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Patterns of African and Asian admixture in the Afrikaner population of South Africa
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.ORCID iD: 0000-0002-1567-8450
Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.ORCID iD: 0000-0002-9122-4530
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2020 (English)In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 18, no 1, article id 16Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2020. Vol. 18, no 1, article id 16
Keywords [en]
Afrikaner, South Africa, Admixture, Slave trade, Colonial times
National Category
Genetics Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-335377DOI: 10.1186/s12915-020-0746-1ISI: 000518016100001PubMedID: 32089133OAI: oai:DiVA.org:uu-335377DiVA, id: diva2:1162591
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2014-5211; 642-2013-8019Available from: 2017-12-04 Created: 2017-12-04 Last updated: 2020-05-28Bibliographically approved
In thesis
1. Population genetic history and patterns of admixture: Examples from northeastern and southern Africa
Open this publication in new window or tab >>Population genetic history and patterns of admixture: Examples from northeastern and southern Africa
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa.

Both of these regions are population melting-pots, with many historically known major migrations.

In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper.

I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations.

The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population.

Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy.

This thesis contributes to a deeper understanding of African demographic history in general and of some previously understudied populations and geographic areas in particular.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2018. p. 57
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1614
Keywords
population structure, genetic admixture, genomic variation, Africa, population genomics, lactase persistence, sex-biased admixture, human evolutionary genetics
National Category
Evolutionary Biology Genetics Bioinformatics (Computational Biology)
Research subject
Biology with specialization in Evolutionary Organismal Biology
Identifiers
urn:nbn:se:uu:diva-335214 (URN)978-91-513-0193-8 (ISBN)
Public defence
2018-02-16, Lindahlsalen, Norbyvägen 18A, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2018-01-24 Created: 2017-12-13 Last updated: 2018-03-07

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Hollfelder, NinaHammarén, RickardVicente, MárioJakobsson, MattiasSchlebusch, Carina

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