Note: my own understanding is that Kennewick Man is broadly similar to other Paleoindians, and that historical Amerindians probably derive most of their ancestry from Paleoindians (with some later Asian gene flow and evolution in a more Mongoloid direction). On the other hand, it appears W. Eurasian-affiliated ancient Central Asians did contribute significantly to the ancestry of Paleoindians (and, to a lesser extent, to the ancestry of modern E. Eurasians in general), which is what I expect most of the heightened affinity between Northern Europeans and Amerindians found by Reich et al. is attributable to.
The skeleton, more than 9,500 years old, has long been at the center of a rift between tribal members and scientists, led by Doug Owsley, a physical anthropologist at the Smithsonian Institution's National Museum of Natural History who spearheaded the legal challenge to gain access to the skeleton for scientific study.
Owsley says study shows that not only wasn't Kennewick Man Indian, he wasn't even from the Columbia Valley, which was inhabited by prehistoric Plateau tribes. [. . .]
Isotopes in the bones told scientists Kennewick Man was a hunter of marine mammals, such as seals, Owsley said. "They are not what you would expect for someone from the Columbia Valley," he said. "You would have to eat salmon 24 hours a day and you would not reach these values.
"This is a man from the coast, not a man from here. I think he is a coastal man." [. . .]
Pressed by Armand Minthorn of the Umatilla Board of Trustees, who asked Owsley directly, "Is Kennewick Man Native American?" Owsley said no. "There is not any clear genetic relationship to Native American peoples," Owsley said. "I do not look at him as Native American ... I can't see any kind of continuity. He is a representative of a very different people."
His skull, Owsley said, was most similar to an Asian Coastal people whose characteristics are shared with people, later, of Polynesian descent.
And, while tribes want the remains returned for reburial, Owsley said there is still much more to learn from the skeleton, which has largely been inaccessible but for two instances, in which a team of about 15 scientists could study it for a total of about two weeks.
Kennewick Man update
Kennewick Man bones not from Columbia Valley, scientist tells tribes