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

Abstract

Background: The Afrikaner population of South Africa is 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. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%. Results: To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five 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 amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population. Conclusions: While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to currentday European populations.

Male-biased migration from East Africa introduced pastoralism into southern Africa

“…Consequently, they provide a higher affinity to the ancestral population in MOSAIC analyses than other South African Bantu speakers who contain a significant portion of Khoe-San admixture in their genomes. Our results contrast to findings for the Afrikaner community of South Africa, where the Afrikaner West African-associated ancestry had higher affinities with the Yoruba population from Nigeria [ 96 ]. Different sources of slaves and different population interactions across geography and time during the colonial era could explain differences in West African ancestries.…”

Globally Rare BRCA2 Variants With Founder Haplotypes in the South African Population: Implications for Point-of-Care Testing Based on a Single-Institution BRCA1/2 Next-Generation Sequencing Study

“…With genetic drift and natural selection, these major events have created uniquely admixed populations residing at Africa's southern-most region. Their composition and heritage have incited various population studies that attempted to identify each group's genetic architecture (10)(11)(12)(13)(14).…”

Bantu-speaker migration and admixture in southern Africa

“…The third and final major migration into southern Africa dates back to over the last four centuries. In addition to the arrival of several waves of colonial settlers from Europe, slave trade across the Indian Ocean also introduced ancestries from South Asia, East Asia and Madagascar ( 18 ). Subsequent admixture between these settlers, and between them and the local populations, gave rise to complex patterns of genomic admixture in some regions of southern Africa ( 15 , 18–22 ).…”