Amazing Ancient Skeleton Discovered in an Underwater Cave Reveals History of Native Americans

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May 15 2014 2:00 PM

Water Nymph

A newly discovered ancient skeleton, found in an underwater cave, answers an anthropological mystery.

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.
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

She was only about 13 years old. She must have been thirsty or perhaps, for a moment, incautious, for she fell through a sinkhole where freshwater gathered, and she was trapped. The cave she fell into has since been submerged by the sea. When it was discovered off the coast of the Yucatán Peninsula, her bones were inside, her skull featuring “deep eye sockets, staring back at us,” as Alberto Nava Blank, one of the divers who found her, put it. They named her Naia—Greek for “water nymph.”

Naia’s sad end enabled an amazing discovery, described Thursday in Science. Buried for 12,000 or 13,000 years, she is one of the oldest and perhaps the most complete ancient American skeleton ever found. Researchers analyzed her DNA, and in doing so may have answered a decades-old archeological question about the origin of the first North Americans.

Paleo-Americans lived more than 9,000 years ago as hunter-gatherers who used stone tools. They looked different from modern Native Americans: Their remains have smaller, narrower skulls and sharply projected faces. Scholars suspected that they might have come from a different lineage than modern American Indians. The 1996 discovery of Kennewick Man, an approximately 9,600-year-old skeleton with distinctive Paleo-American features, lent credence to the idea that they came from a separate provenance.


But Naia’s genes show that this is not the case. Her mitochondrial DNA—genetic material passed down from mother to child through the egg—displayed a combination of genetic sequences similar to that found in modern Native Americans. In other words, the same matrilineal genetic signature runs through Naia as through about 11 percent of Native Americans, according to Deborah Bolnick of the University of Texas, one of the research team members. This suggests that Paleo-Indians and modern Native Americans are descendants of some of the same prehistoric migrants from across the Bering Straits. Naia makes this connection.

Finding Naia and validating her ancestry were incredible feats of science. An Ice Age has passed since her time, and melting glaciers raised sea levels dramatically, turning her grave into a watery one. It now lies 20 meters below the ocean’s surface, in the Caribbean Sea, so dark that the cave is called Hoyo Negro, or “Black Hole” in Spanish. Excavation of the skeleton would have been nearly impossible and caused ruinous disruption to the site. Researchers used a sample of her tooth and some scrapings of crystals from a bone that were brought to the surface by divers to find out when she lived and to read her genetic code. The results were confirmed in three different labs, using three different chemical dating methods.

Along with Naia, Hoyo Negro contains an astonishing trove of preserved Paleolithic specimens, including fossils of now-extinct animals. The paper’s authors have compared it to the La Brea Tar Pits of California, where many ancient creatures became trapped and preserved. James Chatters, a lead researcher on the report on Naia (and also the one who uncovered Kennewick Man), says that he and his colleagues are now attempting DNA extraction of species of a bear, a ground sloth, and a gomphothere, a prehistoric elephantine animal, who had all fallen to their deaths in Hoyo Negro’s vast caverns.

Boer Deng is a Slate editorial assistant. Follow her on Twitter



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