Patterns of African and Asian admixture in the Afrikaner population of South Africa

Abstract

The Afrikaner population of South Africa are the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the "Coloured" populations of South Africa. Ancestry, social class, culture, sex ratio and geographic structure affected admixture patterns and caused different ancestry and admixture patterns in Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records estimated the non-European contributions into the Afrikaners to 5.5%-7.2%. To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization) we genotyped ~5 million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture among diverse groups during early colonial times might have counterbalanced the effects of a founding population with a small census size. SIGNIFICANCE STATEMENTAfrikaners are a southern African ethnic group primarily descended from colonial settlers (population ~2.8-3.5 million). Genome-wide studies might offer interesting insights into their ancestry, not the least due to South Africas history of segregationist laws known as "apartheid", resulting in an expectation of low levels of admixture with other groups. Originating from a small founder population, their genetic diversity is also interesting. In our genome-wide study of 77 Afrikaners we found their majority ancestry (average 95.3%) came from Europeans, but almost all Afrikaners had admixture from non-Europeans (Africans and Asians). Despite their small founding population, we found no signs of decreased genetic diversity. Admixture among diverse groups during colonial times might have counterbalanced effects of a small founding population.