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Hello, Naia! 12,000-Year-Old Girl's DNA Reveals First Americans' Roots

Image: Divers transport the Hoyo Negro skull

Divers Alberto Nava and Susan Bird transport the Hoyo Negro skull to an underwater turntable so that it can be photographed in order to create a 3-D model. Courtesy of Paul Nicklen / National Geographic

In the depths of an underwater cave in Mexico, the bones of an unlucky girl named Naia preserved clues to the origins of the First Americans for 12,000 dark years. Now her bones, and those clues, have finally come to light.

The shape of Naia's skull and the DNA in her bones have led researchers to the conclusion that there was only one major migration to the Americas, over an ancient land bridge that spanned what is now the Bering Strait.

University of New Mexico geochemist Yemane Asmerom, who helped determine how long ago Naia lived, compared her story to that of Lucy, the 3.2 million-year-old human ancestor whose bones were found in Ethiopia 40 years ago.

"Just like the story of Lucy, from where I originated myself, and our rovers right now on Mars, Naia's story touches, I believe, on our hunger for deep human connection in space and time," Asmerom told reporters during a teleconference.

Asmerom and more than a dozen other researchers tell Naia's story in this week's issue of the journal Science.

Image: A broad view of Hoyo Negro
A broad view of Hoyo Negro, shot from the floor near the south edge, showing the immensity of the chamber and the complexity of the boulder-strewn bottom. One access tunnel can be seen near the ceiling at top left. This photo was taken by the “painting with light” method on a 30 second exposure. Roberto Chavez Arce

Naia's significance stems from the fact that the teenage girl's bones were so well-preserved in the cold, dark waters of a vast, 100-foot-deep (30-meter-deep) grotto on Mexico's Yucatan Peninsula, known as Hoyo Negro (Spanish for "Black Hole").

For decades, anthropologists have fleshed out the idea that modern-day Native Americans are the descendants of ancient peoples who made their way from Siberia to the Americas over Beringia, that now-submerged land bridge. But scientists have also puzzled over curious skeletal remains that look as if they came from Africa or the South Pacific rather than Siberia or the Americas.

One of the best examples is Kennewick Man, a 9,300-year-old skeleton found in 1996 on the banks of the Columbia River in Washington state. Such finds led scientists to wonder whether these different-looking immigrants, referred to as Paleoamericans, made their way to the Americas via different routes.

Earlier this year, researchers traced the connections between Native Americans and ancient Beringians by analyzing the DNA from a set of 12,600-year-old human remains that was found in Montana, known as Anzick-1. But they couldn't make a solid connection between those populations and the Paleoamericans. That's where Naia enters the picture.

Image: A diver inspecting a forelimb of an extinct Shasta ground sloth
Alberto Nava at 145-ft depth in Hoyo Negro, inspecting a forelimb of an extinct Shasta ground sloth, one of two sloth species found in the cave. The Shasta ground sloth has not previously been found so far south in the Americas. Roberto Chavez Arce

The modern-day chapters of Naia's story began in 2007, when a trio of divers discovered Hoyo Negro. "The moment we entered the site, we knew it was an incredible place," one of the divers, Alberto Nava, told reporters.

As the divers explored the vast chamber, they found that it was littered with the bones of now-extinct animals, including ground sloths and elephantlike creatures known as gomphotheres. They also found a human skull, lying upside down on a ledge, surrounded by other bones. The skeleton was nicknamed "Naia," echoing the Greek term for a water nymph.

Naia's skull had the look of the Paleoamericans: a broad forehead, narrow face, wide-set eyes and outward-jutting jaw. "About the opposite of what Native Americans look like," said Applied Paleoscience anthropologist James Chatters, the principal author of the Science paper.

Several methods were used to determine how old the remains were, including radiocarbon dating of tooth enamel and uranium-thorium dating of crystals that accumulated on the bones. Those methods indicated that Naia was somewhere between 12,000 and 13,000 years old.

Image: The skull of Naia as it was discovered in 2007
The skull of Naia as it was discovered in 2007, resting against the left humerus (upper arm bone). Daniel Riordan Araujo

The genetic verdict was the clincher: Mitochondrial DNA extracted from one of Naia's teeth confirmed a common genetic lineage with the ancient Beringians and modern-day Native Americans.

"What this study is presenting for the first time is the evidence that Paleoamericans with those distinctive features can be directly tied to the same source population as contemporary Native Americans," said Deborah Bolnick, an anthropologist at the University of Texas at Austin who helped with the genetic analysis.

Such findings suggest that the physical differences between Paleoamericans and Native Americans are due to population changes that took place in Beringia and the Americas, and are not the result of separate migrations. That scenario meshes with the prevailing view about the First Americans — so much so that some anthropologists wonder whether the Science study breaks all that much new ground.

"It doesn't say anything new and doesn't dispute any of our findings, but likely overreaches in its conclusions because the DNA information falls short of being complete," Montana State University's Shane Doyle, one of the authors of the Anzick-1 study, told NBC News. Doyle pointed out that mitochondrial DNA doesn't provide nearly as much information as the nuclear DNA that he and the other Anzick-1 researchers studied.

But for Chatters, who was one of the leading scientists behind the study of Kennewick Man, Naia's story is a game-changer.

"For the nearly 20 years since Kennewick Man turned up, I've been trying to understand why the Paleoamericans and the Native Americans look so different," Chatters told NBC News. "Were they separate immigrations, or was evolution the issue? This is one step toward resolving that question."

Image: Skull
Working at the bottom of Hoyo Negro, diver Susan Bird carefully brushes the human skull found at the site while her team members take detailed photographs. Paul Nicklen / National Geographic

Chatters acknowledged that much more work still has to be done. The next step is to try to decode Naia's complete genome and compare it with other ancient DNA. Scientists would also like to find more specimens from the age of the First Americans.

As for Naia: Her skull and some of her other bones had to be removed from the cave, due to concerns about unauthorized divers disturbing the evidence. But most of the remains have been left where the girl fell more than 12,000 years ago. "We make all the attempts to work in situ," said Pilar Luna, an archaeologist at Mexico's National Institute of Anthropology and History.

Chatters speculated that Naia — like the animals whose bones were found lining the floor and the walls of Hoyo Negro — became trapped in the bottom of the pit while she wandered through the cave, during an age when sea levels were lower than they are today.

"It appears that she fell quite a distance, and struck something hard enough to fracture her pelvis," Chatters said. "You can imagine a young woman either lost in the dark in a cave ... [or] she may have been looking for water, even with a group looking for water, and getting water out of the little puddle that was in the bottom of Hoyo Negro periodically, and fallen in. And no one could get her out once it happened."

That's how Naia's deep misfortune turned out to be a stroke of luck for science.

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The Hoyo Negro project was led by Mexico’s National Institute of Anthropology and History and supported by the National Geographic Society. The project will be featured in National Geographic magazine and on a National Geographic Television program airing as part of PBS' "Nova" documentary series in 2015.

In addition to Chatters, Asmerom, Bolnick, Nava and Luna, the authors of "Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans" include Douglas Kennett, Brian Kemp, Victor Polyak, Patricia Beddows, Eduard Reinhardt, Joaquin Arroyo-Cabrales, Ripan Malhi, Brendan Culleton, Dominique Rissolo, Shanti Morell-Hart and Thomas W. Stafford Jr.