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

N Hollfelder,M Jakobsson,M Jakobsson,M Jakobsson,J C Erasmus,J M Greeff,M Vicente,R Hammaren,C M Schlebusch,C M Schlebusch,C M Schlebusch

doi:10.1186/s12915-020-0746-1

Abstract

BackgroundThe 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%.ResultsTo 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.ConclusionsWhile 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 current-day European populations.

Highlights

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 population structure analysis (Fig. 1) [46], Afrikaners cluster with non-Africans (K = 2 to K = 9) and Europeans (K = 3 to K = 9) before receiving their own cluster at K = 10
Afrikaners contain significantly more northern European ancestry component compared to CEU and GBR (P < 0.00001, Mann-Whitney U test)

Summary

Introduction

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. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. The seventeenth-century European colonization of the southern tip of Africa resulted in the influx of two groups of people, European colonists and slaves. The subsequent admixture between these external groups. While both the Afrikaner and Coloured populations have ancestry from many populations from different continents, the ancestry proportions differ substantially between the groups. The admixture proportions of these populations do not reflect the historical local census sizes of the parental populations (Additional file 1: Hollfelder et al BMC Biology (2020) 18:16

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