Technical Report: Assessment of the genetic analyses of Rasmussen et al. (2015)

The primary aim of the analysis reported in this 22-page report (undertaken with the support of the 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 Rasmussen et al. publication 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.