Wide-scale geographical analysis of genetic ancestry in the South African Coloured population

Abstract

Background The South African Coloured (SAC) population, a prominent admixed population in South Africa, reflects centuries of migration, admixture, and historical segregation. Descendants of local Khoe-San and Bantu-speaking populations, European settlers, and enslaved individuals from Africa and Asia, SAC individuals embody diverse ancestries. This study investigates the genetic makeup of SAC individuals, utilizing autosomal genotypes, mitochondrial DNA and Y-chromosome data. We analyse new genotype data for 125 SAC individuals from seven locations. Results Our analysis, based on a dataset comprising 356 SAC individuals from 22 geographic locations, revealed significant regional variations in ancestry. Khoe-San ancestry predominates in 14 locations, highlighting its lasting influence. Inland regions exhibit higher proportions of Khoe-San ancestry, eastern regions show more Bantu-speaker/West African ancestry, and western/coastal areas, particularly around Cape Town, display increased Asian ancestry. Additionally, sex-biased admixture ratios show male-biased admixture from East Africans and Europeans, and female-biased admixture from Khoe-San populations, which is supported by mitochondrial and Y-chromosome data. Conclusions The observed patterns of significant regional variation in ancestry reflect historical migrations and settlement patterns. This research underscores the importance of studying the SAC population to understand South Africa’s historical migrations, providing insights into the complex genetic heritage of South Africans.