Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry.

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. The unique genetic heritage of the Namib peoples shows how modern DNA research targeting understudied regions of high ethnolinguistic diversity can complement ancient DNA studies in probing the deep genetic structure of the African continent.

Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe.

BACKGROUND: 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). RESULTS: Our results indicate that neither host genetics nor livelihood seem to influence the oral microbiome profile, with Neisseria, Streptococcus, Prevotella, Rothia, and Porphyromonas being the five most frequent genera in southern African groups, in line with what has been shown for other human populations. However, we found that some Tshwa and Twa individuals display an enrichment of pathogenic genera from the Enterobacteriaceae family (i.e. Enterobacter, Citrobacter, Salmonella) of the Proteobacteria phylum, probably reflecting deficient sanitation and poor health conditions associated with social marginalization. CONCLUSIONS: Taken together, our results suggest that socio-economic status, rather than ethnolinguistic affiliation or subsistence mode, is a key factor in shaping the salivary microbial profiles of human populations in southern Africa.

The linguistic and genetic landscape of southern Africa.

The 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. A special focus on modern groups speaking languages of the Khoe-Kwadi family further reveals how contact and admixture led to the generation of new ethnic identities whose diverse subsistence patterns and cultural practices have long puzzled scholars from various disciplines.

The Genes of Freedom: Genome-Wide Insights into Marronage, Admixture and Ethnogenesis in the Gulf of Guinea.

The 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. Our findings show that while all islanders display mixed contributions from the Gulf of Guinea and Angola, the Angolares are characterized by extreme genetic differentiation and inbreeding, consistent with an admixed maroon isolate. In line with a more prominent Bantu contribution to their creole language, we additionally found that a previously reported high-frequency Y-chromosome haplotype in the Angolares has a likely Angolan origin, suggesting that their genetic, linguistic and social characteristics were influenced by a small group of dominant men who achieved disproportionate reproductive success.

Along the Indian Ocean Coast: Genomic Variation in Mozambique Provides New Insights into the Bantu Expansion.

The 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 ∼1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a "late split" between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola.

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.

Matriclans shape populations: Insights from the Angolan Namib Desert into the maternal genetic history of southern Africa.

OBJECTIVES: 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. MATERIALS AND METHODS: We analyzed 295 complete mtDNA genomes and linguistic data from seven groups from the Namib Desert (Himba, Kuvale, Tjimba, Twa, Kwisi, Kwepe) and Kunene Province (!Xun), placing special emphasis on the evaluation of the genealogical consistency of the matriclanic system that characterizes most of these groups. RESULTS: We found that the maternal genetic structure of all groups from the Namib Desert was strongly shaped by the consistency of their matriclanic system. The tracking of the maternal heritage enhanced population differentiation by genetic drift and is likely to have caused the divergent mtDNA profiles of the Kwepe, Twa, and Kwisi, who probably formed a single population within the spectrum of Bantu genetic variation. Model-based analyses further suggest that the dominant pastoral groups Kuvale and Himba may be grouped into a Bantu proto-population which also included the ancestors of present-day Tjimba and Herero, as well as the Khoe-Kwadi speaking Damara foragers from Namibia. DISCUSSION: 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.

Food and pathogen adaptations in the Angolan Namib desert: Tracing the spread of lactase persistence and human African trypanosomiasis resistance into southwestern Africa.

OBJECTIVES: 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. While LP was found to be more frequent in foragers than in pastoralists, the frequencies of the two APOL1 variants associated with HAT-resistance (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 molecularly related to haplotypes found in other African Bantu-speaking populations. The putatively archaic G3 variant displayed more intra-allelic diversity in Africa than in Europe. DISCUSSION: 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.