Bostoen, K. & Van de Velde, M. in The Bantu Languages 2nd edn (eds Van de Velde, M. et al.) 1–13 (Routledge, 2019).
de Filippo, C., Bostoen, K., Stoneking, M. & Pakendorf, B. Bringing together linguistic and genetic evidence to test the Bantu expansion. Proc. Biol. Sci. 279, 3256–3263 (2012).
Bostoen, K. The Bantu Expansion (Oxford Univ. Press, 2018); hdl.handle.net/1854/LU-8560602
Patin, E. et al. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America. Science 356, 543–546 (2017).
Li, S., Schlebusch, C. & Jakobsson, M. Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples. Proc. Biol. Sci. 281, 20141448 (2014).
Tishkoff, S. A. et al. The genetic structure and history of Africans and African Americans. Science 324, 1035–1044 (2009).
Schlebusch, C. M. & Jakobsson, M. Tales of human migration, admixture and selection in Africa. Annu. Rev. Genomics Hum. Genet. 19, 405–428 (2018).
Steyn, M. et al. African farmers, not Stone Age foragers: reassessment of human remains from the Mumbwa Caves, Zambia. Afr. Archaeol. Rev. 40, 53–72 (2023).
Eriksson, A. & Manica, A. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proc. Natl Acad. Sci. USA 109, 13956–13960 (2012).
Vicente, M. & Schlebusch, C. M. African population history: an ancient DNA perspective. Curr. Opin. Genet. Dev. 62, 8–15 (2020).
Hammarström, H. in The Bantu Languages 2nd edn (eds Van de Velde, M. et al.) 17–78 (Routledge, 2019).
Schlebusch, C. M. et al. Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338, 374–379 (2012).
Gurdasani, D. et al. The African Genome Variation Project shapes medical genetics in Africa. Nature 517, 327–332 (2015).
Sengupta, D. et al. Genetic substructure and complex demographic history of South African Bantu speakers. Nat. Commun. 12, 2080 (2021).
Semo, A. et al. Along the Indian Ocean Coast: genomic variation in Mozambique provides new insights into the Bantu expansion. Mol. Biol. Evol. 37, 406–416 (2020).
Currie, T. E., Meade, A., Guillon, M. & Mace, R. Cultural phylogeography of the Bantu Languages of sub-Saharan Africa. Proc. Biol. Sci. 280, 20130695 (2013).
de Maret, P. in Oxford Handbook of African Archaeology (eds Mitchell, P. & Lane, P.) 319–328 (Oxford Univ. Press, 2013).
Grollemund, R. et al. Bantu expansion shows that habitat alters the route and pace of human dispersals. Proc. Natl Acad. Sci. USA 112, 13296–13301 (2015).
Koile, E., Greenhill, S. J., Blasi, D. E., Bouckaert, R. & Gray, R. D. Phylogeographic analysis of the Bantu language expansion supports a rainforest route. Proc. Natl Acad. Sci. USA 119, e2112853119 (2022).
Seidensticker, D. et al. Population collapse in Congo rainforest from 400 CE urges reassessment of the Bantu Expansion. Sci. Adv. 7, eabd8352 (2021).
Bostoen, K. in Language Dispersal, Diversification and Contact (eds Crevels, M. & Muysken, P.) 227–239 (Oxford Univ. Press, 2020).
Russell, T., Silva, F. & Steele, J. Modelling the spread of farming in the Bantu-speaking regions of Africa: an archaeology-based phylogeography. PLoS ONE 9, e87854 (2014).
Wang, K. et al. Ancient genomes reveal complex patterns of population movement, interaction and replacement in sub-Saharan Africa. Sci. Adv. 6, eaaz0183 (2020).
Diamond, J. & Bellwood, P. Farmers and their languages: the first expansions. Science 300, 597–603 (2003).
Ramachandran, S. & Rosenberg, N. A. A test of the influence of continental axes of orientation on patterns of human gene flow. Am. J. Phys. Anthropol. 146, 515–529 (2011).
Busby, G. B. et al. Admixture into and within sub-Saharan Africa. eLife 5, e15266 (2016).
Marks, S. J. et al. Static and moving frontiers: the genetic landscape of Southern African Bantu-speaking populations. Mol. Biol. Evol. 32, 29–43 (2015).
Coelho, M., Sequeira, F., Luiselli, D., Beleza, S. & Rocha, J. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola. BMC Evol. Biol. 9, 80 (2009).
Gunnink, H., Chousou-Polydouri, N. & Bostoen, K. Divergence and contact in Southern Bantu language and population history: a new phylogeny in cross-disciplinary perspective. Lang. Dynam. Change 13, 1–58 (2022).
Choudhury, A. et al. High-depth African genomes inform human migration and health. Nature 586, 741–748 (2020).
Fatumo, S. et al. Uganda Genome Resource: a rich research database for genomic studies of communicable and non-communicable diseases in Africa. Cell Genom. 2, 100209 (2022).
Fan, S. et al. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell 186, 923–939 (2023).
Schlebusch, C. M. et al. Khoe-San genomes reveal unique variation and confirm the deepest population divergence in Homo sapiens. Mol. Biol. Evol. 37, 2944–2954 (2020).
Pagani, L. et al. Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Am. J. Hum. Genet. 96, 986–991 (2015).
Pickrell, J. K. et al. The genetic prehistory of southern Africa. Nat. Commun. 3, 1143 (2012).
Scheinfeldt, L. B. et al. Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation. Proc. Natl Acad. Sci. USA 116, 4166–4175 (2019).
Maples, B. K., Gravel, S., Kenny, E. E. & Bustamante, C. D. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am. J. Hum. Genet. 93, 278–288 (2013).
Almeida, J. et al. The genes of freedom: genome-wide insights into marronage, admixture and ethnogenesis in the Gulf of Guinea. Genes 12, 833 (2021).
Oliveira, S. et al. Matriclans shape populations: Insights from the Angolan Namib Desert into the maternal genetic history of southern Africa. Am. J. Phys. Anthropol. 165, 518–535 (2018).
Scelza, B. A. et al. High rate of extrapair paternity in a human population demonstrates diversity in human reproductive strategies. Sci. Adv. 6, eaay6195 (2020).
Raghavan, M. et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884 (2015).
Bostoen, K. et al. Middle to Late Holocene paleoclimatic change and the early Bantu expansion in the rain forests of Western Central Africa. Curr. Anthropol. 56, 354–384 (2015).
Simwinga, J. Emerging evidence for language shift: the case of Nkoya in Kaoma, Western Zambia. J. Humanit. 9, 61–87 (2009).
Gowlett, D. F. The parentage and development of Lozi. J. Afr. Lang. Ling. 11, 127–150 (1989).
Salter-Townshend, M. & Myers, S. Fine-scale inference of ancestry segments without prior knowledge of admixing groups. Genetics 212, 869–889 (2019).
Ansari Pour, N., Plaster, C. A. & Bradman, N. Evidence from Y-chromosome analysis for a late exclusively eastern expansion of the Bantu-speaking people. Eur. J. Hum. Genet. 21, 423–429 (2012).
Bostoen, K., Pacchiarotti, S. & Hubau, W. À la recherche des sentiers perdus du passé en forêt. Réflexions sur l’effondrement de la population en Afrique centrale il y a 1500 ans. Preprint at Royal Academy for Overseas Science http://www.kaowarsom.be/documents/PDF%20BULLETIN/BOSTOEN.pdf (2023).
Meyer, A., Peyroteo-Stjerna, R., Jolly, C., Schlebusch, C. M. & Steyn, M. A reassessment of archaeological human remains recovered from rock shelters in Cathkin Peak, South Africa. Azania Archaeol. Res. Afr. 56, 508–538 (2021).
Novembre, J. et al. Genes mirror geography within Europe. Nature 456, 98–101 (2008).
Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).
Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).
McInnes, L., Healy, J. & Melville, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://doi.org/10.48550/arXiv.1802.03426 (2020).
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
Diaz-Papkovich, A. & erson-Trocmé, L., Ben-Eghan, C. & Gravel, S. UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts. PLoS Genet. 15, e1008432 (2019).
Ausmees, K. & Nettelblad, C. A deep learning framework for characterization of genotype data. G3 12, jkac020 (2022).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Schlebusch, C. M. et al. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358, 652–655 (2017).
Prendergast, M. E. et al. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 365, eaaw6275 (2019).
Skoglund, P. et al. Reconstructing prehistoric African population structure. Cell 171, 59–71 (2017).
Lipson, M. et al. Ancient West African foragers in the context of African population history. Nature 577, 665–670 (2020).
Coutinho, A. et al. Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups. Am. J. Phys. Anthropol. 174, 701–713 (2021).
Gallego Llorente, M. et al. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 350, 820–822 (2015).
Browning, S. R. & Browning, B. L. Accurate non-parametric estimation of recent effective population size from segments of identity by descent. Am. J. Hum. Genet. 97, 404–418 (2015).
Tournebize, R., Chu, G. & Moorjani, P. Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals. PLoS Genet. 18, e1010243 (2022).
Delaneau, O., Howie, B., Cox, A. J., Zagury, J.-F. & Marchini, J. Haplotype estimation using sequencing reads. Am. J. Hum. Genet. 93, 687–696 (2013).
Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
Bjornstad, O. & Cai, J. ncf: Spatial covariance functions. R package version 1.3-2. CRAN https://cran.r-project.org/web/packages/ncf/ncf.pdf (2022).
Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
Hijmans, R. J., Williams, E. & Vennes, C. Geosphere: spherical trigonometry. R package version 1.5-18. CRAN https://cran.r-project.org/web/packages/geosphere/geosphere.pdf (2015).
Pagani, L. et al. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538, 238–242 (2016).
Petkova, D., Novembre, J. & Stephens, M. Visualizing spatial population structure with estimated effective migration surfaces. Nat. Genet. 48, 94–100 (2016).
Marcus, J., Ha, W., Barber, R. F. & Novembre, J. Fast and flexible estimation of effective migration surfaces. eLife 10, e61927 (2021).
Al-Asadi, H., Petkova, D., Stephens, M. & Novembre, J. Estimating recent migration and population-size surfaces. PLoS Genet. 15, e1007908 (2019).
Bradburd, G. S., Ralph, P. L. & Coop, G. M. A spatial framework for understanding population structure and admixture. PLoS Genet. 12, e1005703 (2016).
Dr. Thomas Hughes is a UK-based scientist and science communicator who makes complex topics accessible to readers. His articles explore breakthroughs in various scientific disciplines, from space exploration to cutting-edge research.
