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Human origins in a southern African palaeo-wetland and first migrations

Abstract

Anatomically modern humans originated in Africa around 200 thousand years ago (ka)1,2,3,4. Although some of the oldest skeletal remains suggest an eastern African origin2, southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1’2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi–Okavango palaeo-wetland of southern Africa7, approximately 200 ka (95% confidence interval, 240–165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast–southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to a sustained effective population size (L0k), whereas wet–dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1’2), as supported by extensive south-coastal archaeological evidence8,9,10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes.

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Fig. 1: Geographical distribution of 1,217 L0 mitogenomes.
Fig. 2: L0 phylogenetic tree, geographical distributions of the major southern African L0 haplogroup and out-of-homeland L0 dispersal routes.
Fig. 3: Reconstructed and simulated climatic conditions during the out-of-homeland migration.

Data availability

The consensus sequences for this set of 198 mitogenomes have been deposited in the NCBI GenBank with accession numbers MK248274–MK248471. Requests for materials should in the first instance be addressed to V.M.H.

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Acknowledgements

We thank all of the study participants, as well as the many people who provided assistance during participant recruitment and recording, or provided critical historical, cultural and linguistic insights including; C. P. Bennett (https://evolvingpicture.com/), R. Wilkinson, J. Sinvula, H. Money, the late C. F. Heyns, R. H. Glashoff, D. de Swart, P. Fernandez, P. A. Venter, S. C. Schuster, M. P. Marx, the late S. M. Kooitjie (39th leader of the ǂAonin clan and chairperson of the Nama Traditional Leaders Association), A. A. Collins, B. Kaesje, J. Kayimbi, H. Mische, F. Naque, D. Naque, H. Oosthuizen, E. Oosthuizen, A. Oosthuysen, E. Oosthuysen, D. Roux, C. Swau and T. Tsebe. We acknowledge the late M. McFarlane, who identified Deception ridge and its importance in the evolution of the Makgadikgadi palaeo-lake. This work was supported by an Australian Research Council Discovery Project grant awarded to V.M.H. (DP170103071) and sampling contributed by the Cancer Association of South Africa to M.S.R.B. and V.M.H. A.T. and S.-S.L. received funding from the Institute for Basic Science (IBS) under IBS-R028-D1. V.M.H. is supported by the University of Sydney Foundation in a Petre Foundation chair position. Computational resources were provided by the Australian Government through the National Computational Infrastructure, the Sydney Informatics Research Hub at the University of Sydney (Artemis HPC) and by the Garvan Institute of Medical Research Data Intensive Computer Engineering team.

Author information

Affiliations

Authors

Contributions

V.M.H. designed the study. M.S.R.B., H.E.A.F. and V.M.H. obtained and maintain study approvals and permits, as well as community leadership support. M.S.R.B., D.C.P. and V.M.H. performed recruitments, consenting, sampling and processing. R.J.L., A.M.F.K. and D.C.P. performed pre-screening and mitogenome data generation. E.K.F.C. performed the bioinformatics and phylogenetic analyses. A.E.M. performed geographical interpretation. S.-S.L. and A.T. performed climatological model analyses and interpretation, with additional local climatology interpretation provided by H.R. V.M.H. led the interpretation of the multiple-discipline analyses, with contributions from all of the authors. E.K.F.C., B.F.B., S.-S.L., A.T. and V.M.H. generated and interpreted the figures. V.M.H., E.K.F.C. and A.T. wrote the manuscript with contributions from all of the authors.

Corresponding authors

Correspondence to Axel Timmermann or Vanessa M. Hayes.

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Competing interests

The authors declare no competing interests.

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Peer review information Nature thanks Victor Brovkin, Rebecca Cann and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Fig. 1 Phylogenetic tree of all 1,217 L0 mitogenomes.

Phylogeny was inferred using FastTree v.2.1.746, displayed using FigTree. Tips belonging to the same haplogroup are collapsed and coloured as in Fig. 2a. Local support values for each node are indicated and branch lengths are proportional to the number of substitutions per site. The tree is rooted to the seven Neanderthal mitogenomes as indicated.

Extended Data Fig. 2 Detailed phylogenetic branching of L0k, L0d3, L0f and L0g.

ad, Expanded sections of the phylogenetic tree depicted in Fig. 2a are shown, including 34 (out of a total of 113) L0k (a), all 40 L0d3 (b), all 27 L0f (c) and all 9 L0g (d) mitogenomes. Each mitogenome is represented as a tip and coloured based on their broad ethno-linguistic classification, if known. KhoeSan is shown in orange, non-KhoeSan in grey and Cape multi-ethnic (KhoeSan ancestral) in green. Publicly available mitogenomes for which we cannot be certain of their broad population identifier are labelled in black font. Proposed new sub-lineages for L0d3, L0f and L0g1 are indicated by red-coloured node labels and are further described in Supplementary Tables 79.

Extended Data Fig. 3 Detailed phylogenetic branching of L0d2.

a, c, d, Expanded branches of the phylogenetic tree depicted in Fig. 2a are shown, including 51 (out of a total of 118) L0d2a (a), 25 (out of 53) L0d2c (c) and all 11 L0d2d (d) mitogenomes. b, For L0d2b, an additional BEAST analysis was performed using an alternate subset of 441 mitogenomes that included all 43 L0d2b samples, as opposed to the n = 461 subset (Fig. 2a) that included only 13 L0d2b. The same model parameters were used for both data subsets. In all panels, each mitogenome is represented as a tip and coloured based on their broad ethno-linguistic classification, as in Extended Data Fig. 2. The previously defined L0d2c1c haplogroup, containing the coastal KhoeSan StHe skeleton6 and other newly proposed sub-lineages are indicated by red node labels (Supplementary Tables 46).

Extended Data Fig. 4 Detailed phylogenetic branching of L0d1.

ac, Expanded branches of the phylogenetic tree depicted in Fig. 2a are shown, including 54 (out of a total of 91) L0d1a (a), 45 (out of 174) L0d1b (b) and 33 (out of 184) L0d1c (c) mitogenomes. Each mitogenome is represented as tips and coloured based on their broad ethno-linguistic classification as in Extended Data Fig. 2.

Extended Data Fig. 5 Detailed phylogenetic branching of L0a.

The L0a branch of the phylogenetic tree displayed in Fig. 2a is shown, which includes a subset of 114 (out of a total of 294) L0a mitogenomes. Each mitogenome is represented as tips and coloured based on their broad ethno-linguistic classification as in Extended Data Fig. 2.

Extended Data Fig. 6 Comparison of the palaeo-data and palaeo-model.

a, Locations of key sites that are used for the comparison of the palaeo-model and palaeo-data in this study are highlighted in red. The map was generated in Paraview v.5.6 (https://www.paraview.org/). b, Simulated tree fraction (%) at Horn of Africa (land grid points nearest to RC09-166) (grey, dark-blue bars) and stable hydrogen isotopic composition of leaf wax, corrected for ice volume contributions from the Gulf of Aden marine sediment core RC09-16630 (orange), indicating changes in hydroclimate. c, Relative precipitation changes (%) simulated by LOVECLIM transient model (all forcings) for 11° E, 19° S (grey, dark-blue bars) and grain-size aridity index reconstructed from sediment core MD96-209432 (orange). d, Grass fraction changes simulated by LOVECLIM transient model (all forcings) at 11° E, 14–17° S (grey, dark-blue bars) and reconstructed δ13C changes of n-alkanes (orange) (South Atlantic sediment core MD08-3167) indicative of abundance of C3 and C4 plants in the Namibian desert and further inland33.

Extended Data Table 1 L0 mitogenomes included in this study
Extended Data Table 2 KhoeSan population identifiers used in this study

Supplementary information

Supplementary Information

This file contains the Supplementary Methods.

Reporting Summary

Supplementary Table 1

L0 study participants. A total of 198 L0 mitogenomes were sequenced and included in this study. Participants were sourced from within the borders of Namibia and South Africa, representing a diverse ethnic background, broadly classified into four ethno-linguistic groups as depicted in Fig. 1b.

Supplementary Table 2

Publicly available L0 mitogenomes. A total of 1,019 publicly available L0 mitogenomes, spanning 26 studies, were downloaded from National Center for Biotechnology Information database between 2015 and 2017. Samples were broadly ethno-linguistically classified, per Fig. 1b as for our 198 samples, based on the samples’ reported population and/or country of origin. Reported haplogroups were confirmed or refined using HaploGrep2 based on PhyloTree Build 17.

Supplementary Table 3

Time to most recent common ancestors within L0. Shown are coalescence time estimates from five replicate BEAST runs, using a subset of 461 L0 mitogenomes described in Supplementary Methods. Combined results from the five replicates are presented in main text and Fig. 2a.

Supplementary Table 4

L0d2c-defining variants. Variants were deduced from all 53 L0d2c mitogenomes available, including the previously identified coastal hunter-gatherer StHe skeleton6. The table shows all variants observed in at least one of the 53 mitogenomes relative to RSRS, providing defining variants for new sub-lineages L0d2c1d’e and L0d2c2c’d’e, and reconfirming previously defined L0d2c1c lineage6. See also Extended Data Fig. 3c.

Supplementary Table 5

L0d2b-defining variants. Variants were deduced from 43 L0d2b complete mitogenomes. The table shows all variants observed in at least one of the mitogenomes relative to RSRS, allowing for the identification of seven new sub-lineages (see also Extended Data Fig. 3b).

Supplementary Table 6

L0d2d-defining variants. The table shows all variants observed in at least one of the 11 L0d2d mitogenomes, relative to RSRS, allowing for the identification of three new sub-lineages: L0d2d1’2’3 (see also Extended Data Fig. 3d).

Supplementary Table 7

L0d3-defining variants. All variants present in at least one of the 40 L0d2d mitogenomes, relative to RSRS, are shown. Along with Extended Data Fig. 2b, this allowed for L0d3b1 to be redefined and for the identification of three new sub-lineages: L0d3b3’4’5.

Supplementary Table 8

L0f-defining variants. Variants were deduced from all 28 L0f mitogenomes, including the mitogenome AF44 with only coding-region sequence available54. The table shows all variants observed in at least one of the 28 mitogenomes relative to RSRS, allowing for the identification of new sub-lineages L0f3, and L0f1a’b’c (Extended Data Fig. 2c).

Supplementary Table 9

L0g-defining variants. Shown are variants observed in at least one of the nine L0g mitogenomes, relative to RSRS, allowing for the identification of a new sub-lineage, L0g1 (Extended Data Fig. 2d).

Supplementary Table 10

Homo sapiens neanderthalensis mitogenomes. Shown are the seven Neanderthal complete mitogenomes were included in this study. Nucleotide sequences were obtained from NCBI, and used to root the phylogenetic trees. Age of the mitogenomes, as reported for the corresponding skeletal remains, were used to calibrate the phylogenetic tree.

Supplementary Table 11

BEAST Tracer Summary. Trace file from each BEAST run was examined using Tracer v1.6 to ensure MCMC convergence with acceptable effective sample sizes for all parameters (> 1,000).

Supplementary Table 12

Bayesian Skyline Plot Summary. For common haplogroups with > 100 mitogenomes, at least five sub-sampling for n=100 were performed. In contrast, for rare haplogroups with < 20 mitogenomes, BSP analyses were performed with varying Group Sizes to ensure this parameter did not dramatically impact the results. While Effective Sample Sizes (ESS) were low for the Posterior of the model, we note ESS for the Tree Likelihood and BSP generally reached acceptable levels (>500). This table shows the best BSP result for each haplogroup.

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Chan, E.K.F., Timmermann, A., Baldi, B.F. et al. Human origins in a southern African palaeo-wetland and first migrations. Nature 575, 185–189 (2019). https://doi.org/10.1038/s41586-019-1714-1

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