The remains of a small, delicate teenage girl who fell to her death in an underground cave system in Mexico 12,000 years ago have thrown fresh light on the origins of the first Americans.

Cave divers chanced upon the girl's skeleton, along with the bones of sabre-tooth cats, giant ground sloths and cave bears, in a vast water-filled cavern they discovered while exploring a submerged network of tunnels reached from a sinkhole in the Yucatan jungle.

Researchers believe the girl, whom they have named Naia, died after breaking her pelvis when she fell into the cave, which would have been dry at the time, apart from a small, occasional pool at the bottom. Like the animals around her, she may have met her death after venturing into the cave system to look for drinking water.

The tunnels and bell-shaped cave, which is 60 metres across and 40 metres deep, filled with brackish water when melting glaciers caused the sea level to rise. The cavern is now well below sea level and can only be reached by technical divers.

Alberto Nava, a diver based in California, found the cavern and Naia's remains with two fellow divers in 2007. Deep inside the jungle, the trio had entered a crystal-clear pool that fed into the cave system. After swimming along a flooded tunnel for more than a kilometre, the cavern opened up before them.

"The moment we entered inside, we knew it was an incredible place. The floor disappeared under us and we could not see across to the other side. We plunged a way down inside. All we could see was darkness," Nava said. The divers named the cavern Hoyo Negra, which is Spanish for "black hole".

As the divers explored the cavern, they spotted a human skull perched on a ledge among some other bones. "It was a small cranium laying upside down with a perfect set of teeth and dark eye sockets looking back at us. The skull was resting on its humerus [an upper arm bone] and we could see the rest of the upper torso spread to the left and down on the ledge," Nava said.

The skeleton belonged to a slight young woman, aged 15 or 16 years old, who was only four feet 10 inches (1.47 metres) tall. To find out how long ago she lived, researchers carbon-dated her tooth enamel and used a separate technique to work out the age of tiny flower-like crystals that had grown on her bones when water rich in calcite dripped onto them from the cavern's damp limestone roof. Together, they put her remains at 12,000 to 13,000 years old.

The origins of the first Americans have been debated by scientists because some of the early skeletons from the region are unlike modern Native Americans. The older humans, known as palaeoamericans, had narrower skulls and other striking features that led some researchers to suggest they had different ancestral roots, perhaps in Australia, southeast Asia, or even Europe.

Modern Native Americans are almost certainly descendants of hunter-gatherers who lived in the ancient region of Beringia around the Bering Strait from 26,000 to 18,000 years ago. Those people crossed into North America and spread south after crossing the exposed Bering land bridge 17,000 years ago.

In a study published in Science on Thursday, a team led by Jim Chatters at Applied Paleoscience, a consultancy based in Bothell, Washington, provide rare genetic evidence that the very first Americans came from Beringian stock. They extracted genetic material from one of Naia's molars, specifically her mitochondrial DNA, which is passed exclusively down the maternal line. The DNA showed that Naia belonged to a lineage shared only with Native Americans.

"What this study is presenting for the first time is evidence that palaeoamericans, with those distinctive features, can also be directly tied to the same Beringian source population as contemporary Native Americans," said Deborah Bolnick, a co-author on the paper at the University of Texas, Austin.

So why do modern Native Americans look so different from the first Americans? Chatters told the journal that Native Americans, who have flatter, rounder faces, represented a more "domesticated" population that settled down as farmers in the Americas. There are other explanations, though. David Meltzer at Southern Methodist University in Dallas puts the differences down to "genetic drift", a random evolutionary process that gradually altered the appearance of Native Americans over thousands of years.

Tom Dillehay, an anthropologist at Vanderbilt University in Nashville, said that while the science was good, the interpretation was overstated. "It is simply one life story of one individual representing one possible interpretative scenario among many other possibilities," he told the Guardian. "It doesn't mean that all early skeletons from the Americas represent the same story."