SEATTLE » After the bruising battle over Kennewick Man died down, Jim Chatters kept a low profile.

As the first scientist to study the skeleton unearthed in Eastern Washington almost two decades ago, Chatters was embroiled in a controversy over race and cultural identity stirred up by the 9,500-year-old bones. His assertion that the mystery man didn’t look anything like modern Native Americans infuriated Northwest Tribes, who consider the remains those of an ancestor and sued for the right to rebury what they call the Ancient One.

Now the Bothell archaeologist is back in the spotlight with another set of prehistoric bones, along with DNA evidence that helps resolve a long-standing puzzle about the first Americans. The findings also suggest — but don’t prove — that the tribes may have been right about Kennewick Man all along.

The new discovery comes from a spectacular underwater cave on Mexico’s Yucatan Peninsula. Divers stumbled across a trove of prehistoric animal bones and one of the oldest, most complete human skeletons in the Western Hemisphere.

In Thursday’s issue of the journal Science, Chatters and an international team of 15 experts report that the human remains are those of a teenage girl, who apparently took a fatal tumble into the limestone cavern between 12,000 and 13,000 years ago, before slowly rising seas engulfed the formation.

The divers who found the skeleton named her "Naia," Greek for water nymph.

The young woman’s skeleton shares many of the physical traits that led Chatters to question Kennewick Man’s relationship to modern Native Americans. "Even though she is extremely feminine looking and he is very masculine, they look a lot alike," he said.

Both skeletons have narrow brain cases, short faces and prominent foreheads typical of people from the Pacific Rim, Australia and Africa.

Native Americans more closely resemble people from northeast Asia. That jibes with genetic studies documenting their descent from Siberians believed to have migrated east into the land mass that once linked Asia and Alaska, and thence into the Americas beginning about 17,000 years ago.

To explain why the bones of the Western Hemisphere’s oldest inhabitants — called paleoamericans — have such an unexpected appearance, Chatters and other scientists hypothesized that the Americas were colonized twice in prehistoric times: First by people from Southeast Asia or even Europe, then by migrants from Siberia.

But DNA extracted from Naia’s teeth changed his mind.

Genetic analyses conducted at Washington State University and other labs show a clear link between the girl in the cave and modern Native Americans.

The study is the first to show that despite having unusual features, at least one paleoamerican — Naia — is descended from the same ancestors as modern Native Americans, said WSU anthropologist Brian Kemp.

That means the physical differences must be due to evolution, as the earliest human occupants adapted to their new environments in the Western Hemisphere.

"For nearly 20 years, since Kennewick Man turned up, I’ve been wondering why these early people looked so different from Native Americans," Chatters said. "This is one step toward resolving that issue."

The study supports the traditional view that most of the people who colonized the Americas had their roots in northeast Asia, whether they came via a Bering land bridge or by sea, said University of New Mexico anthropologist James Dixon, who was not involved in the project.

"It’s a very sound piece of work, and it makes a lot of sense," he said. "All the DNA evidence we have on these early skeletons — which is very meager — points to the northeast Asian origin," he said.

But that doesn’t rule out the possibility of colonists from other parts of the world, he added.

It’s hard to draw sweeping conclusions from a single skeleton, cautioned Smithsonian Institution archaeologist Dennis Stanford. Based on similarities between spear points and stone tools, Stanford is convinced that some of the first people to settle North America came from Europe — and there’s nothing in the new study to rule that out, he said.

DNA has only been extracted from four sets of human remains in the Western Hemisphere older than 10,000 years. Naia’s skeleton, which includes all the major bones and a full set of teeth, is the most complete.

Alberto Nava, one of the divers who discovered the skeleton in 2007, said he and his colleagues swam through a mile-long tunnel before reaching a chamber the size of a basketball arena. They named it Hoyo Negro, or Black Hole, because it was so vast their underwater lights barely penetrated the darkness.

Heaps of bones on the chamber floor, nearly 150 feet below sea level, later were identified as those of sabertooth cats, elephant-like creatures called gomphotheres and giant sloths. Naia’s bones were lying on a small ledge.

The girl probably fell through a sinkhole into the chamber, which at that time was above sea level, Chatters said. Her pelvis was broken. "I think she died almost instantly, if not instantly," he said.

Over the past three years, Chatters worked with divers and Mexican scientists to study her skeleton. Because the bones are fragile and their position in the cave is important to piecing together the scientific puzzle, much of the analysis was conducted underwater by professional divers.

Part of the skeleton was removed to a museum for safe keeping in March, after unauthorized divers moved the skull and broke several bones.

Dating the bones was difficult because the collagen used for standard radiocarbon analysis had decayed away. The scientists got a radiocarbon date from tooth enamel, and used an isotopic method to date small rosettes of calcium carbonate deposited on the bones by water dripping from the roof of the cave.

The researchers estimated that the cave was flooded about 10,000 years ago, as the last ice age came to an end and melting glaciers raised sea levels around the world.

Naia’s third molar was shipped to Kemp’s lab at WSU for DNA extraction. He didn’t think it was going to work because the tooth was in such bad shape. But he was wrong.

"I was surprised at how easy it was," he said.

Kemp enlisted colleagues at two other universities to verify the results.

In the first pass, the scientists only sequenced a tiny fraction of girl’s genome located in cell structures called mitochondria passed down along maternal lines. But they hope to extend their analysis soon, Kemp said.

Although the new study didn’t deal directly with Kennewick Man, the findings raise questions about the fate of the skeleton that remains locked away at the University of Washington’s Burke Museum.

After a lengthy custody battle with Northwest tribes and federal agencies, a group of scientists led by Smithsonian anthropologist Doug Owsley was allowed to study the bones in 2006.

Owsley, who declined to comment on the new report, said his team’s book-length manuscript will be published this fall. Owsley is steadfast in his belief, based on physical features, that the ancient man is not genetically linked to the tribes who still hope to lay the bones to rest someday.

Scientists would love to extract DNA from Kennewick Man, but the agencies who control access to the skeleton won’t allow it. Without those results, it’s impossible to know if Kennewick Man would share Naia’s genetic affinity with Native Americans. But the results from Mexico add ammunition to the tribes’ argument that just because his head is shaped differently from theirs, doesn’t mean they aren’t related, Kemp said.

"If DNA is ever obtained from Kennewick Man, my prediction is that he’s Native American," he said. "I have no reason to believe that he could be anything else."