Complex Patterns of Genomic Admixture within Southern Africa
(A) Boxplots show the estimated ancestral fractions based on ADMIXTURE analysis for six population clusters defined as IND (Indian), IDO (Indonesian), CEU (European), SAN (Ju/'hoan), YRI (Yoruba) and CHB (Han Chinese) for the !Xun, #Khomani, amaXhosa, Baster and regionally defined Coloured (3,725 markers). The red dashed line depicts significance of ancestral contributions. A value of 1.0 indicates that each individual has a significant contribution from the respective ancestral population, a value of <1 indicates that the ancestral contribution is observed only in a proportion of the individuals, while a value of 0 indicates complete absence. (B) Map of India representing the sampling sites for 10 population identifiers and four regionally relevant genetic clusters (GCs). Flags depict the geographical location and date of Dutch East Indian Company (VOC) trading posts, with percentage in red depicting the estimated slave contribution to the Cape Colony. (C) STRUCTURE analysis of 9,317 LD-pruned autosomal markers for three ancestral populations distinguishes between a ‘Sino-Tibetan’ and ‘Indo-European’ population cluster, the latter significantly impacted by colonization of India. This data suggests that both clusters contributed to slavery at the Cape.