The Kennewick Man is Native American.
A genome sequence of the 8,500-year-old male skeleton discovered in 1996 in the Columbia River in Washington contradicts earlier work including a cranial analysis that found he resembled populations in Japan, Polynesia or Europe.
The findings in Nature announced Thursday also should bolster hopes from several tribes in the Northwest that want to repatriate the bones - several of which said they now will push to take possession of Kennewick Man, whose skeleton is kept in the Burke Museum of Natural History & Culture in Seattle. It, however, is not on display for security reasons.
"Comparing the genome sequence of Kennewick Man to genome-wide data of contemporary human populations across the world clearly shows that Native Americans of today are his closest living relatives," said Eske Willerslev, whose Centre for GeoGenetics at the University of Copenhagen led the study.
As part of the study, the researchers took DNA samples from one of the five claimant tribes, the Confederated Tribes of the Colville Reservation. They found the tribe was "one of the groups showing close affinities to Kennewick Man or at least to the population to which he belonged," though they couldn't say exactly which tribe he might come from.
But since the other tribes didn't provide DNA, Willerslev acknowledged Kennewick Man could be more closely related to them. "It is certainly possible," he said. "From my understanding of the history between these tribes, they have been intermarrying with one another for many, many years. So, my expectation is that the other four tribes also would be closely related to Kennewick Man."
They also compared the Kennewick Man's DNA to that of Japanese Ainu and Polynesian populations and found that he didn't have any more of their DNA than contemporary Native Americans.
This marks the latest twist in the saga of Kennewick Man, known by the tribes as the Ancient One, whose discovery sparked a long-running legal battle of who has the rights to the skeleton.
Tribes in the region where Kennewick Man was found demanded the remains be turned over to them for reburial on the basis that he was likely an ancestor to them. The U.S. Army Corps of Engineers, which managed the land where the skeleton was found, agreed.
However, their request was ultimately blocked in 2004 after eight scientists sued, claiming there was no proof the bones were Native American. The lawsuit divided the anthropological community and strained relations with Native American groups.
The ruling gave scientists plenty of time to study the skeleton, allowing them to piece together who he was and how he might have died and making him the most studied Paleoamerican skeleton to date. Among other things they determined he was about 5'7", a muscular 163 pounds, and died when he was about 40 years old.
He also was pretty banged up. He had broken ribs, a bum shoulder and several skull fractures. And when he was a teenager, someone tossed a spear at him and it lodged in his hip.
The debate over his ancestry seemed to be settled with a 2014 study - using isotopic, anatomical and morphometric analysis - that concluded Kennewick Man resembles circumpacific populations, particularly the Japanese Ainu and Polynesians, and also has certain European-like morphological traits, and reinforced the claim that he was anatomically distinct from modern Native Americans.
But that study didn't use DNA analysis, prompting the latest research. Researchers from the Centre for GeoGenetics took advantage of technology advances that allowed them to get much more information from shorter pieces of DNA from the damaged samples. It came from 200 milligrams of hand bone.
"Although the exterior preservation of the skeleton was pristine, the DNA in the sample was highly degraded and dominated by DNA from soil bacteria and other environmental sources," Morten Rasmussen, a co-author on the paper also from the Centre for GeoGenetics, said. "With the little material we had available, we applied the newest methods to squeeze every piece of information out of the bone."
David Meltzer, another author on the study who is an archeologist from Southern Methodist University, said analyzing the DNA proved crucial to solving the mystery.
"The trail from past to present is often poorly marked in the archaeological record, making it difficult to follow a people through time by their changing artifacts or their rarely encountered and often fragmentary skeletal remains," he said. "With the recovery and careful analysis of ancient DNA, we can better follow that trail: in Kennewick's case, it leads unerringly to Native Americans."
Another group of researchers on the paper reexamined the cranial data and concluded it alone was not enough to say much about Kennewick Man's ancestry.
The researchers, whose study was funded entirely by two Danish organizations with no money from the tribes, said they were not taking any position on what should become of the skeleton now.
"We are just putting out the results," Willerslev said. "We don't take any position in the lawsuit case. We are just scientists."
However, the tribes, who had fought to take possession of the body, said they were thrilled with the findings, which only confirmed what they had long believed.
"Obviously it's very good news," Jim Boyd, the chairman of the Colville tribal council, which includes 12 different tribes on a reservation in north central Washington, told CBS News. "We've maintained a belief throughout that this was an ancestor. He was a relative."
Boyd said the tribe would push to rebury the skeleton - though he acknowledged he could be an ancestor of any of several tribes. The others tribes that have demanded the body's return are the Umatilla, Yakama, Nez Perce and Wanapum.
"Our goal all along has been joint repatriation and reburial," he said. "We still want him respectfully buried. With that, we're still in the legal process to be determined so there is still discussion between tribes and even between us and the U.S. Corp of Engineers. We are not exactly sure where we are going to go from here but we do see this as a victory."
The federated Tribes of the Umatilla Indian Reservation, in a statement, said the study should put an end to the dispute:
"Scientists have been studying the Ancient One for almost 20 years and, in light of these recent results, the (federation) believes that additional studies should cease and the Ancient One should be repatriated for reburial."
Brig. Gen. John Kem, commander of the Northwestern Division of the Corps of Engineers, will study the findings over the next couple of weeks so he can decided a path forward.
But even the Native American designation is not enough to turn over the bones, since the Native American Graves Protection and Repatriation Act (NAGPRA) requires that the remains also have to be linked to a specific tribe - something the Nature study couldn't do with certainty and likely will require much more information including geographic, kinship and archeological evidence.
"Just because we have DNA evidence now, it doesn't mean that he's Native American," under NAGPRA, Gail Celmer, the regional archeologist for the Northwestern Division, told CBS News. "It's going to be a big piece in the complete picture but it's not everything we need to know. We're going to take one step at a time and be very careful because this thing has been in litigation for so many years. So, we have to make sure we have thorough documentation and a very clear path forward."