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PreprintCited by 19

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Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago

Schlebusch, Carina M., Malmström, Helena, Günther, Torsten, Sjödin, Per, Coutinho, Alexandra, Edlund, Hanna, Munters, Arielle R., Steyn, Maryna, Soodyall, Himla, Lombard, Marlize, Jakobsson, Mattias·2017
DOI 10.1101/145409
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Abstract

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens . To examine the region’s human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300–500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9–22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|‘hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) ‘hot spot’ for the evolution of our species.

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Figure 1 (A) Locations of the archaeological sites and the geographic centers of comparative populations from Schlebusch et al 8 . (B) PCA with southern African, African and global comparative data. (C) Admixture analysis, displayed for selected number of clusters (K), see figure S6.5 for all K values.
Figure 1 (A) Locations of the archaeological sites and the geographic centers of comparative populations from Schlebusch et al 8 . (B) PCA with southern African, African and global comparative data. (C) Admixture analysis, displayed for selected number of clusters (K), see figure S6.5 for all K values.CC-BY-NC-ND · From the PDF
Figure 2 (A) East African/Eurasian admixture proportions (inferred with f4 ratio test using Amhara) in a southern African comparative dataset 8 . Circles are San and Khoekhoe populations and diamonds are Bantu-speakers. (B) Runs of Homozygosity of the 200-500 Kb bin in Africans (see fig S7.2 for inclusion of non-Africans).
Figure 2 (A) East African/Eurasian admixture proportions (inferred with f4 ratio test using Amhara) in a southern African comparative dataset 8 . Circles are San and Khoekhoe populations and diamonds are Bantu-speakers. (B) Runs of Homozygosity of the 200-500 Kb bin in Africans (see fig S7.2 for inclusion of non-Africans).CC-BY-NC-ND · From the PDF
Figure 3 Demographic model of African history and estimated divergences . (A) The estimated age of the Florisbad skull from southern Africa is indicated by a dashed line. The ancient southern African individuals in this study are denoted using the labels in Fig 1A, where the Stone Age hunter-gatherers are shown by red symbols, and Iron Age farmers of West African origin as green symbols. The depiction of population split-times, hierarchy and population sizes (width along a horizontal axis for populations) are a summary of the results presented in Extended Data Figures 1-2, 4-6. (B) Estimated population split times using the Gronau et al. approach (G-PhoCS) 15 and the novel Two-by-Two (TT) method described in SI 9. The deepest divergence among humans is estimated to 260-360 kya. Divergence time estimates for human vs Neandertal, and non-Africans vs Africans (indicating the out of Africa event) are given for reference, and these estimates are consistent with recent estimates in the literature 4 . NKSP-SKSP shows the estimated split time between Ballito Bay A and Ju|'hoansi.
Figure 3 Demographic model of African history and estimated divergences . (A) The estimated age of the Florisbad skull from southern Africa is indicated by a dashed line. The ancient southern African individuals in this study are denoted using the labels in Fig 1A, where the Stone Age hunter-gatherers are shown by red symbols, and Iron Age farmers of West African origin as green symbols. The depiction of population split-times, hierarchy and population sizes (width along a horizontal axis for populations) are a summary of the results presented in Extended Data Figures 1-2, 4-6. (B) Estimated population split times using the Gronau et al. approach (G-PhoCS) 15 and the novel Two-by-Two (TT) method described in SI 9. The deepest divergence among humans is estimated to 260-360 kya. Divergence time estimates for human vs Neandertal, and non-Africans vs Africans (indicating the out of Africa event) are given for reference, and these estimates are consistent with recent estimates in the literature 4 . NKSP-SKSP shows the estimated split time between Ballito Bay A and Ju|'hoansi.CC-BY-NC-ND · From the PDF
Image 4
CC-BY-NC-ND · From the PDF
Extended Data Fig. 2: A population and admixture graph model of Ju|'hoansi as an admixed population between southern Africans and an admixed (Eurasian/East African) population is consistent with the data. The numbers next to edges represent the amount of drift between the nodes (multiplied by 1000). The model is including Yoruba as a potential source of Bantu-speaking ancestry. Ju|'hoansi as a Khoe-San population without admixture from Bantu-speakers is also consistent with the data. Alternative tested models constructed in a hierarchical way are discussed in SI section 6.5. The most likely model for the Ju|hoansi is shown here.
Extended Data Fig. 2: A population and admixture graph model of Ju|'hoansi as an admixed population between southern Africans and an admixed (Eurasian/East African) population is consistent with the data. The numbers next to edges represent the amount of drift between the nodes (multiplied by 1000). The model is including Yoruba as a potential source of Bantu-speaking ancestry. Ju|'hoansi as a Khoe-San population without admixture from Bantu-speakers is also consistent with the data. Alternative tested models constructed in a hierarchical way are discussed in SI section 6.5. The most likely model for the Ju|hoansi is shown here.CC-BY-NC-ND · From the PDF
Extended Data Fig. 3: Heterozygosity estimates based on stringently filtered sites. Red points indicates heterozygosity based on all sites with coverage >7x, black circles on sites with coverage >1x and blue points have additional applied quality filters, including >13x (see SI section 7.1). Points are sorted in ascending order based on the more stringently filtered sites (blue points).
Extended Data Fig. 3: Heterozygosity estimates based on stringently filtered sites. Red points indicates heterozygosity based on all sites with coverage >7x, black circles on sites with coverage >1x and blue points have additional applied quality filters, including >13x (see SI section 7.1). Points are sorted in ascending order based on the more stringently filtered sites (blue points).CC-BY-NC-ND · From the PDF
Extended Data Fig. 4: MSMC plot of 11 HGDP genomes together with the diploid full genome of Ballito Bay A (BBayA).
Extended Data Fig. 4: MSMC plot of 11 HGDP genomes together with the diploid full genome of Ballito Bay A (BBayA).CC-BY-NC-ND · From the PDF
Image 8
CC-BY-NC-ND · From the PDF
Extended Data Fig. 6 : Estimates of split time between pairs of individuals using the TT method. The populations displayed on top and in larger font are focal populations while the populations below in smaller font are the contrasting populations. We assume a mutation rate of 1.25×10 -8 per site and generation, and a generation time of 30 years to translate the estimated parameter T to time in calendar years.
Extended Data Fig. 6 : Estimates of split time between pairs of individuals using the TT method. The populations displayed on top and in larger font are focal populations while the populations below in smaller font are the contrasting populations. We assume a mutation rate of 1.25×10 -8 per site and generation, and a generation time of 30 years to translate the estimated parameter T to time in calendar years.CC-BY-NC-ND · From the PDF
Extended Data Fig. 7: Outgroup-f3 between Ballito Bay A and Khoe-San and Bantu-speaker individuals from Schlebusch et al 8 . Ancestral sites are inferred from the genomes of three great apes and are used as outgroup.
Extended Data Fig. 7: Outgroup-f3 between Ballito Bay A and Khoe-San and Bantu-speaker individuals from Schlebusch et al 8 . Ancestral sites are inferred from the genomes of three great apes and are used as outgroup.CC-BY-NC-ND · From the PDF
Extended Data Fig. 8: Pairwise FST between Ballito Bay A and the individuals in Schlebusch et al 8 .
Extended Data Fig. 8: Pairwise FST between Ballito Bay A and the individuals in Schlebusch et al 8 .CC-BY-NC-ND · From the PDF

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Metadata

Authors
Schlebusch, C. M., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., Munters, A. R., Steyn, M., Soodyall, H., Lombard, M., & Jakobsson, M.
Publisher
openRxiv
Published
2017-06-05
DOI
10.1101/145409
Cited by
19
References
5
Type
Preprint
Licence
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)

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CoChat. (2026). Citation check: Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. https://app.cochat.ai/papers/10.1101/145409
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Schlebusch, C. M., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., Munters, A. R., Steyn, M., Soodyall, H., Lombard, M., & Jakobsson, M. (2017). Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago. https://doi.org/10.1101/145409