Ancient DNA studies reveal the genetic structure of Africa before the expansion of Bantu-speaking agriculturalists; however, the impact of now extinct hunter-gatherer and herder societies on the genetic makeup of present-day African groups remains elusive. Here, we uncover the genetic legacy of pre-Bantu populations from the Angolan Namib Desert, where we located small-scale groups associated with enigmatic forager traditions, as well as the last speakers of the Khoe-Kwadi family's Kwadi branch. By applying an ancestry decomposition approach to genome-wide data from these and other African populations, we reconstructed the fine-scale histories of contact emerging from the migration of Khoe-Kwadi-speaking pastoralists and identified a deeply divergent ancestry, which is exclusively shared between groups from the Angolan Namib and adjacent areas of Namibia.
View Article and Find Full Text PDFBackground: While the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood. To gain better insights into the general composition of the microbiome on a global scale, the characterization of microbiomes from a broad range of populations, including non-industrialized societies, is needed. Here, we used the portion of non-human reads obtained through an expanded exome capture sequencing approach to characterize the saliva microbiomes of 52 individuals from eight ethnolinguistically diverse southern African populations from Angola (Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, !Xun) and Zimbabwe (Tshwa), including foragers, food-producers, and peripatetic groups (low-status communities who provide services to their dominant neighbors).
View Article and Find Full Text PDFThe present-day diversity of southern African populations was shaped by the confluence of three major pre-historic settlement layers associated with distinct linguistic strata: i) an early occupation by foragers speaking languages of the Kx'a and Tuu families; ii) a Late Stone Age migration of pre-Bantu pastoralists from eastern Africa associated with Khoe-Kwadi languages; iii) the Iron Age expansion of Bantu-speaking farmers from West-Central Africa who reached southern Africa from the western and eastern part of the continent. Uniting data and methodologies from linguistics and genetics, we review evidence for the origins, migration routes and internal diversification patterns of all three layers. By examining the impact of admixture and sex-biased forms of interaction, we show that southern Africa can be characterized as a zone of high contact between foraging and food-producing communities, involving both egalitarian interactions and socially stratified relationships.
View Article and Find Full Text PDFThe forced migration of millions of Africans during the Atlantic Slave Trade led to the emergence of new genetic and linguistic identities, thereby providing a unique opportunity to study the mechanisms giving rise to human biological and cultural variation. Here we focus on the archipelago of São Tomé and Príncipe in the Gulf of Guinea, which hosted one of the earliest plantation societies relying exclusively on slave labor. We analyze the genetic variation in 25 individuals from three communities who speak distinct creole languages (Forros, Principenses and Angolares), using genomic data from expanded exomes in combination with a contextual dataset from Europe and Africa, including newly generated data from 28 Bantu speakers from Angola.
View Article and Find Full Text PDFThe Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using ∼1.
View Article and Find Full Text PDFSouthwestern 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.
View Article and Find Full Text PDFObjectives: Southern Angola is a poorly studied region, inhabited by populations that have been associated with different migratory movements into southern Africa. Apart from Kx'a-speaking San foragers and Bantu-speaking pastoralists, ethnographic and linguistic studies have suggested the existence of an enigmatic array of pre-Bantu communities, like the Kwepe (formerly Khoe-Kwadi speakers), Twa and Kwisi. Here, we evaluate previous peopling hypotheses by assessing the relationships between different southern Angolan populations, based on newly collected linguistic data and complete mtDNA genomes.
View Article and Find Full Text PDFObjectives: We investigated the frequency distribution and haplotype diversity of human African trypanosomiasis (HAT) resistance and lactase persistence (LP) variants in populations from the Angolan Namib 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 short tandem repeat loci in six groups with different subsistence traditions living in the Angolan Namib, and in a comparative dataset including other populations from Africa and Europe. LP in the Angolan Namib is represented by the -14010*C allele, which is associated with a predominant haplotype that is shared with other southern and eastern African populations.