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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.Researchers detailed their analysis of the oldest most complete, genetically intact human skeleton discovered in the New World in a paper published today in the journal Science. This project was led by the Mexican government’s National Institute of Anthropology and History and supported by the National Geographic Society.Paul Nicklen

She was young, no more than 16, and feeling her way through a dark cave, perhaps lured by the quest for water in a land with no surface rivers or streams.

One can imagine her terror as the cave suddenly opened into a yawning chasm, with a sheer drop to a shallow pool far below. A step too far took her over the unseen edge. In pitch blackness she fell as much as 30 metres – about eight storeys. The echoes of her scream and the sound of her body as it hit bottom would have echoed off the limestone walls for a few moments. Then eons of silence.

After more than 12,000 years, the girl scientists call Naia has returned from the underworld. Her bones, long preserved in their watery tomb in Mexico's Yucatan peninsula, offer a direct link to a mysterious past. And now her DNA is helping to answer one of the most enduring questions in prehistory: Who were the first people to populate the new world?

The newly emerging answer amounts to a convergence of theories. It suggests people reached North America earlier that once thought, and that those same people are also the ancestors of living native Americans.

"This is a bonanza find," said Eduard Reinhardt, a micropaleontologist at McMaster University in Hamilton, Ontario. "The quality of the data that we're getting is exceptional."

An experienced diver, Dr. Reinhardt is one of the scientists directly involved in examining the site where the Naia skeleton was first discovered in 2007. After many millennia, the change in sea level since the end of the last ice age has put the floor of the vast chamber under 40 metres of water. Researchers in scuba gear must swim through the passage where Naia took her final steps, and glide over the precipice where she plunged to her death into what has been named Hoyo Negro, or "black hole".

"The bottom drops out as you get into that big cavern," Dr. Reinhardt said. "It's like a cathedral. Your light just dances off the walls."

The scientific payoff has been equally impressive.

Naia's skull is intact and well preserved, which reveals what she looked like when she was alive. At the same time she has yielded her mitochondrial DNA – a form of DNA that is inherited only along the maternal line – which scientists successfully extracted from one of her teeth.

Together, these two pieces of information speak to a debate over the true identity of "paleo-Americans", the oldest people discovered in the western hemisphere.

Naia's DNA contains the D1 haplogroup, a genetic feature that is widespread in native populations across North and South America. This indicates she is descended from the same Siberian-based population that is thought to have given rise to all existing groups of indigenous people in the new world today.

"This girl was maternally related to living Native Americans," said Deborah Bolnick an anthropologist at the University of Texas at Austin and one of the researchers involved in a detailed analysis of the Naia find, published Thursday in the journal Science.

Yet, based on her prominent forehead and narrow face, Naia looked nothing like a Native American. On their own, her features might be taken as evidence that the new world was once home to a different line of people that were later replaced by the ancestors of living Native Americans.

But scientists have instead arrived at a different conclusion: The features that are typically associated with Native Americans likely evolved after their ancestors arrived, either in response to the environment – likely a very cold one – or through a random process known as genetic drift.

"The take-home story is that there was no replacement," said Michael Waters, director of the Center for the Study of the First Americans at Texas A&M University, who was not involved with the Naia find.

In February Dr. Water and colleagues published the genome of a male infant whose bones were found at a site in Montana in connection along with spear points that are representative of the Clovis culture, a stone-age group of big game hunters.

For years, the dominant theory about how the Americas were first settled involved the arrival of Clovis people via the land bridge that once connected Siberia with Alaska and then down an ice-free corridor that opened up between two major continental glaciers some 12,000 years ago.

However, evidence of human habitation in the new world that predates the opening of this inland route has grown in recent decades, generating a fierce debate over the "Clovis first" theory.

Now many anthropologist favour a model in which the first Americans showed up as early as 16,000 years ago, perhaps along a western coastal route and perhaps giving rise to Clovis culture after their arrival – but exactly who those people were has remained an open question. Naia strongly supports the growing consensus that they were Siberians too, and genetically related to any who may have come later by other routes.

"It's a contribution to the solution of the puzzle," said James Chatters, a forensic anthropologist based in Bothell, Washington, who is lead author of the Naia study. Dr. Chatters is known for his previous investigations of "Kennewick Man", an ancient skeleton found on the banks of the Columbia River in 1996 which sparked a legal battle between scientists and local native groups over ownership.

Dr. Chatters added that the new find does not speak to that controversy because it does not establish a direct ancestral link between either Kennewick Man or Naia and modern Native Americans – though it suggests they all share a common ancestry.

Scientists say there is more to come. The cave that trapped Naia also trapped a wide range of ice age animals, from sabre tooth cats and giant sloths to gomphotheres, an extinct cousin to modern elephants. Bones of sixteen mammal species have so far been identified in Hoyo Negro.

But the work, conducted at a depth where professional divers have minutes rather than hours to work on specimens, is time consuming and exhausting.

"It's like being an astronaut," said Patricia Beddows, a Canadian researcher at Northwestern University in Evanston, Illinois.

Dr. Beddows, a specialist in hydrogeochemisty, collected and analyzed calcium deposits that grew on Naia's bones and help establish the skeleton's age.

"When you start getting involved and looking at all sorts of details that tell you what someone's life was like, it does become very personal," said Dr. Beddows.

Although most of Naia's skeleton is still in the cave where they are being studied in place, the skull and a few other bones were removed in March after it was discovered that unauthorized divers had entered the site and disturbed the remains.