Abstract: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-spe… Show more
“…1 ). Similarly low levels of local group admixture have been noted for Bantu speakers from Malawi 16 and Mozambique 21 . A recent attempt to reconstruct the route of Bantu migration across central Africa concluded that populations from Angola were the best source of Bantu speakers for east and south African Bantu speakers, and suggested a westerly route of Bantu-speaker migration via Angola 9 .…”
Section: Insights Into Migration and Admixturementioning
The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.
“…1 ). Similarly low levels of local group admixture have been noted for Bantu speakers from Malawi 16 and Mozambique 21 . A recent attempt to reconstruct the route of Bantu migration across central Africa concluded that populations from Angola were the best source of Bantu speakers for east and south African Bantu speakers, and suggested a westerly route of Bantu-speaker migration via Angola 9 .…”
Section: Insights Into Migration and Admixturementioning
The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.
“…In addition, the extent of the gene-flow also varies considerably between the SEB groups clearly differentiating them from one other. For example, the Khoe-San ancestry levels vary from >20% in the South African Tswana and Sotho to only around 3% in the Chopi and Tswa from south Mozambique, whereas central and north Mozambican populations, Zambian and Malawian populations have no admixture signals with Khoe-San ( 16 , 37–39 , 46 ) ( Fig. 1 ).…”
Section: Admixture Of Bantu-speakers With Resident Hunter-gatherer Populationsmentioning
The presence of Early and Middle Stone Age human remains and associated archaeological artefacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of southern Africa have largely been reshaped by three major sets of migrations over the last 2000 years. These migrations have led to a confluence of four distinct ancestries (San hunter-gatherer, East African pastoralist, Bantu-speaker farmer and Eurasian) in populations from this region. In this review, we have summarized the recent insights into the refinement of timelines and routes of the migration of Bantu-speaking populations to southern Africa and their admixture with resident southern African Khoe-San populations. We highlight two recent studies hinting at the emergence of fine-scale population structure within some South-Eastern Bantu-speaker groups. We also accentuate whole genome sequencing studies (current and ancient) that have both enhanced our understanding of the peopling of southern Africa and demonstrated a huge potential for novel variant discovery in populations from this region. Finally, we identify some of the major gaps and inconsistencies in our understanding and emphasize the importance of more systematic studies of southern African populations from diverse ethnolinguistic groups and geographic locations.
“…The intensity of this sex bias increases from North to South, possibly indicating changes in social interactions between immigrating groups and autochthonous peoples over time ( 35 ). Such changes in interactions are also implied by the varying levels of Khoisan-related ancestry detectable in modern-day Bantu-speaking populations of southern Africa: populations from Malawi do not show any evidence for Khoisan-related ancestry ( 14 ), and populations from southern Mozambique show only low levels of such ancestry [4–5% maximum ( 43 )]. This is in contrast to populations such as the Kgalagadi and Tswana from Botswana with 33–39% and 22–24% Khoisan-related ancestry, respectively ( 29 , 36 ), or the Sotho, Xhosa and Zulu from South Africa with between ~10–24% Khoisan-related ancestry ( 43 , 44 ).…”
Section: Admixture With Immigrating Food-producing Populationsmentioning
confidence: 99%
“…Such changes in interactions are also implied by the varying levels of Khoisan-related ancestry detectable in modern-day Bantu-speaking populations of southern Africa: populations from Malawi do not show any evidence for Khoisan-related ancestry ( 14 ), and populations from southern Mozambique show only low levels of such ancestry [4–5% maximum ( 43 )]. This is in contrast to populations such as the Kgalagadi and Tswana from Botswana with 33–39% and 22–24% Khoisan-related ancestry, respectively ( 29 , 36 ), or the Sotho, Xhosa and Zulu from South Africa with between ~10–24% Khoisan-related ancestry ( 43 , 44 ). Such changes in social interactions between immigrating Iron Age agropastoralists and resident Khoisan-speaking populations might also explain variable patterns of click borrowing in Bantu languages ( 18 , 45 ).…”
Section: Admixture With Immigrating Food-producing Populationsmentioning
Peoples speaking so-called Khoisan languages—that is, indigenous languages of southern Africa that do not belong to the Bantu family—are culturally and linguistically diverse. They comprise herders, hunter-gatherers, as well as groups of mixed modes of subsistence and their languages are classified into three distinct language families. This cultural and linguistic variation is mirrored by extensive genetic diversity. We here review the recent genomics literature and discuss the genetic evidence for a formerly wider geographic spread of peoples with Khoisan-related ancestry, for the deep divergence among populations speaking Khoisan languages overlaid by more recent gene flow among these groups, and for the impact of admixture with immigrant food-producers in their prehistory.
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