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Population genetic history and patterns of admixture: Examples from northeastern and southern Africa
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
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
Keyword [en]
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: urn:nbn:se:uu:diva-335214ISBN: 978-91-513-0193-8 (print)OAI: oai:DiVA.org:uu-335214DiVA, id: diva2:1165836
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
List of papers
1. Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations
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2017 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 8, article id e1006976Article in journal (Refereed) Published
Abstract [en]

Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gateway out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping similar to 3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400-200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2017
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-333162 (URN)10.1371/journal.pgen.1006976 (DOI)000408763800042 ()28837655 (PubMedID)
Available from: 2017-11-07 Created: 2017-11-07 Last updated: 2017-12-13Bibliographically approved
2. The genetic variation of lactase persistence alleles in northeast Africa
Open this publication in new window or tab >>The genetic variation of lactase persistence alleles in northeast Africa
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(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-336177 (URN)
Available from: 2017-12-12 Created: 2017-12-12 Last updated: 2017-12-13
3. Patterns of African and Asian admixture in the Afrikaner population of South Africa
Open this publication in new window or tab >>Patterns of African and Asian admixture in the Afrikaner population of South Africa
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(English)Manuscript (preprint) (Other academic)
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-335377 (URN)
Available from: 2017-12-04 Created: 2017-12-04 Last updated: 2017-12-13
4. Genetic patterns of sex-biased admixture in southern African populations
Open this publication in new window or tab >>Genetic patterns of sex-biased admixture in southern African populations
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(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-335212 (URN)
Available from: 2017-12-01 Created: 2017-12-01 Last updated: 2017-12-13

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