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

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-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.

High-depth African genomes inform human migration and 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 .…”

Bantu-speaker migration and admixture in southern Africa

“…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 ).…”

The genomic prehistory of peoples speaking Khoisan languages

“…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 ).…”

“…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 ).…”