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Genomic Analysis of Kennewick Man Indicates Relationship to Modern Native Americans

NEW YORK (GenomeWeb) – A genomic analysis of a bone from the Kennewick Man indicates that he is most closely related to modern Native Americans.

Remains from the Kennewick Man, also called the Ancient One by Native Americans, were uncovered in Washington State in 1996. An initial assessment concluded that the approximately 8,500-year-old man was not Native American. Based largely on that, the request from five Native American tribes in the Pacific Northwest seeking repatriation of the remains for burial was denied by a court in 2004.

However, the University of Copenhagen's Eske Willerslev and his colleagues have sequenced ancient DNA isolated from the Kennewick Man and compared it to other global populations, as they reported today in Nature.

Rather than concluding that the Kennewick Man resembled European Americans as the initial assessment did, or that he was similar to Polynesians and the indigenous Ainu people of Japan as a subsequent morphology study did, Willerslev and his colleagues found that he is most closely related to modern Native Americans, including the Confederated Tribes of the Colville Reservation, one of the five tribes that sued for the repatriation of the remains.

"We have basically managed to obtain the genome sequence from the Kennewick Man to address the question about his ancestry and his affiliations to contemporary people," Willerslev said during a press teleconference.

Though previous attempts to analyze DNA from the Kennewick Man were unsuccessful, Willerslev and his colleagues managed to obtain about 1X coverage of his genome from 200 milligrams of metacarpal bone specimen, due to, he said, a combination of improved technology and techniques, and a dash of luck.  

The ancient DNA was an average length of 53.6 basepairs, Willerslev noted, adding that the patterns of damage were typical for that of ancient DNA.

They also sequenced the mitochondrial genome to about 71X coverage, and placed it at the root of haplogroup X2a. Meanwhile, analysis of the Y chromosome indicated it belonged to the Q-M3 haplogroup. Both of these lineages, the researchers noted, are nearly exclusively found among Native Americans.

Also, based on the X chromosome sequence, the researchers estimated a 2.5 percent contamination rate, mostly of European origin, but within the normal range for ancient human remains.

Willerslev and his colleagues developed a reference set based on published SNP array data as well as new genomic data from the Colville to use as global comparisons for the Kennewick Man data.

The researchers masked recent European ancestry among Native Americans to account for the effect of recent admixture, but did not apply the same masking technique to the Kennewick Man.

Through both principal components analysis and f3-outgroup statistics, the researchers found that Kennewick Man has a clear genetic similarity to Native Americans. Further, they rejected the hypothesis that he was more closely related to the Ainu or Polynesians.

"It's very clear that the genome sequence shows that he is most closely related to contemporary Native Americans," Willerslev said.

Model-based clustering using the ADMIXTURE software tool also revealed that Kennewick Man's ancestry is most similar to that of Native Americans, including the Colville, Ojibwa, and Algonquin. Among solely Native American groups, f3-outgroup statistical and D-statistical analysis found that the Kennewick Man shared a high degree of ancestry with Native Americans from Central and South America, but also with the Colville.

Comparing the Kennewick Man, two members of the Colville tribe, two Northern Athabascan individuals from Canada, and two Karitiana individuals from Brazil discounted direct ancestry between Kennewick Man and these groups, though the researchers noted it was weakly rejected in the case of the Colville.

This suggests two possible scenarios. First, the Colville could be direct descendants of the population to which the Kennewick Man belonged, with additional gene flow into that group from other populations in the 8,500 intervening years.

At the same time, it could also mean that the Colville descend from a population that, some 8,500 years ago, had slightly diverged some 600 years to 700 years prior from the population to which the Kennewick Man belonged to.

However, the researchers suspect the first scenario is more likely, given the evidence that the Colville have had gene flow from other populations, co-author Rasmus Nielsen from the University of California, Berkeley, noted during the press briefing.

The researchers said, though, that despite Kennewick Man's close affinity to the Colville, it's not possible to identify which modern Native American groups he is most closely related to because of a dearth of data.