Table 1.
Genome-wide population diversity studies of Southern African populations.
| Population | Country | Genotyping method | Marker | Major findings | Reference |
|---|---|---|---|---|---|
| Khoe-San and Bantu speakers | Namibia, South Africa | Microarray (genome-wide) | Autosomal SNPs and CNVs | Khoe-San and Bantu speakers are genetically different. | (Jakobsson et al., 2008; Li et al., 2008) |
| Bantu speakers, SAC and Khoe-San | South Africa | Panel sequencing | Autosomal SNPs, indels, and microsatellites | Khoe-San, SAC and Bantu speakers are genetically divergent. SAC show the highest level of intercontinental admixture. | (Tishkoff et al., 2009) |
| Khoe-San and Bantu speakers | Botswana, Namibia, South Africa | Microarray (genome-wide) | Autosomal SNPs | Structure observed among the Khoisan, and between the Khoisan, SAC, and Bantu speakers. | (Pickrell et al., 2012; Schlebusch et al., 2012) |
| Khoe-San | South Africa | Microarray (genome-wide) | Autosomal SNPs | Precolonial Eurasian admixture observed in Khoe-San populations. | (Pickrell et al., 2014) |
| Khoe-San | Angola, Botswana, South Africa | Microarray (genome-wide) | Autosomal SNPs, mtDNA, and Y-chromosome | Khoe-San show high genetic differentiation and have sex-biased Bantu speakers and European admixture. | (Henn et al., 2011; Montinaro et al., 2017; Uren et al., 2016; Choudhury et al., 2017; Oliveira et al., 2019) |
| Bantu speakers and SAC | South Africa | Microarray (genome-wide) and WGS | Autosomal SNPs | Multiway admixture including Khoe-San ancestry observed in the SAC population. Differential Khoe-San admixture detected in Bantu speakers. | (de Wit et al., 2010; Chimusa et al., 2013a, Gurdasani et al., 2014; Chimusa et al., 2015; Uren et al., 2016; Choudhury et al., 2017; Chimusa et al., 2018) |
| Bantu speakers | South Africa | Microarray (genome-wide) | Autosomal SNPs | Weak clustering of southeastern Bantu speakers possibly due to admixture with Khoe-San. | (May et al., 2013) |
| Khoe-San and Bantu speakers | South Africa, Namibia, Malawi | Microarray (genome-wide) | Autosomal SNPs | Admixture in Malawian population supports the late split of the Eastern Bantu speakers. Eurasian admixture detected in South African Khoe-San, dating back to European colonial period settlement in Southern Africa. | (Busby et al., 2016) |
| Bantu speakers and Khoe-San | Botswana | Microarray (whole exome) and WES | Autosomal SNPs | Within population structure of Botswana was not observed. Genetic differentiation was observed between Sotho, Zulu (of South Africa), and the Botswana population. | (Retshabile et al., 2018) |
Indels, insertions/deletions; SAC, The “Coloured” of South Africa; SNP, single nucleotide polymorphism; CNV, copy number variation; mtDNA, mitochondrial DNA; WES, whole exome sequencing; WGS, whole genome sequencing. Details on specific groups within Khoe-San and Bantu speakers can be obtained from original publications.