We find the Kennewick sample has the highest shared similarity to Native American populations with the highest values observed being with populations from South America (Figure 7), in line with the observations from Rasmussen et al.Hopefully this will end the campaign to put him back to the ground. I have added a horizontal line to the new study's Figure 7 to mark the population claiming the skeleton among the huge number considered, showing that there's no particularly strong relationship to it (the strongest connection is at the bottom of the figure).
The Rasmussen et al. and Novembre et al. studies are really science working at its best: simultaneously falsifying claims that Kennewick was some sort of Australoid (or even more implausibly Caucasoid) based on its craniofacial morphology, but not overreaching to validate emotional appeals to make him into an ancestor he wasn't. Thankfully, the way forward is to keep studying Kennewick Man (and modern Native Americans) with ever-better data and techniques which may turn up (who knows?) a real (rather than imagined) ancestral link.
Technical Report: Assessment of the genetic analyses of Rasmussen et al. (2015)
John Novembre, PhD, David Witonsky, Anna Di Rienzo, PhD
The primary aim of the analysis undertaken here (U.S. Army Corps of Engineers, St Louis District Contract #W912P9-16-P-0010) is to provide an independent validation of the genetic evidence underlying a recent publication by Morten Rasmussen and colleagues on July 23rd, 2015, in Nature (Vol 523:455–58). Based on our analysis of the Kennewick Man’s sequence data and Colville tribe genotype data generated by Rasmussen et al., we concur with the findings of the original paper that the sample is genetically closer to modern Native Americans than to any other population worldwide. We carried out several analyses to support this conclusion, including (i) principal component analysis (PCA; Patterson et al. 2006), (ii) unsupervised genetic clustering using ADMIXTURE (Alexander, Novembre, and Lange 2009), (iii) estimation of genetic affinity to modern human populations using f3 and D statistics (Patterson et al. 2012), and (iv) a novel approach based on the geographic distribution of rare variants. Importantly, these distinct analyses, spanning three non-overlapping subsets of the data, are each consistent with Native American ancestry.