Introduction: We investigated the frequency distribution and haplotype diversity of APOL1 and LCT variants associated with human African trypanosomiasis (HAT) resistance and lactase persistence (LP), respectively, in populations from southern Angola to trace the spread of these genetic adaptations into southwestern Africa.
Materials and Methods: We resequenced two fragments of the LCT-enhancer and the APOL1 gene and genotyped flanking STRs in six groups from the Angolan Namib with different subsistence traditions, and in other populations from Africa and Europe for comparative purposes. The age and selection coefficient of these variants were estimated.
Results: LP in the Angolan Namib is represented by the -14010*C allele, which is associated with a predominant haplotype shared with other southern and eastern African populations. While LP was more frequent in foragers than in pastoralists, the frequencies of the two APOL1 variants (G1 and G2) did not differ between the two groups. The G1 allele is mostly associated with a single widespread haplotype. The G2 allele is linked to several haplotypes that are related to haplotypes found in African Bantu-speaking populations. The putatively archaic G3 variant displayed more intra-allelic diversity in Africa than in Europe.
Conclusions: The LP adaptation was carried to southern Africa from eastern Africa, probably by non-Bantu speaking pastoralists, although we could not confirm a direct link with groups speaking Khoe-Kwadi family languages. The presence of APOL1 variants G1 and G2 is linked to the Bantu expansions. Our results suggest that the G3 variant was retained in modern humans by incomplete lineage sorting.