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

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 current-day European populations.


SUPPLEMENTARY FIGURES AND TABLES
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Supplementary Text
This supplementary note discusses the populations from which the Afrikaner population arose, it summarizes genealogical information of admixture and presents genetic information of admixture.

Khoekhoe and San
The

European colonists
Europeans started independent settlement at the Cape from 1658. Since they were to some extent independent of the Dutch East Indian Company (DEIC) they were initially called "free citizens" and as the populations' identity evolved they were referred to as Afrikaners (although "Africander" was initially used to indicate locally born slaves). The population had a high growth rate of about 2.6% per annum [6]. Although a small part of this increase was the result of a continuous arrival of immigrants, it is mostly due to the population's high fecundity ( Figure S12).
The immigrants from Europe originated from many different countries and the DIC encouraged immigration by offering free passage to the Cape and granting land for farming [7]. The Netherlands, Germany and France were the most important sources of immigrants with them respectively donating 34%-37%, 27%-34% and 13%-26% of the immigrants. Figure S12. The population size of adult Afrikaner men (solid heavy line) and women (solid lighter line) as a function of time. Data was obtained from Gouws [8]. The yearly average number of immigrants that married into Afrikaner families is given in dashed lines with men in heavy and women in lighter lines. Data was counted from Heese [9]. These values are averages for 30 year periods, so for instance, from 1808 to 1837, 970 men who were not born at the Cape, got married in the colony, giving a yearly rate of 32⅓. Note the different scales on the y-axes. The Y-axis in the second panel starts where the axis ends in the first panel.

Slaves
Starting with two boats carrying about 400 slaves from West Africa in 1658 the slave population grew to 36,169 in 1834 when slavery was abolished at the Cape [10]. The total number of slaves and their origin has to be inferred indirectly, because records are missing and many arrivals were not recorded (Worden pers comm). Even so, Shell [4] argued that about 63,000 slaves arrived in the colony between 1658-1807. He calculated that roughly a quarter came from each of; Africa  [4]. Based on household inventories, Worden [11,12] estimated that more slaves came from Asia, especially South Asia, and that substantially fewer came from Madagascar and Africa. Both sources suggest marked temporal variation in the origin of slaves, with Asian slaves predominating in the 17 th and earlier 18 th centuries and African slaves dominating towards 1807 ( Figure S13). Initially the DEIC owned most slaves but after 1692 colonists owned the majority [10]. Shortly after 1710 slaves outnumbered the colonists and this situation remained until the abolition of slave trade in 1807 [10]. Although the slave population creolized (>50% locally born) in 1770 [4], the local growth was lower than that of the colonists [10]. After emancipation in 1834 slaves were freed after a four-year apprenticeship and formed the backbone of the Coloured community. Figure S13. The origins of slaves arriving in the Cape. Estimates based on Shell [4] (A-D) and Worden [11,12] (E-H). Shell's [4] data were read off his figure 2-1, rounded to the nearest 20, with slight adjustments to 1) fit the time line of arrivals from 1658 -1807, and to 2) correct for the first two vessels that arrived from Western Africa in 1658. Worden's [11,12]

Absence of South African Bantu-speakers
Bantu-speakers originated from West Africa and started to expand to the rest of sub-Saharan Africa around 4,000 years ago, reaching the northern parts of current-day South Africa around 1,800 years ago. During the 1600s the edge of the Bantu-expansion (specifically Xhosa speakers) reached as far south as the Fish River in the Eastern Cape Province of current day South Africa (approximately 1000 km from Cape Town). Therefore, Bantu-speakers were only encountered at a much later stage during the frontier wars in 1779-1851 by expanding Afrikaner frontier farmers [13]. Although initial interactions between the frontier farmers and Bantu-speaking Xhosa populations were peaceful with trade between groups, relations quickly turned aggressive and conflicts erupted. It is unlikely that much gene flow occurred between South African Bantu-speakers and Afrikaners, since during this relatively late time period, the Afrikaner population identity had already culminated, which resulted in social hinders to relationships between groups.

Genealogical evidence of admixture
Historians in South Africa compiled genealogical registries for the Afrikaner population based on church records (summarized in Greeff & Erasmus [14]). From these records it is clear that the Afrikaner population is admixed (Table S7). The estimates vary, but the non-European contribution is between 5.4 and 7.2 percent. While many unions between slaves were recorded in church records, only one instance of a union between a European and Khoe-San was solemnized at the Cape [3]. People that are given the toponym "van die Kaap" (meaning from the Cape) rather than a surname are of uncertain heritage. While these individuals were born at the Cape their parent(s) may have been a slave, Khoe-San or even European [15]. For this reason and for other reasons given in the main text, a genetic analysis is required to make an accurate calculation of the population's constitution.

Genetic structure of the Afrikaner population
Surprisingly little is known about the genetic structure of the Afrikaner population. The few genetic studies on Afrikaners suggested admixture between European and non-European populations. 1) For some loci Afrikaners have more alleles than Europeans [16] and 2) Afrikaners have non-European alleles at some loci [17]. Botha & Pritchard [18] estimated that slaves from Africa and Asia, and/or Khoe-San, contributed between 6 -7% of genes to the Afrikaner population. They based their estimate on blood group allele frequencies.
A number of familial diseases are more common in Afrikaners than in European populations [19][20][21][22][23][24][25][26][27]. These data supports the notion of a significant founder effect during the formation of the population [17,28,29]. While a deep routing pedigree of one Afrikaner clearly illustrated the existence of many common ancestors, these were so distant that his pedigree-inbreeding coefficient was not higher than European averages [30].  This sample represents about 15% of the entire Afrikaner population at the time. c Percentages divided by 82.81 from Greeff [30]. It corrects for incomplete lineages. d numbers in bold are totals of normal type indented from each area listed underneath. e The expression "van die Kaap" was given as a toponymical surname and means "from the Cape". It was given to children born at the Cape and was presumably used to hide the fact that their parents were slaves or manumitted slaves. However, their parents may have been Khoe-San or even European [15].