The view from southwestern Angola offers a new perspective on the populating history of southern Africa and the Bantu expansions by showing that social stratification and different subsistence patterns are not always indicative of remnant groups, but may reflect Bantu-internal variation and ethnogenesis.

The LP adaptation was carried to southern Africa by non-Bantu speaking pastoralists from eastern Africa, but an obvious link between its presence in southern Angola and groups speaking languages of the Khoe-Kwadi family, as previously found in other areas, could not be confirmed. 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.

Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx'a, Khoe-Kwadi, and Bantu languages. Although present-day Bantu speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been thought to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the male-specific region of the Y chromosome (MSY) from 170 individuals with previously reported mitochondrial DNA (mtDNA) genomes, to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun), and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu MSY lineages among Bantu-speaking groups, except for small amounts of "Khoisan" introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for MSY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.

Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx'a, Khoe-Kwadi and Bantu languages. Although presentday Bantu-speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been though to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the non-recombining Y chromosome (NRY) from 170 individuals with previously reported mitochondrial genomes (mtDNA), to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun) and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu NRY lineages among Bantu-speaking groups, except for small amounts of "Khoisan" introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for NRY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.