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The divers could scarcely believe their eyes.

Swimming deep into a vast, pitch-dark underwater pit in a Yucatan cave, lead diver Alberto Nava felt like he was in “an outer space black hole.” Then their headlamps shone on a huge trove of ancient fossils scattered across the floor of the flooded pit. These included parts of over 30 animal skeletons, many of them extinct Ice Age megafauna such as saber-tooth cats and huge Shasta ground sloths. Preserved 130 feet down in cool water, the ancient bones were in pristine condition.

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But the real prize was an incredible rarity: the nearly intact skull and skeleton of one of the earliest humans in the Americas. The bones belonged to a teenage girl of around 16 who had fallen to her death in the pit at the end of the last Ice Age some 13,000 years ago. Barely half-a-dozen other human remains in the New World date back so far.

The challenging dig deep in a cave in Mexico revealed new information about the First Americans. Photo: Roberto Chávez.

The team named her Naia, after a water nymph in Greek mythology. As told in NOVA’s “First Face of America,” Naia’s skeleton was so complete that scientists are able to reconstruct her life and death in intimate detail and add a crucial new piece to the long-standing puzzle about when and how humans first populated the Americas.

There was one serious problem, though: the 130-foot deep Hoyo Negro—“Black Hole”—was accessible only to highly experienced cave divers who could stay down in the flooded pit for no more than 90 minutes at a time. With such limitations, how could scientists properly map the cave, study the unique fossils in place, and then systematically retrieve them?

The answer was a state-of-the art, high-resolution 3D virtual reality space also known as a CAVE (Cave Automatic Virtual Environment) that scientists could walk into, map and measure the fossils, and plan future diving missions. It was created by the University of California at San Diego’s Cultural Heritage Engineering Initiative (CHEI) , a lab dedicated to applying high end digital tools to analyzing and preserving evidence from the past. Archaeologist Dominique Rissolo, a lead member of the CHEI team, says that its aim is to take “an underwater archaeological site topside, so archaeologists and paleontologists can spend time looking at the relationships between a particular bone and another bone, for example.

“If we can document all the fossils, make a photo map of the bottom of the pit, and create a 3D visualization that puts the archaeologists and paleontologists there without ever getting wet, those discoveries and interpretations are made possible.”

The 3D virtual cave depended not only on high-tech ingenuity, but on the courage and dedication of Alberto Nava and his team. Since Hoyo Negro’s discovery in 2007, Nava has led repeated, risky missions back to the submerged pit. Team photographer Roberto Chávez has shot thousands of photos at every scale and angle to provide the raw data for the 3D cave. The CHEI team uses then uses what’s known as structure-from-motion photogrammetry software to track and line up features in the different photos. Using that information, the software then stitches the photos together to form the 3D model. It’s similar in principle to how our own eyes and brains determine the structure of objects in the real world. In areas around key fossils, the images have a resolution of less than a millimeter.

The virtual model has transformed the sleuthing, according to archaeologists James Chatters and Pilar Luna of Mexico’s National Institute of Anthropology and History. The duo is co-directing the investigation. “The model is hugely important,” Chatters says. “You can resolve details that are simply not visible in normal photographs, and spot things that even the divers can’t see. We can peer in between and behind rocks that divers can’t do because of all the gear they’re wearing.”

Lead diver Alberto Nava inside the virtual cave. Photo: Dominque Rissolo

Poring over images from the latest dive inside the computer cave, team members spotted bones from a pair of fossil bobcats and a coatimundi hidden behind rocks that “you could never have seen by just swimming around,” he says.

Not only is the virtual cave essential for a comprehensive fossil inventory, Chatters says, it enables the team to take measurements and print accurate 3D replicas of specific bones, including Naia’s skull. Before divers finally retrieved the skull from the cave, the model helped Chatters design a padded box of exactly the right size to prevent damage during its journey to the surface.

The most recent National Geographic-funded mission to the cave in November and December 2017—the result of intricate planning inside the virtual cave—was phenomenally productive. The team brought up parts of eleven animals, including bobcats, a previously unknown species of ground sloth, and rare limb bones of two Shasta ground sloths, not to mention two saber tooth cats, three bears, and a lot more.

“It was a whole menagerie of creatures that we were able to target carefully beforehand, based on their research value,” Chatters says. “We’re busy narrowing down the age represented by the animals, but it’s pretty clear they could span at least 20,000 years of the last Ice Age.”

Back then, sea levels were appreciably lower and most of the cave system was dry. Chatters thinks the animals—and Naia, too—were probably drawn to the cave to find water, then got lost in the dark and tumbled into the deep pit. “You just don’t see sites as rich as this. We don’t have as many fossils as the La Brea tar pits but ours are in almost perfect condition,” Chatters adds. “And we don’t have the tar.”

The discovery of Hoyo Negro’s fossil treasures has come at a key moment in our understanding of the First Americans. Converging clues from genetics and archaeology are bringing new clarity to contentious debates about the timing and origins of their entry into the continent.

Geneticists successfully extracted mitochondrial DNA, a significant indicator of ancestry passed down only through the female line, from one of Naia’s wisdom teeth. The results of that work confirm other recent findings that suggest today’s Native Americans can trace their heritage to a single founding population somewhere on the Bering land bridge around 25,000 years ago. Eventually, this population began spreading south around 14, 000 years ago as the ice sheets retreated, opening up the new continent to the first humans. Naia’s people were relative newcomers in a very new world.