Errors in estimating ancestral allele frequencies lead to bias in estimating ancestry fractions ( Q ), with many individuals ascribed too much admixture. The plot shows an estimate of the relationship between the true ancestry fraction q
1 (fraction of ancestry attributed to population 1) and the resulting estimate as determined via a nonparametric regression (LOESS) model fitted to the results from analyses of 100 simulated datasets. Reference individuals are excluded from the plots and regression analyses. The dotted line y = x is tracked closely by the conditional mean of supervised estimates, suggesting little bias. However, in panel (a) (simulations with F
= .01) the conditional mean of the unsupervised estimates deviates substantially, exhibiting an upward bias for low q
1 and a downward bias for high q
1. The bias is mitigated using simulations with F
= .05, as shown in panel (b), or by using a larger number of markers (J = 300, 000, not shown).