a) Principal components plot of individual pairwise genetic distance estimates. Panel 1 – most New World Totonac and Bolivian individuals are clustered and have smaller estimated distances to the HapMap CHB/JPT than to the CEU or YRI (~815 K SNPs). Panel 2 – data merged with five Native American HGDP populations typed on the Affymetrix 6.0 platform (~470 K SNPs). Each individual (+) is color coded by population. The percent variance accounted for by each principal component is indicated on the axes. b) Population structure analysis of Totonac and Bolivian individuals at K inferred ancestral populations using a genome-wide panel of 120,958 SNPs (r2 ≤ 0.2). Each individual is shown as a vertical bar with proportionate ancestry indicated by color. The top two panels show European attributable ancestry in ten Bolivians at K = 2, 3. The bottom two panels demonstrate greater similarity between the Totonacs and Bolivians than between other World populations (K = 4, 5), including CHB and JPT samples.