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Patterns of African and Asian Admixture in the Afrikaner bioRxiv preprint doi: https://doi.org/10.1101/542761; this version posted February 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Patterns of African and Asian admixture in the Afrikaner population of South 2 Africa 3 4 N Hollfelder1*, JC Erasmus2*, R Hammaren1, M Vicente1, M Jakobsson1,3,4+, JM Greeff2#+, CM 5 Schlebusch1,3,4#+ 6 7 8 1 Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 9 SE-752 36 Uppsala, Sweden 10 11 2 Department of Genetics, University of Pretoria, Pretoria, 0002, South Africa 12 13 3 Science for Life Laboratory, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, 14 Sweden 15 16 4 Centre for Anthropological Research & Department of Anthropology and Development Studies, 17 University of Johannesburg, Johannesburg, South Africa 18 19 20 Running Title: Admixture into the Afrikaner population of South Africa 21 * Equal contribution 22 + Equal contribution 23 24 # Correspondence: Carina Schlebusch 25 Email: [email protected] 26 27 # Correspondence: Jaco Greeff 28 Email: [email protected] 29 30 31 32 Keywords: Afrikaner, South Africa, admixture, slave trade, colonial times 33 34 35 1 bioRxiv preprint doi: https://doi.org/10.1101/542761; this version posted February 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 36 ABSTRACT 37 The Afrikaner population of South Africa are the descendants of European colonists who started 38 to colonize the Cape of Good Hope in the 1600’s. In the early days of the colony, mixed unions 39 between European males and non-European females gave rise to admixed children who later 40 became incorporated into either the Afrikaner or the “Coloured" populations of South Africa. 41 Ancestry, social class, culture, sex ratio and geographic structure affected admixture patterns and 42 caused different ancestry and admixture patterns in Afrikaner and Coloured populations. The 43 Afrikaner population has a predominant European composition, whereas the Coloured population 44 has more diverse ancestries. Genealogical records estimated the non-European contributions into 45 the Afrikaners to 5.5%-7.2%. To investigate the genetic ancestry of the Afrikaner population today 46 (11-13 generations after initial colonization) we genotyped ~5 million genome-wide markers in 77 47 Afrikaner individuals and compared their genotypes to populations across the world to determine 48 parental source populations and admixture proportions. We found that the majority of Afrikaner 49 ancestry (average 95.3%) came from European populations (specifically northwestern European 50 populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European 51 admixture originated mostly from people who were brought to South Africa as slaves and, to a 52 lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding 53 population, there is no sign of a recent bottleneck in the Afrikaner compared to other European 54 populations. Admixture among diverse groups during early colonial times might have 55 counterbalanced the effects of a founding population with a small census size. 56 57 58 59 60 61 SIGNIFICANCE STATEMENT 62 Afrikaners are a southern African ethnic group primarily descended from colonial settlers 63 (population ~2.8–3.5 million). Genome-wide studies might offer interesting insights into their 64 ancestry, not the least due to South Africa's history of segregationist laws known as “apartheid”, 65 resulting in an expectation of low levels of admixture with other groups. Originating from a small 66 founder population, their genetic diversity is also interesting. In our genome-wide study of 77 67 Afrikaners we found their majority ancestry (average 95.3%) came from Europeans, but almost all 68 Afrikaners had admixture from non-Europeans (Africans and Asians). Despite their small 69 founding population, we found no signs of decreased genetic diversity. Admixture among diverse 70 groups during colonial times might have counterbalanced effects of a small founding population. 71 72 2 bioRxiv preprint doi: https://doi.org/10.1101/542761; this version posted February 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 73 INTRODUCTION 74 The seventeenth century European colonization of the southern tip of Africa resulted in the influx 75 of two groups of people, European colonists and slaves. The subsequent admixture between these 76 external groups and the local southern African Khoe-San populations resulted in two admixed 77 populations – the Afrikaner population and the “Coloured” population of South Africa (1). (In this 78 article we use the term “Coloured” following the current-day continued use of the term as self- 79 identification (2)). 80 81 While both the Afrikaner and Coloured populations have ancestry from many populations from 82 different continents, the ancestry proportions differ substantially between the groups. The 83 admixture proportions of these populations do not reflect the historical local census sizes of the 84 parental populations (supplementary text), rather, ancestry, social class, culture, sex ratio and 85 geographic structure affected admixture patterns (3-7). 86 87 The most dominant contribution to the Afrikaner population came from European immigrants ((8- 88 10) and supplementary text), whereas the Coloured population has more diverse ancestries (11- 89 20). The colonization of southern Africa started in 1652 when Jan van Riebeeck established a 90 refreshment station for the Dutch East India Company (DEIC) at the Cape of Good Hope (Cape 91 Town today). In 1657 a few employees of the DEIC were released from their services to start 92 farming (4) (numbering 142 adults and children in 1658). They were initially called free citizens 93 and later Afrikaners (supplementary text). The DEIC continued to support the settlement of Dutch 94 nationals and other Europeans by offering free passage to the Cape and granting land for farming 95 (4). The other major sources of immigrants were 156 French Huguenots that arrived in 1688 and 96 an unknown number of German laborers and soldiers that were financially marginalized (4). 97 Estimates vary but Dutch, German and French respectively contributed 34%-37%, 27%-34% and 98 13%-26% ((8-10) and supplementary text). Immigrants from Europe continued to arrive at the 99 Cape from 1658 onwards, but the very rapid population growth of the local established population 100 (almost 3% per annum; (5, 21) and supplementary text) and lower fecundity in the new immigrants 101 (5) meant that the genetic contribution of later arrivals was less ((8) and supplementary text). 102 103 While the DEIC did not encourage admixture with local populations and slaves, the strongly male- 104 biased ratio of immigrants lead to mixed-ancestry unions (3), especially between European males 105 and non-European females (however there are recorded cases of European women marrying non- 106 European men) (7). The offspring from these unions were frequently absorbed into the Afrikaner 107 population (8). As time progressed relationships between Europeans and non-Europeans became 108 more infrequent (8) and as early as 1685, commissioner van Rheede outlawed marriages between 109 Europeans and non-Europeans (marriages to admixed individuals, with some European ancestry, 110 were still allowed though) (7). In early colonial times, mixed marriages were more acceptable than 111 later on, and due to the population’s fast growth rate, early unions likely contributed exponentially 112 more to the Afrikaner population. Elphick and Shell (3) distinguish two admixture patterns in 113 Afrikaners based on historical records – in Cape Town and the surrounding area admixture was 114 predominantly between European men and female slaves or former slaves, and in the outlying 115 areas between European pastoralist frontier farmers (“trekboere”) and Khoe-San women. 3 bioRxiv preprint doi: https://doi.org/10.1101/542761; this version posted February 7, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 116 117 Admixture with slaves (and former slaves) resulted from informal as well as formal associations 118 (3). The church recorded many marriages between Europeans and manumitted slaves (7, 8). 119 Husbands-to-be frequently had to buy their future slave wife’s freedom (7). It is unclear what the 120 input of informal relationships into the Afrikaner gene pool was, as the outcome of these 121 relationships and the population affiliation of the resulting offspring is not clear. Informal liaisons 122 resulted, for example, from the slave lodge that served as a brothel for one hour a day for passing 123 sailors and other European men (3, 22). This practice was so extensive that many children in the 124 slave lodge clearly had European fathers (3/4 in 1671; 44/92 in 1685), prompting commissioner 125 van Rheede to decree that these children should be manumitted and baptized (3). A census of the 126 slave lodge in 1693 revealed 29/61 admixed school children and 23/38 admixed children under the 127 age of three (3). Many women that married at the Cape during the early years used the toponym 128 “van de Kaap” (meaning from the Cape) which may indicate a locally born slave.
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