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.
Highlights
Southern Africa is home to populations carrying significant human genomic variation
The pattern of genomic variation in contemporary southern African populations resulted from unions between the most diverse genomes found within Africa to the least differentiated as represented by populations impacted by a severe founder effect associated with the out-of-Africa dispersal [2,10,11,12,13]
While we have previously alluded to the unlikely ancestral contribution of Han Chinese to the Coloured [17], we provide evidence for lack of the East Asian specific ‘dry earwax’ (ABCC11 rs17822931-AA) [41] and the ‘alcohol-induced flush’ genotypes (ALDH2 rs671 A-allele) [42] in our study subjects
Summary
The analysis of patterns of DNA variation, have placed modern human origins within Africa [1], with the most divergent contemporary lineages found in the indigenous Khoesan inhabitants of southern Africa [2,3,4,5,6]. African homeland beginning roughly 1,500 years ago [7,8], followed over a millennium later by the arrival of European settlers and East-Indian slaves [9], shaped the ancestral contributions of contemporary southern Africans. These intra- and intercontinental contributions led to historical events that perpetuated population dispersals, isolations and assimilation between populations, giving rise to complex genomic admixture. The pattern of genomic variation in contemporary southern African populations resulted from unions between the most diverse genomes found within Africa to the least differentiated as represented by populations impacted by a severe founder effect (bottleneck) associated with the out-of-Africa dispersal [2,10,11,12,13]
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