Genome-Wide SNP Analysis of Southern African Populations Provides New Insights into the Dispersal of Bantu-Speaking Groups

Abstract

The expansion of Bantu-speaking agropastoralist populations had a great impact on the genetic, linguistic, and cultural variation of sub-Saharan Africa. It is generally accepted that Bantu languages originated in an area around the present border between Cameroon and Nigeria approximately 5,000 years ago, from where they spread South and East becoming the largest African linguistic branch. The demic consequences of this event are reflected in the relatively high genetic homogeneity observed across most of sub-Saharan Africa populations. In this work, we explored genome-wide single nucleotide polymorphism data from 28 populations to characterize the genetic components present in sub-Saharan African populations. Combining novel data from four Southern African populations with previously published results, we reject the hypothesis that the “non-Bantu” genetic component reported in South-Eastern Africa (Mozambique) reflects extensive gene flow between incoming agriculturalist and resident hunter-gatherer communities. We alternatively suggest that this novel component is the result of demographic dynamics associated with the Bantu dispersal.

Mozambican genetic variation provides new insights into the Bantu expansion

“…This pattern suggests that Bantu speakers scarcely admixed with local foragers, in agreement with recent findings about Bantu speakers from Malawi, who displayed no Khoisan ancestry, despite the confirmed presence of a Khoisan-related genetic component in ancient samples from the region (34). It therefore seems that the processes governing earlier admixture events between Bantu-speakers and local huntergather groups in modern-day Mozambique and Malawi were very different from what has been reported for South Africa and Botswana (7,30,35). As previously suggested on the basis of genetic variation in uniparental markers and archaeological modeling, the differences in admixture dynamics leading to increased Bantu/Khoisan admixture beyond the southern border of Mozambique could have been caused by a slowdown of the Bantu expansion due to adverse ecoclimatic conditions (36 is located in Angola (Kimbundu) rather than in East Africa (as represented by the Bakiga and Luhya from around the Great Lakes) (20).…”

Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations

“…At $K=12,$ the component common in Niger-Congo speaking populations splits into two, one common in Western and Central African populations and in Western Bantu speakers, the other more common in Southeastern Bantu speakers, consistent with these representing the last stage of the Bantu migration process (González-Santos et al 2015). Interestingly, this Southeastern Bantu component is present in most Khoesan populations from Botswana, Lesotho, and South Africa, providing evidence for admixture during the expansion of Bantu-speaking populations (Tishkoff et al 2009; Pickrell and Pritchard 2012; Schlebusch et al 2012; Barbieri et al 2013b; Petersen et al 2013; González-Santos et al 2015; Marks et al 2015; Busby et al 2016). The presence of ancestry related to Western Bantu speakers in some of the Western Khoesan populations such as the Khoe, the Hai||om, and the Nama, is consistent with their current geographic position, and could be interpreted as a signature of admixture events.…”

“…Forty-four of these individuals from four Bantu speaking groups (MbukushuM, OwamboM, Kwangali, and Sotho), and a Khoesan-speaking group (NamaM), have been published previously (González-Santos et al 2015), using a subset of the markers (∼2000). Eight individuals each from the Damara and Hai||om, collected in the Khorixas and Etosha areas of Namibia, respectively, are presented here for the first time.…”

“…Eight individuals each from the Damara and Hai||om, collected in the Khorixas and Etosha areas of Namibia, respectively, are presented here for the first time. Detailed information about the collecting process and samples are available elsewhere (Marks et al 2012, 2015; González-Santos et al 2015). Full ethical approval for the collections was provided by the Oxford Tropical Research Ethics Committee (OxTREC), the Lesotho Ministry of Health and Social Welfare, the Lesotho Ministry of Local Government, the Lesotho Ministry of Tourism, Environment and Culture, and the Namibian Ministry of Health and Social Services.…”

Investigating racial differences in clinical and pathological features of prostate cancer in South African men

“…The age standardised rate of prostate cancer in Kampala, Uganda was calculated as Genetic admixture seems to have been relatively minimal during much of this process, resulting in a good correlation between genetic and linguistic lineage (61,62). So despite the fact that within population genetic diversity is greatest in African populations (63), it is plausible that a genetic risk factor for prostate cancer might be shared by populations as widely separated as African Americans and Southern African Bantu speakers.…”