To analyse populations with substantial historical admixture, statistical methods were applied to each individual to infer regions of the genome with different ancestries. Populations and individuals vary substantially in admixture proportions. For example, the MXL population contains the greatest proportion of Native American ancestry (47% on average compared to 24% in CLM and 13% in PUR), but the proportion varies from 3% to 92% between individuals (Fig. S9a). Rates of variant discovery, the ratio of nonsynonymous to synonymous variation and the proportion of variants that are novel vary systematically between regions with different ancestries. Regions of Native American ancestry show less variation, but a higher fraction of the variants discovered are novel (3.0% of variants per sample, Fig. 3c) compared to regions of European ancestry (2.6%). Regions of African ancestry show the highest rates of novelty (6.2%) and heterozygosity (Fig. S9b,c).
