For about 9,000 years, his bones lay entombed in earth, an unknown record of early life in the Americas. But since a chance find in the 1990s, the remains have been at the nexus of a scientific and political firestorm over the ancestry of this ancient individual. Now, the first genome analysis of Kennewick Man, or “the wise one”, is adding fresh fuel to the flame.

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Contrary to previous results based on the size and shape of the skeleton, the DNA analysis, published today in Nature, suggests that Kennewick Man is more closely related to modern Native Americans than any other population of modern humans. While the researchers were not able to link the skeleton to a specific contemporary Native American group, the study could have implications for the fierce debate over who should be its modern caretakers.

“We will never be able to say what population, what individual in the Americas, is most closely related to [Kennewick Man] simply because most Native Americans haven’t been sequenced,” says Eske Willerslev, a geneticist at the University of Copenhagen and a co-author on the study. “What we can say is that Kennewick Man is more closely related to some Native American groups than others.”

The modern saga of Kennewick Man began in 1996, when college students stumbled upon some bones along the Columbia River in Kennewick, Washington, and called the police. Radiocarbon dating put the skeleton at about 9,000 years old. The remains consist of roughly 300 bone fragments, making it one of the most complete ancient skeletons unearthed in the Americas.

Because the bones were discovered on federal land, they fell into the hands of the U.S. Army Corps of Engineers. When five tribes from the area claimed Kennewick Man as their ancestor and called for his return and reburial under the Native American Graves Protection and Repatriation Act (NAGPRA), the corps was inclined to grant their request. Once reburied, the skeleton would no longer be available for scientific study.

However, early analysis suggested that the bones might be anatomically different from those of modern Native Americans, in which case NAGPRA might not apply. The results sparked an eight-year-long legal conflict between a group of scientists who wanted to study Kennewick Man, the tribes and the corps. In 2004, a court ruled in favor of the scientists.

“It was always about being able to ask questions,” says Doug Owsley, an anthropologist at the Smithsonian’s National Museum of Natural History and a plaintiff on the lawsuit. Figuring out Kennewick Man's lineage would not only establish the legal case but might also provide important clues to the peopling of the Americas, such as who the first Americans were and what they were like. Ancient human skeletons are incredibly rare, especially in the Americas. Thus far, only a few significant remains have been found in a cave in Mexico and on the plains of Montana.

Subsequent studies linked Kennewick Man to Europeans, Native Americans and Asian populations. Led by Owsley, a team undertook a thorough analysis of the Kennewick Man’s life history—from what he looked like to when he died. Based on skull morphology, the team suggested that his bones most resembled those of the Ainu people of Japan and a Polynesian group called the Moriori.

One thing lacking from this extensive skeletal study was DNA—it degrades over time, and it can be difficult to extract from ancient remains, depending on their condition. Attempts to extract and sequence samples from Kennewick Man in the 1990s and early 2000s were fruitless.

But genetic technology has come a long way since then. “We can now get information out of shorter pieces of DNA, and given the very degraded DNA in Kennewick Man, that’s absolutely key for addressing these questions,” says Morten Rasmussen, a geneticist and co-author on the study. Rasmussen, Willerslev and their colleagues have had previous successes reconstructing ancient human genomes and determining their ancestry. When a colleague offered them a Kennewick Man bone sample with permission from the corps, they jumped at the opportunity.

From 200 milligrams of a hand bone, the team carefully extracted pieces of DNA, pasted these fragments together, reconstructed a genome and sequenced it. Using a few different statistical strategies, they compared Kennewick Man to genomes from around the world, including the Ainu and Polynesians, as well as DNA sequences from other ancient American skeletons. One of the five Native American tribes claiming ancestry, the Confederated Tribes of the Colville Reservation, also submitted genetic samples for comparison.

The team found that Kennewick Man’s genes have more in common with Native Americans than any other group alive today. The results show “convincingly that Kennewick is a member of the same broad population as most present-day Native Americans,” says David Reich, a geneticist at Harvard University who was not affiliated with the study.

Though they were not able to directly link the Kennewick Man to any specific modern tribe, the researchers argue that the Colville people may be more closely related to Kennewick Man than other Native Americans. Two possible scenarios emerge from the analysis. First, around 9,200 years ago, an ancient population of humans in North America split into two branches. One produced Kennewick Man a few hundred years later, and one gave rise to modern Native Americans, including the Colville. In the second scenario, Kennewick Man could be a direct ancestor of the Colville, and over time, an influx of DNA from other groups could have made that connection hard to distinguish.

That said, it is still possible that other tribes are even more closely related to Kennewick Man than the Colville. Reich is optimistic that the findings might encourage other tribes to donate genetic samples. Sequencing more genomes and unearthing more skeletons could provide some context, Owsley points out. “It doesn’t surprise me one bit that you could show connections with Asia and connections in the Americas,” he says. “It’s fantastic that more research is continuing. It’s amazing that we can get DNA analysis at all.”

While this isn’t the final word on Kennewick Man’s ancestry, the new analysis makes a compelling argument for what can be learned from ancient DNA, notes Mark Stoneking, a geneticist at the Max Planck Institute in Germany. “Morphology is not always a reliable indicator [of ancestry],” he says. Anthropologists on Willerslev’s team also reevaluated Kennewick Man’s skull, and they argue that connecting him to any population based on the shape of his bones would require more skeletons from the same culture.

As to the case for reburial, Owsley points out that the way NAGPRA defines “Native American” requires a link to a specific modern tribe or culture, so even with the new DNA work in hand, the case isn't conclusive. But he ultimately plans to leave that decision to the judiciary system.