The genetic legacy of the expansion of Bantu-speaking peoples in Africa

DATA AVAILABILITY : SNP array genotype data of modern-day African populations and whole-genome data of aDNA individuals generated in this project were made available through the European Genome-Phenome Archive (EGA) data repository (EGA accessory nos. EGAS50000000006 and EGAS00001007519 for modern and aDNA, respectively). Controlled-access policies guided by participant consent agreements will be implemented by the AfricanNeo Data Access Committee (AfricanNeo DAC accessory no. EGAC00001003398). Authorized NIH DAC granted data access to C.M.S. for the controlled-access genetic data deposited in the NIH dbGAP repository (accession code phs001396.v1.p1 and project ID 19895). C.M.S. was granted data access to whole-genome sequencing data deposed by the H3Africa Consortium (EGA dataset accessory nos. EGAD00001004220, EGAD00001004316, EGAD00001004334, EGAD00001004393, EGAD00001004448, EGAD00001004505, EGAD00001004533, EGAD00001004557 and EGAD00001005076). Interactive map-based visualizations were created using the Python library bokeh v.3.0.0 and maps were provided by CartoDB (CARTO 2023), other base maps were provided by GoogleMaps (Google 2023) or created using Python libraries (plotly v.5.17.0 and shapely v.1.8.4); R packages (rworldmap v.1.3.6, plotmaps v.1.0, rEEMSplots and rEEMSplots2); and one inhouse vector map in MapInfo interchange format based on the WGS-84 projection.CODE AVAILABILITY : Code and interactive plots used for plotting are available in two online repositories (GitHub https://github.com/Schlebusch-lab/Expansion_of_BSP_peer-reviewed_article and figshare https://doi.org/10.6084/m9.figshare.24107718).SUPPLEMENTARY INFORMATION. Supplementary Methods, Notes 1–12, Figures 1–107, and references.SUPPLEMENTARY TABLES. Supplementary Tables 1–15.The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000–4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.Open access funding provided by Uppsala University.http://www.nature.com/naturehj2024BiochemistryGeneticsMicrobiology and Plant PathologyNon

The genetic legacy of the expansion of Bantu-speaking peoples in Africa.

The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations

The Malian Lakes Region redefined : archaeological survey of the Gorbi Valley

The Malian Lakes Region of West Africa has long been overlooked in favour of better-known basins of the Niger River. New archaeological survey of this region, however, shows a history far more complex than had previously been thought, with settlement mounds and multiple phases of migration and eventual abandonment in a landscape of shifting power structures between the first millennium BC and second millennium AD. With the establishment of a relative chronology, the archaeology of this region now holds great potential for a better understanding of the broader cultural history of the Ghana Empire

A fluid past : socio‐hydrological systems of the West African Sahel across the long durée

Since the end of the last glacial period (similar to 12.4 ka bp) the African continent has undergone no less than 30 dramatic climate transitions. West Africa in particular witnessed abrupt climate oscillations-between humid optima and hyper-aridity-which lasted anywhere between 10 and 15 years and a millennium. Such unpredictable shifts forced local communities to develop a suite of risk-buffering strategies that could withstand climate change on various scales. Both archeological and palaeoclimatic research has begun to reveal how these societies engaged with their erratic environment over the span of the Holocene. The adoption of pastoral lifeways, the domestication of cereal crops, and the emergence of monumentality or urbanism may indeed be viewed through the lens of environmental risk-buffering strategies. Yet, these developments proceeded along trajectories that belie traditional narratives rooted in environmental determinism and underscore the unique cultural processes at play, which do not conform to presumptions imported from outside regions. Revised narratives, therefore, must take into account cultural perceptions of climate change, and the localized nature of landscape. This article is categorized under: Human Water > Water as Imagined and Represented Science of Water > Water Extreme