ancestry in African American populations ranges from 3.5% to 22.5% [Parra et al., 1998; Parra et al., 2001], but the admixture proportion in a given individual may range from as low as 1.2% to 77.3% [Xu et al., 2007] and these estimates have been shown to vary by chromosome [Lind et al., 2007]. We therefore think that incorporating local admixture estimates for individuals will be likely necessary for efficient combination of imputed genotypes. Second, we suggest that MACH may be improved by expanding the prior model to explicitly allow for multiple reference populations and gene flow among those populations.
