The divers found her on a ledge, her skull at rest on an arm bone. Ribs and a broken pelvis lay nearby. She was only 15 years old when she wandered into the cave on the Yucatan Peninsula, and in the darkness she must not have seen the enormous pit looming in front of her.

More than 12,000 years later, in 2007, after the seas had risen and the cave system had filled with water, her skull — upside down, teeth remarkably intact — caught the eye of a man in scuba gear.

He and his two fellow divers gave the girl a name: Naia. Her remains may help determine the origins of the earliest Americans and finally solve the mystery of why they looked so dramatically different from the Native Americans of recent millennia.

A paper published Thursday online in the journal Science argues that the discrepancy in appearance between the Paleoamericans and later Native Americans is most likely the result of recent, and relatively rapid, human evolution — and not the result of subsequent migrations of people into the Americas.

Tests on mitochondrial DNA taken from Naia show that she had a genetic marker common today across the Americas, one that scientists say evolved in a prehistoric population that had been isolated for thousands of years in Beringia, the land mass between Alaska and Siberia that formed a bridge between the continents during the Ice Ages.

View Graphic Paleoamerican remains found in the Yucatan

Thus, according to the report, the Native Americans and the Paleoamericans are the same people, descended from the same Beringia population. They just look different because of recent evolution.

“This is truly an extraordinary discovery,” said Yemane Asmerom, a geochemist at the University of New Mexico who co-wrote the report. He compared the cave, known as Hoyo Negro (“black hole”), to the Awash Valley of Ethi­o­pia — the site of the 1974 discovery of “Lucy,” an early human ancestor.

Most scientists have assumed that the first humans to come to the Americas traveled from Eurasia across the Bering land bridge that existed before the oceans rose after the Ice Ages. But there is great debate about whether this represented a single migratory event or multiple pulses of people from different parts of Eurasia and via different routes, including a coastal migration. One maverick theory, based on archeological finds, contends that people came from Europe, following the edge of the ice around the North Atlantic.

Adding to the mystery is that the Paleoamericans, such as Naia, didn’t look like later Native Americans. Naia had a small, projecting face, with narrow cheekbones, wide-set eyes and a prominent forehead. Native Americans of later millennia tended to have broader, longer, flatter faces, and rounder skulls, said James Chatters, an independent researcher based in Washington state and the lead author of the paper.

The distinct morphology of the Paleoamericans is most famously found in the “Kennewick Man,” a 9,000-year-old skeleton discovered two decades ago along the Columbia River in Washington state. Facial reconstruction resulted in someone who looked a bit like the actor Patrick Stewart (“Star Trek: The Next Generation,” “X-Men”). Scientists theorized that he could have been related to populations in East Asia that spread along the coast and eventually colonized Polynesia. Under that scenario, more recent Native Americans could be descended from a separate migratory population.

Chatters said in an interview, “For 20 years I’ve been trying to understand why the early people looked different. The morphology of the later people is so different from the early ones that they don’t appear to be part of the same population.”

He went on: “Do they come from different parts of the world? This comes back with the answer, probably not.”

1 of 8 Full Screen Autoplay Close Skip Ad × An underwater cave reveals bones and clues about the first Americans View Photos Inside a 100-foot-deep chamber near Mexico’s Yucatan Peninsula, divers discovered a skull at least 12,000 years old. DNA from this skeleton is helping scientists address a puzzle about the settling of the Americas. Caption Inside a 100-foot-deep chamber near Mexico’s Yucatan Peninsula, divers discovered a skull at least 12,000 years old. DNA from this skeleton is helping scientists address a puzzle about the settling of the Americas. Diver Susan Bird works at the bottom of a large underwater cave near Mexico’s Yucatan Peninsula. She carefully brushes the human skull found at the site while her team members take detailed photographs. Researchers published their analysis of a nearly complete skeleton, dated to between 12,000 and 13,000 years old, in the journal Science on May 15, 2014. The project was led by the Mexican government’s National Institute of Anthropology and History and supported by the National Geographic Society. Paul Nicklen/National Geographic Buy Photo Wait 1 second to continue.

One of the co-authors of the paper, Deborah Bolnick, an anthropologist at the University of Texas at Austin, said the new genetic tests support the hypothesis of a single ancestral population for Native Americans.

“It’s a lineage that we see across the Americas,” she said, “and a variety of different studies, different lines of evidence over several decades — archaeological studies, genetic studies, morphological studies — all suggest that Native Americans can be traced to a Beringian source population.”

Douglas Owsley, a forensic anthropologist at the Smithsonian’s National Museum of Natural History, and a leading expert on the Kennewick Man, cautioned that the new study is based on “a sample of one.” He said he hadn’t

read the paper — titled “Late Pleistocene Human Skeleton and

mtDNA Link Paleoamericans and Modern Native Americans” — and would like to see more genetic evidence to bolster the report’s central hypothesis.

When there is a rapid change in the appearance of a population, he said, “I have to think you’re talking about migrations and people coming in.”

But, he added, “I think it’s a great discovery.”

In 2007, three divers explored the Hoyo Negro cave, which is about five miles inland on Mexico’s Yucatan Peninsula in an area dotted with sinkholes. When Naia (named for a mythical Greek “water nymph”) was alive, the cave network would have been dry but for ephemeral pools. Now it is entirely flooded, the water mostly fresh.

Three-fifths of a mile from the cave entrance, having penetrated a narrow tunnel, the divers came upon an astonishing sight: a massive pit, at least 150-feet deep.

“Imagine a basketball stadium dome in the ground,” said diver Alberto Nava, who is based in Monterey, Calif.

Two months after they found the pit, during another dive, Nava and his two colleagues reached the boulder-covered bottom of the pit and discovered a virtual museum of animal bones. The first was the femur of a creature called a gomphothere — an elephant-like animal that, like most other megafauna of the Americas, went extinct approximately at the same time as the arrival of humans (whether a causal connection was there is another enduring mystery).

Nava’s fellow explorer Alex Alvarez spotted the skull on the ledge.

“It was a small cranium lying upside down with a perfect set of teeth and dark eye sockets looking back at us,” Nava said.

The divers did not attempt to move the bones.

“When you find remains, you don’t want to touch anything. It took 10,000 years for it to be the way it is,” he said.

The divers contacted archeologist Pilar Luna of Mexico’s National Institute of Anthropology and History, and with support from the National Geographic Society they continued to explore the pit and document the fossils at the bottom, including two saber-toothed cats, six bears, three cougars and two ground sloths.

A series of delicate measurements followed. Scientists examined material scraped from the surface of the bones, and used multiple techniques to probe one of Naia’s molars. They estimated the age of the skeleton at 12,000 to 13,000 years old, and found the genetic marker linking Naia to the Beringia population. The paper concludes, “The differences in craniofacial form between Native Americans and their Paleoamerican predecessors are best explained as evolutionary changes that postdate the divergence of Beringians from their Siberian ancestors.”

Scientists became concerned that some divers coming into the cave may have moved or accidentally broken bones in the pit. Naia’s skull and four of her other bones have been removed to a research institute.

Chatters, the lead author, said he is working on another paper in which he will lay out his theory of the “Human Wild Style” population.

He believes that these early migrants were an aggressive breed — risk-takers and novelty-seekers. They chased wild game, including megafauna such as mastodons and saber-toothed cats, into unpopulated lands far from their ancestral hunting grounds.

But later, as their descendants settled down and adopted agriculture, natural selection favored a gentler sort of personality, and men and women took on softer, more feminine features, Chatters argues. This tendency toward “neotony,” or natural selection of more childlike features, has been seen across much of the world, he said.

That is all material for the future paper, however, and the report published Thursday sticks to the Paleoamerican girl and the cave of fossil wonders.

Why did Naia go into that cave and to her doom? Perhaps, Chatters said, she was in search of water in an era when the Yucatan was parched. Or perhaps she was following an animal. She would have been, under his scenario, a Wild Style person, a risk-taker. And so she went forward — into the cave, through the darkness, falling into the distant future.