographic modeling, the researchers concluded that the founding population of Native Americans began splitting from their ancestors in East Asia around 36,000 years ago. By 25,000 years ago, they had made a complete split. By 20,000 years ago, another divergence had happened, this time between the Ancient Beringians and the rest of the Native Americans. And within the next 3,000 to 6,000 years, the Native Americans further divided into Northern and Southern groups.

All this, from the ancient DNA of one long-dead child.

Genetics Rewrites the History of Early America—And, Maybe, the Field of Archaeology
Members of the archaeology field team watch as University of Alaska Fairbanks professors Ben Potter and Josh Reuther excavate at the Upward Sun River site. courtesy Ben Potter

“Now we have these bounds on the formation of Native Americans,” says Victor Moreno Mayar, another author of the paper and geneticist at the Center for GeoGenetics. “We think the explanation for this pattern, the one that requires the least movement, was that Native Americans were somewhere in Beringia 20,000 years ago. The best supported archaeological site in Alaska is only 15,000 years old, so we’re pushing the dates back, and it will be controversial because of this.”

The authors were well aware of the possibility for controversy going into the study. To that end, they included two different models to explain how the Ancient Beringians came to be. In one version, the Beringians split from the rest of the Native Americans before crossing the land bridge into North America, meaning multiple waves of migration. In the second, the group traveled across Beringia as one group, only splitting afterwards. Archaeologist Ben Potter, one of the authors, favors the former.

“I tend to support that on the archaeological side because that fits with the vast majority of archaeological evidence we have,” says Potter, who has worked at the Upward Sun River site since 2006 and was the one who discovered the children in 2013. “It’s not just a lack of sites [on Beringia and North America], it’s also the presence of a robust dataset of sites that shows a clear expansion from northeast Asia into the Aldan region, into northeast Siberia, and then finally into Beringia at around 14,500.”

But how can two such different scientific interpretations coexist side by side? Welcome to the real struggle with the story of human history: the question of whose facts come first, those of archaeologists or those of geneticists. As Potter puts it, genetics provides information about the populations and their splits, while archaeology points to the physical location of these populations and how they interacted with their environment. 

Today, scientists find themselves having to incorporate these two strands of information in ways that don't always seem to agree. 

“We should remember that the earliest proven trace of human activity in eastern Beringia dates to around 14.1-thousand-years-ago, making the Upward Sun River site nearly 3,000 years too young to be representative of the initial human colonization of the New World,” said archaeologist Brian T. Wygal of Adelphi University by email. “Based solely on the archaeological data, human variability in the late Pleistocene was already quite diverse by the time of the Upward Sun River child burials.”

Geneticist and archaeologist Dennis O’Rourke of the University of Kansas, whose lab sequenced the mitochondrial DNA of the Upward Sun River infants several years ago but wasn’t involved in this study, agrees that there are some growing pains in the field now that archaeology and genetics are becoming more mixed.

“It’s a continuing challenge to figure out how to integrate these different types of data and ways of approaching the past,” O’Rourke says. “Questions can be raised [with this paper] where the archaeological and the genetic data might point to different geographic populations, but I think those will ultimately be resolved with more archaeological and genomic data from different geographic regions.”

This isn’t the first time such questions have been raised. As East Asian historian Nicola Di Cosma writes for the Institute of Advanced Study, “The tendency to explain the distribution of genes according to assumed patterns of behavior of certain peoples and societies is quite common in ancient DNA studies. Ultimately, these assumptions go back to historical, anthropological, and archaeological models, and sometimes not the best of them.”

That leads to the other issue with this new research: it relies on a single sample. “We could know something about the extent of diversity in this early Beringian population with greater certainty if we had multiple genomes,” O’Rourke says.

Di Cosma is even more blunt. “The samples from which the ancient DNA information is extracted are miniscule: how relevant are they to population movements across Eurasia over a couple of millennia?” he writes.

But ancient remains are exceedingly rare, and even when they’re found, using them for science is fraught with ethical complications. Perhaps most well known is the Kennewick Man, a 9,000-year-old man discovered in Washington who ignited a legal battle between scientists and local indigenous groups who wanted to rebury him. Willerslev ultimately used DNA samples to prove the genetic link between the ancient skeleton and modern Native Americans, allowing him to be returned under the Native American Graves Protection and Repatriation Act.

Potter and the rest of the team worked hard to avoid any missteps in their analysis of the Upward Sun River children, cooperating with the local tribes before doing any testing and trying to answer questions they might be interested in. reached out to the Tanana Chiefs Conference, a consortium of 42 member tribes in Alaska that includes the region where Upward Sun River is located, but didn’t receive a response before publication.

The team's analysis has already uncovered fascinating insights. For instance, findings from Upward Sun “represents the first evidence of human use of salmon in the New World,” Potter says. “One of the elements we can develop through the bones is that we want to look at the mother’s diet and potential changes through time that might let us understand if people were storing salmon over the winter.”

In the end, the most valuable knowledge from this and future discoveries will likely be some combination of genetics, artifacts and paleo-environmental data, says O’Rourke. Taken all together, the amalgam of sciences could show how humans created material culture to interact with and survive in their environment.

“We’re always reaching a little further in one place than another,” O’Rourke says. “That’s the challenge—how to integrate these different streams of knowledge.” 

Editor's Note, January 5, 2018: This article has been updated to clarify how the new paper presented different models for the origins of the Ancient Beringians.

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