Inferred human tree.

A. Maximum likelihood tree. Plotted is the maximum-likelihood tree. Populations are colored according to geographic location (black: archaic humans, red: Africa, brown: Middle East, green: Europe, blue: Central Asia, purple: America, orange: East Asia). The scale bar shows ten times the average standard error of the entries in the sample covariance matrix (). For analysis including Oceania, see Figures S11 and S12. B. Residual fit. Plotted is the residual fit from the maximum likelihood tree in A. We divided the residual covariance between each pair of populations and by the average standard error across all pairs. We then plot in each cell this scaled residual. Colors are described in the palette on the right. Residuals above zero represent populations that are more closely related to each other in the data than in the best-fit tree, and thus are candidates for admixture events.