Divers mapping the underwater caves within Mexico's Eastern Yucatan Peninsula came upon a surprising find -- a superbly preserved skeleton dating close to the time when people first entered the New World.

"It was like a magnet and I remember swimming over to her remains and hovering in place about 12 inches from the skull, absolutely spellbound, for several moments," Susan Bird, a Bay Area Underwater Explorers diver, told Discovery News.

Subsequent underwater testing and analysis of this oldest, most complete skeleton found in the Americas has since provided evidence that modern Native Americans are directly related to the earliest inhabitants of the Americas, according to a study published today in the journal Science.

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Dating close to the time when people first entered the New World, the early American, or Paleoamerican, skeleton features Native American DNA while showing a distinctly different skull shape. The research provides new clues to how the Americas were first populated.

It suggests the morphological differences between Paleoamericans, the first people to inhabit the Americas after the most recent ice age, and modern Native Americans are not the result of separate migrations from southeast Asia or even Europe. Rather, they belong to the same population that "evolved in place" in the Americas and Beringia, a now partially submerged landmass including parts of Siberia, Alaska and the Yukon.

Belonging to an adolescent girl, the skeleton was found in 2007 in a submerged chamber named Hoyo Negro (Spanish for Black Hole), deep inside a cave system on Mexico's Eastern Yucatán Peninsula, about 12 miles north of the city of Tulum.

"The moment we entered the site, we knew it was an incredible place. The floor disappeared under us, and we could not see across to the other side. We pointed our lights down and to the sides. All we could see was darkness," Alberto Nava of Bay Area Underwater Explorers, one of the divers who found the skeleton, told Discovery News.

About two months later, armed with powerful underwater lights, the divers reached the floor of the pit at about 170 feet. They found themselves in a bell-shaped structure 200 feet in diameter, whose center was littered with large boulders stacked on top of each other.

"As our eyes got accustomed to the environment, we started to notice large animal bones resting at the bottom and on the walls of the pit," Nava said.

Then one of the divers spotted a human skull resting on the top of a small ledge. The small cranium lay upside down and rested on the left humerus (upper arm bone) with other remains nearby.

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"It had a perfect set of teeth and dark eye sockets looking back at us. We could see the rest of the upper torso spread to the left and down on the ledge," Nava said

Using photography, videography, three dimensional modeling and minimal sampling, researchers studied the skeleton without removing it from its watery grave. Only recently, due to unauthorized dives risking to damage the remains, the skull and other four bones were recovered and placed in an artifact conservation lab in Campeche, Mexico.

The international team of anthropologists, archaeologists, geneticists, and geologists was led by anthropologist James Chatters, owner of Applied Paleoscience, a consulting service in Bothell, Wash. He was the first to study Kennewick Man, a 9,300-year-old skeleton found in Washington in 1996.

Also showing the distinctive Paleoamerican rather than modern Native American traits, the Kennewick skeleton triggered a nine-year legal battle between scientists, the U.S. government and Native American tribes who claimed him as one of their ancestors and sought permission for reburial.

In 2004, a U.S. court ruling established there was no evidence connecting Kennewick Man with any existing tribe because the remains date back before recorded history and no cultural or biological link could reasonably be made.

The Hoyo Negro skeleton, which might reopen the debate, turned out to be much older than Kennewick Man.

"The skeleton produced the earliest radiocarbon age, confirmed in two separate laboratories, of any on the Americas," Chatters told Discovery News.

Indeed the human remains were dated between 12,700 and 12,900 years old.

"However, because the material we had to use for the age is one that is not entirely safe from contamination by old carbon in the rocks, we are being more conservative and giving the age as between 13,000 and 12,000 years," Chatters added.

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.Roberto Chavez Arce

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.

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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.

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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.