PCA and ADMIXTURE Analysis
PCA (A) and ADMIXTURE analysis (B) of the newly sequenced samples (Egyptian, pink; Amhara, yellow; Oromo and Ethiopian Somali, light orange; Wolayta, red; and Gumuz, blue) and a subset of 1000 Genomes samples (CHB, dark gray; TSI, light gray; ASW [African ancestry in Southwest USA], green; and LWK [Luhya in Webuye, Kenya] and YRI, light green). ADMIXTURE was run with different values of K (K = 5 was the smallest cross-validation error). The top ADMIXTURE plot shows five ancestral components tentatively describable as West African (green), East African (orange), European (light gray), East Asian (dark gray), and putatively Middle Eastern (pink). The phased and imputed genotypes from the low-coverage sequences were processed with PLINK19 for the removal of variants with a minor allele frequency < 1% (--maf 0.01 --geno 0.01) and pairwise linkage disequilibrium above 0.1 (--indep-pairwise 50 10 0.1). The pruned dataset was then analyzed by ADMIXTURE17 with the --cv option for assessing the most plausible value of K and also by PCA.18 The proportion of the total variance explained by each principal component is reported as a percentage next to each axis label.