Confirmation came from uranium-thorium dating of calcite encrusted on the bones, which provided a minimum age of 12,000 years ago, making the skeleton one of the six oldest humans yet found in the Americas, certainly the oldest most complete.
Anthropological analysis revealed the small skeleton, named "Naia" by the dive team (meaning water nymph in Greek) belonged to a slight female measuring only 4'10" tall. She is estimated to have been between 15 and 16 years old at the time of her death.
Chatters and colleagues also identified the remains of more than 26 large mammals which met their death in the pit. They included a gomphothere, an extinct elephant-like creature, which was dated to around 40,000 years ago, saber-toothed cats and giant ground sloths, which were largely extinct in North America by 13,000 years ago.
Extant species included puma, bobcat, coyote, Baird's tapir, collared peccary and a bear.
"When Naia and the animals entered the cave, the near-surface tunnels were dry, so they walked in from a ground-level entrance, probably a sink hole. They walked a considerable distance, as much as 600 meters," Chatters said.
He speculates that Naia, and the larges animals in particular, were drawn by a large, ephemeral pool of water in the bottom of Hoyo Negro.
"Yucatan was a dry place back then. Walking in the dark, they fell into the deep pit, from which there was no exit," Chatters said.
Indeed, Naia’s remains show fractures of pubic bones, which are consistent with a fall into a shallow pool from one of the upper passages.
"I think she died almost instantly, if not instantly," Chatters said.
The water level was down in the bottom of the shaft when Naia fell. Then, between 9,700 and 10,200 years ago, global glacier melted enough that rising sea levels submerged everything.
Like Kennewick Man, Naia does not feature the broader and rounder skulls of today's Native Americans. She bore a long and high cranium, a pronounced forehead, a low and flat nose. Her teeth projected outward from her small face.
Such different faces, skulls and teeth have led speculations that prehistoric Americans might represent an earlier migration from Southeast Asia or even Europe via a now submerged land mass where the Bering Sea is now.
But mitochondrial DNA testings -- maternally inherited DNA -- carried out from Naia's upper right third molar suggest a different scenario: Paleoamericans and Native Americans descended from the same land in Beringia.
"We found that the Hoyo Negro girl belonged to a mitochondrial lineage known as haplogroup D1," Deborah Bolnick, assistant professor of anthropology at the University of Texas at Austin, said.
Derived from an Asian lineage, haplogroup D1 is common to modern Native Americans and is found only in the Americas. The presence of this genetic marker indicates that the girl was maternally related to living Native Americans.
"She traces ancestry to the same Beringian source population as contemporary Native Americans," Bolnick said.
According to the researchers, the craniofacial divergences are probably the result of evolutionary changes that happened in Beringia and the Americas over the last 9,000 years.
"We now have a better idea of who the Paleoamericans were," Chatters said.
A facial reconstruction to see how Naia might have looked is planned for next month, while future analysis of her nuclear DNA should help to clarify her biologic ancestry and that of the earliest Americans more generally.