Principal components analysis plots based on the r2 values obtained for neighbouring markers. Populations with more than three missing r2 values were excluded in the analysis (Surui, San, Non-Austronesian (NAN) Melanesian, Colombian, Karitiana, Pima and Papuan). 42.1% and 18.9% of the variance is explained by the first and second components, respectively. The plot of the two first components pools the populations into two groups: East Asia and European/Western Eurasians. African populations are scattered due their lack of a single linkage disequilibrium pattern. Note that four Native American populations were excluded from the analysis and only one such population (Mayans, from Mexico) could be included.