Complex patterns of genomic admixture within Southern Africa
Date
2013-03
Authors
Petersen, Desiree C.
Libiger, Ondrej
Tindall, Elizabeth A.
Hardie, Rae-Anne
Hannick, Linda I.
Glashoff, Richard H.
Mukerji, Mitali
Indian Genome Variation Consortium
Fernandez, Pedro
Haacke, Wilfrid
Journal Title
Journal ISSN
Volume Title
Publisher
PLOS
Abstract
Within-population genetic diversity is greatest within Africa, while between-population genetic diversity is directly
proportional to geographic distance. The most divergent contemporary human populations include the click-speaking
forager peoples of southern Africa, broadly defined as Khoesan. Both intra- (Bantu expansion) and inter-continental
migration (European-driven colonization) have resulted in complex patterns of admixture between ancient geographically
isolated Khoesan and more recently diverged populations. Using gender-specific analysis and almost 1 million autosomal
markers, we determine the significance of estimated ancestral contributions that have shaped five contemporary southern
African populations in a cohort of 103 individuals. Limited by lack of available data for homogenous Khoesan
representation, we identify the Ju/’hoan (n = 19) as a distinct early diverging human lineage with little to no significant non-
Khoesan contribution. In contrast to the Ju/’hoan, we identify ancient signatures of Khoesan and Bantu unions resulting in
significant Khoesan- and Bantu-derived contributions to the Southern Bantu amaXhosa (n = 15) and Khoesan !Xun (n = 14),
respectively. Our data further suggests that contemporary !Xun represent distinct Khoesan prehistories. Khoesan
assimilation with European settlement at the most southern tip of Africa resulted in significant ancestral Khoesan
contributions to the Coloured (n = 25) and Baster (n = 30) populations. The latter populations were further impacted by 170
years of East Indian slave trade and intra-continental migrations resulting in a complex pattern of genetic variation
(admixture). The populations of southern Africa provide a unique opportunity to investigate the genomic variability from
some of the oldest human lineages to the implications of complex admixture patterns including ancient and recently
diverged human lineages.
Description
The original publication is available at www.plosgenetics.org
Keywords
Human genetics, Genetic diversity, Genomic variability, Gender-specific analysis
Citation
Petersen, D.C et al. 2013. Complex patterns of genomic admixture within Southern Africa. PLoS Genetics 9(3), 1-17, e1003309. doi:10.1371/journal.pgen.1003309