Admixture and population structure.

Plots of principal components A) 1 versus 2 and B) 2 versus 3 calculated using 1M SNP data from 67 Pygmy and 58 Bantu samples. The proportion of variance explained by PCs 1, 2, and 3 is 0.245, 0.0192, and 0.0109, respectively. The three Pygmy ethnic groups are clearly distinguished from their neighboring Bantu populations by the first two PCs, while the third differentiates the three Pygmy groups from one another. C) Regression of height on Pygmy ancestry inferred using STRUCTURE (K = 2). Higher levels of Pygmy ancestry are associated with shorter stature. The trend line intersects the intercept from the full model and has a slope equal to the regression coefficient for percent ancestry. D) Visualization of percent ancestry inferred using STRUCTURE at K = 2, 3, and 4.