Native American autosomal genetic tree. Each language stock is given a color, and if all populations subtended by an edge belong to the same language stock, the clade is given the color that corresponds to that stock. Branch lengths are scaled according to genetic distance, but for ease of visualization, a different scale is used on the left and right sides of the middle tick mark at the bottom of the figure. The tree was rooted along the branch connecting the Siberian populations and the Native American populations, and for convenience, the forced bootstrap score of 100% for this rooting is indicated twice. In the neighbor-joining tree, a reasonably well-supported cluster (86%) includes all non-Andean South American populations, together with the Andean-speaking Inga population from southern Colombia. Within this South American cluster, strong support exists for separate clustering of Chibchan–Paezan (97%) and Equatorial–Tucanoan (96%) speakers (except for the inclusion of the Equatorial–Tucanoan Wayuu population with its Chibchan–Paezan geographic neighbors, and the inclusion of Kaingang, the single Ge–Pano–Carib population, with its Equatorial–Tucanoan geographic neighbors). Within the Chibchan–Paezan and Equatorial–Tucanoan subclusters several subgroups have strong support, including Embera and Waunana (96%), Arhuaco and Kogi (100%), Cabecar and Guaymi (100%), and the two Ticuna groups (100%). When the tree-based clustering is repeated with alternate genetic distance measures, despite the high Mantel correlation coefficients between distance matrices (0.98, 0.98, and 0.99 for comparisons of the Nei and Reynolds matrices, the Nei and chord matrices, and the Reynolds and chord matrices, respectively), higher-level groupings tend to differ slightly or to have reduced bootstrap support.