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A. Patterns of admixture in the AFRIKANER population of South Africa
(Adapted from Patterns of African and Asian admixture in the Afrikaner population of South Africa N. Hollfelder, J. C. Erasmus, R. Hammaren, M. Vicente, M. Jakobsson, J. M. Greeff & C. M. Schlebusch 24 February 2020)
The most dominant contribution to the Afrikaner population came from European immigrants, whereas the Coloured population has more diverse ancestries. The colonization of southern Africa started in 1652 when the Dutch East India Company (DEIC) established a refreshment station at the Cape of Good Hope (Cape Town today).
- In 1657, employees of the DEIC were released from their services to start farming. This group, numbering 142 adults and children in 1658, continued to grow due to high fecundity (almost 3% per annum) and continued immigration, and their descendants became the Afrikaners
Two other major sources of immigrants were
- 156 French Huguenots that arrived in 1688
- and an unknown number of German labourers and soldiers that were financially marginalized.
Estimates, based on genealogical research, vary but Dutch, German and French respectively contributed 34–37%, 27–34% and 13–26%.
While the DEIC did not encourage admixture with local populations and slaves, the strongly male-biased ratio of immigrants led to mixed-ancestry unions , especially between European males and non-European females. The offspring from these unions were frequently absorbed into the Afrikaner populatio. As time progressed, relationships between Europeans and non-Europeans became more infrequent, and as early as 1685, marriages between Europeans and non-Europeans were outlawed (marriages to admixed individuals, with some European ancestry, were still allowed though). In early colonial times, mixed marriages were more acceptable than later on, and due to the population’s fast growth rate, early unions likely contributed exponentially more to the Afrikaner population.
Elphick and Shell distinguish two admixture patterns in Afrikaners based on historical records
- —in Cape Town and the surrounding area admixture was predominantly between European men and female slaves or former slaves,
- and in the outlying areas between European pastoralist frontier farmers (“trekboere”) and Khoe-San women.
Admixture with slaves (and former slaves) resulted from informal as well as formal associations. The church recorded many marriages between Europeans and manumitted slaves. It is unclear what the input of informal relationships into the Afrikaner gene pool was, as the outcome of these relationships and the population affiliation of the resulting offspring were not recorded. One source of informal liaisons was the slave lodge that served as a brothel for 1 h a day for passing sailors and other European men. This practice was so extensive that many children in the slave lodge clearly had European fathers (3/4 in 1671; 44/92 in 1685; 29/61 of school children and 23/38 children younger than 3 years in 1693). Many women that married at the Cape during the early years used the toponym “van de Kaap” (meaning from the Cape) which may indicate a locally born slave. European men also sometimes had a “voorkind” (meaning “before child”) with a slave in the household before they got married to a European woman. These children could also have been absorbed into the Afrikaner population (as opposed to becoming part of the Coloured population).
To understand the characteristics of the genetic contributions that slaves made, it is necessary to know from where and when they came to Cape Town and see that in the light of European male partner choices. Shell claimed that from 1658 to 1807, roughly a quarter of the slaves in the Cape colony came from Africa, Madagascar, South Asia and Southeast Asia each. Slave trade in the Cape was stopped in 1807, and slavery as such was stopped in 1834. Worden estimated that more slaves came from Asia, specifically South Asia, and fewer from Madagascar and Africa. Nevertheless, we do not expect an exact reflection of these ratios in Afrikaners. European men had a clear preference for Asian and locally born slaves over African and Malagasy women. Despite only two ships, containing West African slaves, that moored at the Cape in 1685, we can expect the West African per capita contribution to exceed later arrivals because the fast population growth rate meant earlier contributions benefitted more from the exponential growth.
The “trekboere” were European farmers who followed a nomadic lifestyle in harsh conditions along the frontier. Informal unions with Khoe-San women were more frequent amongst the “trekboere”, but it is unclear if children from these relationships were absorbed into the Coloured and/or Afrikaner community. Poor record keeping and a reduced presence of the church on the frontier meant that recorded information is incomplete for this section of the population. In the Cape, formal unions between European men and Khoe-San women were very unusual with only one known example.
By using church records, genealogists calculated the contribution of non-Europeans to be between 5.5 and 7.2% . These estimates may be biased because the registers (a) only reflect the Christian fraction of the population, (b) were less complete at the frontier where admixture may have been more frequent, (c) could be incorrectly pieced together from church records and (d) list people of unknown heritage, such as “van de Kaap”. In addition, records may be incorrect or unrecorded for children born out of wedlock. Populations that would have been excluded were a substantial Muslim community amongst manumitted slaves, a small Chinese population resulting from exiles and banned political prisoners and the indigenous Khoe-San who were not partial to the Christian religion. The presence of the Coloured population compounded these difficulties as genes may have exchanged between the Coloured and Afrikaner populations.
Genealogical records suggest that Afrikaners have their main ancestry components from Europeans (Dutch, German and French) and estimate the non-European contributions to the Afrikaner to be between 5.5 and 7.2%. Our genetic study that included 77 Afrikaners inferred a slightly lower non-European contribution than predicted by genealogical studies. From population structure analyses, we saw that Afrikaners have their main ancestry component (95.3%) from European populations. The European component is a more northwestern (than southern or eastern) European component which is in agreement with genealogical records of most ancestry coming from Dutch and German (61–71%), intermediate from French (13–26%), with much smaller fractions from other European groups. Of note, Afrikaners group separately from populations from the UK despite the fact that the Cape was a British colony from 1806 onwards. This confirms the relatively small contributions from British people to the Afrikaner population as predicted by genealogical records.
The non-European fraction in Afrikaners was estimated to be 4.7% on average. More of the non-European admixture fraction appeared to have come from people who were brought to the Cape as slaves (3.4%) during colonial times than from local Khoe-San people (1.3%). Indeed historical records of the early Cape Colony record more instances of unions between European men and slaves or former slaves than to local Khoe-San women. Only one example of a Khoe-San-European union in the Cape colony is known. A local Khoekhoe woman from the Goringhaicona group, Eva (or Krotoa) van de Kaap, was an interpreter and ambassador between the colonists and Khoekhoe people and married Pieter Van Meerhof in 1664. Since unions between Khoe-San women and the frontier farmers were thought to be more frequent, it may account for the 1.3% observed admixture in the Afrikaner population. The 1.3% observed Khoe-San ancestry calculates to 26.6 Khoe-San women out of 2048 ancestors 11 generations ago. However, we know that one Afrikaner had for example only 299 ancestors in colonial times because many Afrikaner ancestors enter pedigrees multiple times. These 26.6 Khoe-San women that contributed to the average Afrikaner should thus not be seen as 26 separate women (i.e. the same woman could have contributed many times). The Khoe-San admixture component is the most ubiquitous non-European admixture component and only 6 out of the 77 Afrikaners had no Khoe-San ancestry.
South and East Asians contribute cumulatively to an average of 2.6% of the Afrikaner ancestry (53.2 out of 2048 ancestors 11 generations ago). Elphick and Shell noted that European men more often mixed with Asian and locally born slaves than African and Malagasy women. Although many other additional factors might have played a role in the resultant current-day Afrikaner admixture fractions, the genetic admixture fractions of South and East Asians were higher in current-day Afrikaners than Khoe-San fractions (1.3%) and West/East African fractions (0.8%) and slightly higher than the combined African fractions (2.1%). South Asian contributions outweigh East Asian contributions. The South Asian contribution seems to have come predominantly from Indian populations.
West/East Africans contributed an average of 0.8% of the Afrikaner ancestry (16.3 out of 2048 ancestors 11 generations ago). Shell estimated that about 63,000 slaves arrived in the Cape colony between 1658 and 1807 and a quarter came from West/East coastal Africa (26.4%, east coast and only 2.5% from West Africa). Only two ships brought West African slaves to the Cape in 1685. When one takes into account that only 2.5% of African slaves came from West Africa, it is surprising that just over half of this signal is from West Africans rather than East Africans. This discrepancy could possibly be explained by West Africans arriving four generations earlier than East Africans. More frequent admixture during early years and fast population growth could have caused the genetic footprint of West Africans to exceed that of East Africans. Another explanation that likely contributes to this observation is that a large fraction of the East African slaves brought to the Cape colony might have been East African Bantu speakers and thus they would also trace most of their ancestry to West Africa.
The shared allele analysis indicates that the West African fraction in the Afrikaners mostly came from West (and possibly East) African slaves and not from southern African Bantu speakers. Afrikaners shared the most alleles with the West African Yoruba from Nigeria, intermediate levels with East African Bantu speakers (LWK from Kenya) and the lowest level with local South African Bantu speakers (southeast Bantu speakers).Although current-day South African Bantu speakers trace the majority of their ancestry (80%) to West Africa, there were no Bantu speakers present in the southwestern part of Africa during colonial times.
While admixture fractions between East Asians, South Asians and Khoe-San correlate well with each other in Afrikaner individuals , West/East African fractions do not correlate significantly with South Asian and East Asian fractions and a high number of Afrikaners had no West/East African admixture (26/77). These patterns could possibly be explained by the fact that there were relatively few West African slaves at the Cape, that the arrival of West African slaves was contained in a very limited time period and that East African slaves arrived later in time.
Although the different admixture events into the Afrikaners could not be distinguished in the admixture time estimates (probably because they all occur during the same time period), the estimated time of 9.3 (SD = 0.99) generations compares well with genealogical estimates. In the Afrikaner population, the average generation time for men is 32.92 years whereas for women it is 27.36. Using a mean generation time of 30 years, the time of admixture equates to 279 years ago. The average date of birth of the study participants was 1960—which resolves to an estimated admixture date of 1681 (± 30 years). This date falls during early colonial times at the Cape and since most admixing events are thought to have occurred during this time period, the genetic dating falls into the expected range.
Afrikaners showed several clear local genomic signals where allele frequencies significantly deviate from the frequencies of comparative northwestern European groups. A gene associated to the top signal is expressed in the testes and has sperm antigen functions, which might suggest reproduction adaptation in the Afrikaners. Scans for haplotypes under selection in the Afrikaners implicated several genes associated with diet, i.e. intestinal function, lipid and glucose metabolism, possibly indicating adaptation to modified or novel food sources.
It is interesting to observe that Afrikaners do not present a signal of a population bottleneck compared to European groups, even though they had a very small founding population. This could be explained by the fact that even though the initial founding population of the Afrikaners was small, they were from diverse origins in Europe. Additionally, some of the initial unions resulted in admixed children who were incorporated in the resultant population. The very high population growth rate means that alleles were unlikely to coalesce in the recent past. For example, one Afrikaner individual’s parents had 125 common ancestors, but these were so distant (paths longer than 16 steps) from each other that his inbreeding coefficient is only 0.0019. Until recently, most humans were sedentary and populations were small so that inbreeding due to distant relations was not unusual. However, a number of founder effects for specific diseases have been identified in Afrikaners. These founder effects however need not imply inbreeding but rather suggest a sampling effect, i.e. some disease alleles were present in original founders and were amplified through exponential population growth. https://www.geni.com/documents/view?doc_id=6000000203176378872