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Link to original content: https://doi.org/10.1038/s41586-021-03457-8
Earliest known human burial in Africa | Nature
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Earliest known human burial in Africa

Nature volume 593, pages 95–100 (2021)Cite this article

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Abstract

The origin and evolution of hominin mortuary practices are topics of intense interest and debate1,2,3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1,2,3,4,5,6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya7,8. Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead.

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Fig. 1: Location of PYS and stratigraphic context of burial.
Fig. 2: PYS human fossil.
Fig. 3: Mtoto’s preservation and position in the pit.

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The data that support the findings of this study are available from the corresponding authors upon reasonable request.

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Acknowledgements

Funding for this project was provided by the SEALINKS project under a European Research Council (ERC) grant (no. 206148) and the Max Planck Society (to N.B.). Funding for the hominin analyses was from the Dirección General de Investigación of the Ministerio de Ciencia, Innovación y Universidades, grant numbers PGC2018-093925-B-C31 and C33 (MCI/AEI/FEDER, UE) and The Leakey Foundation, through the personal support of G. Getty (2013) and D. Crook (2014-2020) to M.M.-T.; analyses were also carried out at the laboratories of the CENIEH-ICTS with the support of the CENIEH staff. E.S. has a Ramón Areces/Atapuerca Foundation postdoctoral grant. L.M.-F. is a beneficiary of an Atapuerca Foundation postdoctoral grant. S.J.A. and F.d’E. acknowledge support from the Research Council of Norway, through its Centres of Excellence funding scheme, SFF Centre for Early Sapiens Behaviour (SapienCE) (no. 262618). F.d’E. was funded by the ERC grant TRACSYMBOLS (no. 249587), the Agence Nationale de la Recherche (ANR-10-LABX-52), LaScArBx Cluster of Excellence, and the Talents programme of the University of Bordeaux, Initiative d’Excellence. A.P.M. was funded by the Beatriu de Pinós postdoctoral programme (2017 BP-A 00046) of the Government of Catalonia’s Secretariat for Universities & Research of the Ministry of Economy and Knowledge. We thank B. Kimeu for the extraction of Mtoto in the field, N. Blegen for conducting the digital work in the field, R. Blasco for insights about taphonomy, R. García and P. Saladié for assisting in anatomical identification, S. Sarmiento for the tooth photographs and M. O’Reilly for assisting with graphic design. We thank G. Musuko and family for permission to excavate the site. Permission to conduct the research was granted by the National Commission for Science, Technology and Innovation Office of the President of the Republic of Kenya through affiliation with the National Museums of Kenya (NMK). We are grateful for the support of the NMK administration, staff from the preparation and archaeology section, and the British Institute in Eastern Africa.

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Authors and Affiliations

  1. CENIEH (National Research Center on Human Evolution), Burgos, Spain

    María Martinón-Torres, Ana Álvaro Gallo, José María Bermúdez de Castro, Pilar Fernández-Colón, David Larreina, Laura Martín-Francés & Belén Notario

  2. Anthropology Department, University College London, London, UK

    María Martinón-Torres, José María Bermúdez de Castro & Laura Martín-Francés

  3. UMR 5199 CNRS De la Préhistoire à l’Actuel: Culture, Environnement, et Anthropologie (PACEA), Université Bordeaux, Talence, France

    Francesco d’Errico, Africa Pitarch Martí, Alain Queffelec & Solange Rigaud

  4. SFF Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Bergen, Norway

    Francesco d’Errico & Simon J. Armitage

  5. Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Instituto de Salud Carlos III, Madrid, Spain

    Elena Santos & Juan Luis Arsuaga

  6. Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales - Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares, Spain

    Elena Santos

  7. Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany

    Noel Amano, James Blinkhorn, Alison Crowther, Katerina Douka, Patrick Faulkner, Julio Mercader, Jennifer M. Miller, Emmanuel Ndiema, Patrick Roberts, Mohammad Javad Shoaee, Nicole Boivin & Michael D. Petraglia

  8. Department of Archaeology and Anthropology, National Museum, Bloemfontein, South Africa

    William Archer

  9. Department of Archaeology, University of Cape Town, Cape Town, South Africa

    William Archer

  10. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

    William Archer

  11. Department of Geography, Royal Holloway, University of London, Egham, UK

    Simon J. Armitage & James Blinkhorn

  12. Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain

    Juan Luis Arsuaga

  13. Pan-African Evolution Research Group, Max Planck Institute for the Science of Human History, Jena, Germany

    James Blinkhorn

  14. School of Social Science, The University of Queensland, Brisbane, Queensland, Australia

    Alison Crowther, Patrick Roberts, Nicole Boivin & Michael D. Petraglia

  15. Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK

    Katerina Douka

  16. UMR 5060 CNRS-Université Bordeaux Montaigne IRAMAT-CRP2A: Institut de recherche sur les Archéomatériaux – Centre de recherche en physique appliquée à l’archéologie, Maison de l’archéologie, Pessac, France

    Stéphan Dubernet & François-Xavier Le Bourdonnec

  17. Faculty of Arts and Social Sciences, Department of Archaeology, The University of Sydney, Sydney, New South Wales, Australia

    Patrick Faulkner

  18. Centre for Open Learning, University of Edinburgh, Edinburgh, UK

    Nikos Kourampas & Ian Simpson

  19. Biological and Environmental Sciences, University of Stirling, Stirling, UK

    Nikos Kourampas & George MacLeod

  20. 3D Applications Engineer and Heritage Specialist Digital Heritage and Humanities Collections, University of South Florida, Tampa, FL, USA

    Jorge González García

  21. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

    Diyendo Massilani

  22. Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada

    Julio Mercader & Nicole Boivin

  23. National Museums of Kenya, Department of Earth Sciences, Nairobi, Kenya

    Emmanuel Ndiema

  24. Seminari d’Estudis i Recerques Prehistòriques (SERP), Facultat de Geografia i Història, Departament d’Història i Arqueologia, Universitat de Barcelona, Barcelona, Spain

    Africa Pitarch Martí

  25. Department of Anthropology, Rice University, Houston, TX, USA

    Mary E. Prendergast

  26. Institute of Archaeology, University College London, London, UK

    Ceri Shipton

  27. Centre of Excellence for Australian Biodiversity and Heritage, The Australian National University, Canberra, Australian Capital Territory, Australia

    Ceri Shipton

  28. Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA

    Nicole Boivin

  29. Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA

    Michael D. Petraglia

  30. Australian Research Centre for Human Evolution (ARCHE), Griffith University, Brisbane, Queensland, Australia

    Michael D. Petraglia

Authors
  1. María Martinón-Torres
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  2. Francesco d’Errico
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  3. Elena Santos
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  4. Ana Álvaro Gallo
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  5. Noel Amano
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  6. William Archer
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  7. Simon J. Armitage
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  8. Juan Luis Arsuaga
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  9. José María Bermúdez de Castro
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  10. James Blinkhorn
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  11. Alison Crowther
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  12. Katerina Douka
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  13. Stéphan Dubernet
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  14. Patrick Faulkner
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  15. Pilar Fernández-Colón
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  16. Nikos Kourampas
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  17. Jorge González García
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  18. David Larreina
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  19. François-Xavier Le Bourdonnec
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  20. George MacLeod
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  21. Laura Martín-Francés
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  22. Diyendo Massilani
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  23. Julio Mercader
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  24. Jennifer M. Miller
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  25. Emmanuel Ndiema
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  26. Belén Notario
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  27. Africa Pitarch Martí
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  28. Mary E. Prendergast
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  29. Alain Queffelec
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  30. Solange Rigaud
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  31. Patrick Roberts
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  32. Mohammad Javad Shoaee
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  33. Ceri Shipton
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  34. Ian Simpson
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  35. Nicole Boivin
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  36. Michael D. Petraglia
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Contributions

N.B., M.D.P. and E.N. designed and directed the PYS research; C.S. and J.B. directed the field excavations; M.M.-T., J.M.B.d.C., J.L.A., E.S. and L.M.-F. analysed the hominin fossil; P.F.-C. conducted the mechanical restoration and conservation of the hominin; E.S. and J.G.G. conducted the virtual restoration and reconstruction of the hominin; F.d’E., N.A., W.A., S.J.A., J.B., A.C., S.D., K.D., F.-X.L.B., A.A.G., B.N., D.L., N.K., G.M., D.M., J.M., J.M.M., A.P.M., M.E.P., A.Q., S.R., P.R., M.J.S., C.S. and I.S. conducted analytical studies; M.M.-T., M.D.P., F.d’E. and N.B. wrote the paper with contributions of all authors.

Corresponding authors

Correspondence to María Martinón-Torres, Nicole Boivin or Michael D. Petraglia.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks Louise Humphrey, Richard Klein, Wu Liu and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 PYS MSA lithics.

Top, the relative sizes of flakes through layers 18–17 (MSA) and layer 16 (early LSA) visualized with a violin plot, illustrating the density of values by layer as a continuous distribution. Note the decrease across layers 17–16. The flakes recovered from the burial (n = 14), shown here with a box plot, fall within the variation in product weight for the MSA. The box plot shows the median value for burial lithics at the centre, with two neighbouring hinges marking the 25th and 75th percentiles. The whiskers plot the distance from the hinge values to the largest and smallest values in the burial dataset, to a maximum distance of 1.5 times the interquartile range (data beyond this range, if present, would have been plotted as individual outlier points). Below, facetted limestone flakes from MSA layers of PYS. A, limestone flake from burial context (809) with facetted dihedral platform; B, retouched limestone flake with large facetted platform from layer 17.

Extended Data Fig. 2 Bayesian model for the age estimation of PYS.

Left, Bayesian model of all available age determinations from PYS, produced using OxCal 4.4.2 and IntCal20. Right, age estimate of the burial determined using Bayesian model. A full description (OxCal code) of the age model is provided in Supplementary Information C.

Extended Data Fig. 3 Reconstruction of key taphonomic events of Mtoto’s burial.

a–c, The 3D sequence illustrates the reconstruction of the key taphonomic events that affected the shape and relationship of the head and the spine. a, Original right lateral decubitus position of the child in the burial pit. b, Lateral compression of the thorax because of the sediment weight; the ribs are flattened but the rib cage does not collapse, as is common in decomposition in filled space (earth grave). c, The head dislocates, as is typical in the case of burials with perishable head support. d, Ideal reconstruction of Mtoto’s original position at the moment of its discovery at the site.

Extended Data Fig. 4 Analysis of sediment from the stratigraphic sequence and the burial pit.

a, Particle size ternary diagram indicating the higher content of sand and silt in the burial pit in comparison to the encasing archaeological layers, and in particular layer 19. b, Examples of particle size distribution and multimodal decomposition showing the similarities of sand and silt modes between the burial samples and samples 137 (base of layer 17) and 138 (top of layer 18). c, Elemental profiles of sediment from layers 17, 18, 19 and the burial pit. Element concentrations are expressed in percentages. Data are presented as mean values. Sediment samples from the burial pit display an elemental composition notably similar to the three samples identified as an anomaly at the top of layer 18 and the base of layer 17. d, Results of PCA of the centre log ratio data (selected elements: SiO2, K2O, TiO2, MnO, Fe2O3, Zn, Ga, As, Rb, Y, Zr and Ba). Confidence ellipses at 95%. The burial pit samples markedly differ from layer 19.

Extended Data Fig. 5 Micromorphological and histological analysis.

a–h, Polarizing microscopy (a, c–f) and SEM (g, h) images of bone and sediment from Mtoto’s burial and from surrounding contexts (b). a, Ferruginous microfacies (MF-fer: here a coarser-grained variant) adhering on cancellous bone (PPL). b, Small vertebrate bone fragment from ferruginous sediment at the top of layer 18, about 20 cm above Mtoto’s skeleton. Note the good histological preservation and longitudinal and transverse fracturing (PPL). c, Mtoto’s bone fragment. A Fe-oxide-stained calcite crust (Ca) covers the bone surface. A thin zone of non-clouded bone (HAP—conventionally ‘hydroxyapatite’) immediately beneath the bone surface is underlain with clouded, Ca-enriched bone of the mesosteum (CLb). Note the sharp boundary between HAP and CLb (especially on the left side), and the dense non-Wedl bioerosion foci within CLb (linear longitudinal tunnels at about 45°; budding tunnels (dark spots), attributed to bacteria) and enlarged osteocyte lacunae (smaller dark spots). Double arrow shows two possible Wedl tunnels (PPL). d, As in c, but in XPL. The calcitic crust (Ca) comprises two layers: an Fe-oxide-stained, microcrystalline layer, and a latter layer of clear, coarser-crystalline calcite (grey arrow). Birefringent areas within CLb mark osteons. Note the loss of birefringence in bioerosion foci (for example, lower right corner). e, Enlarged osteocyte canaliculi and lacunae, possibly due to fungal or fungal and bacterial action, in clouded, Ca-enriched bone (PPL). f, Advanced alteration of putative human bone (general histological index: 2), with small areas of preserved histology, pervasive clouding, fissuring (for example, blue arrow), dissolution pores (for example, green arrow) and Fe and Mn impregnation (black spots). Note the spatial patterning of bioerosion, with domains of larger, circular, coalescent non-Wedl (bacterial) MFD (for example, red arrow) and smaller, more typical tunnels (budding and linear longitudinal: for example, white arrow). A crust of calcite speleothem (grey arrows) encrusts a transverse fracture across the bone (PPL). g, Budding and linear longitudinal tunnels in highly altered bone (area marked with white arrow in f). Some smaller-scale, spongiform bioerosion is also shown, surrounded with permineralized rims (white) of redeposited ‘hydroxyapatite’ (light blue arrows) (SEM image). h, Periosteum of clouded bone (Cb), encrusted with carbonate deposits (MF-carb). Larger circular-elliptical pores (blue/turquoise) are Haversian canals. Dashed circles show foci of fine-scale (0.1–1 μm) bacterial bioerosion within clouded bone (SEM image, with colour temperature filter to enhance resolution).

Extended Data Fig. 6 Histological analysis of Mtoto’s bone.

Elemental composition of clouded bone (Cb) and encrusting calcium carbonate precipitate (Cc) (SEM–EDS image and spectra). The pictured area corresponds to that of Fig. 3c, d. Diffuse lighter grey areas within the clouded bone may be permineralized rims around fine-scale (0.1–1 μm) bioerosion foci. Note the variable enrichment in Ca (especially in spectrum 21) and the low concentrations of Fe, Al, and Mg in the authigenic Ca-P phase that makes up the clouded bone. The pervasive recrystallization of the bone hydroxyapatite into a Ca-enriched, amorphous or cryptocrystalline calcium phosphate appears to be associated with fine-scale bacterial microtunnelling.

Extended Data Fig. 7 PYS shell analysis.

a, Fragments of Achatina cf. fulica found in close association with the child’s skeleton. Observation of anatomical features allows precise identification of the provenance of the fragments on the shell. Fragments PYS-2017-200407 and PYS-2017-200404 come from the area of the body whorl adjacent to the middle portion of the parietal callus. Fragment PYS-2017-200405 must come from a portion of the shell close to that of the previous fragment and may derive from the same individual. Fragment PYS-2017-200406 comes from the middle of the body whorl, on its dorsal aspect. Although anatomically it is compatible with provenance from the same individual, its very dark colour, suggestive of a higher Mn intake, and different texture of the concretion coating its outer surface indicate that it had a different taphonomic history and may derive from a different shell. Fragment PYS-2017-200086.D comes from the middle of the body whorl, on its ventral aspect. b, Refitting of fragments PYS-2017-200407 and PYS-2017-200404. The two large fragments refit along an ancient fracture perpendicularly intercepting the shell growth lines. c, Modern striations on the inner surface of specimen PYS-2017-200406, probably produced during excavation or cleaning of the fragments. The modern origin of the striations is shown by their random orientation and absence of the thin manganese patina adhering to the inner surface of this specimen. d, Micrographs and 3D reconstruction of an area of the outer surface of fragment PYS-2017-200404 showing two grooves obliquely crossing the decussated sculpture of the outer shell surface. The internal morphology and outlines of the grooves indicate that they were made by a pointed agent, possibly a stone tool, following the irregular morphology of the shell natural surface and slightly changing direction when falling into concave areas. The antiquity of the lines is demonstrated by the red sediment coating the specimen, which fills in the striations and almost completely buries them when they run into natural grooves of the shell. e, Fragments of Achatina cf. fulica found in feature 809 (bottom) and their anatomical origin (top). The twelve fragments mostly come from body whorls and last whorls of the spire of Achatina snails, with only two from the parietal wall and the apex. They present a similar state of preservation, colour, taphonomic modifications and type of concretions to the five fragments found in direct association with the skeleton. None of them bears incisions similar to those recorded on specimen PYS-2017-200404. Fragments comprising the control sample from layer 18 are, in general, more free from concretions than those from the skeleton and feature 809. f, Biplot and linear regression correlating the length and width of Achatina cf. fulica fragments from the grave pit (n = 12) and the skeleton (n = 5) with those from layer 18 (n = 581) (top), and box plots of length and width distributions of Achatina cf. fulica fragments from these two contexts (bottom). Rectangles in the box plots show the second and third quartiles, central bar indicates the median, and whiskers the extreme values. The fragments from the burial pit are significantly larger in size (P = 0.001) while displaying the same length/width ratio. Incorporation in the grave infilling have preserved Achatina fragments from the higher levels of fragmentation that have affected fragments exposed to trampling on the occupation surface in layer 18.

Extended Data Fig. 8 PYS human dental remains.

a, PYS dental remains: isolated teeth (left) and mCT 3D reconstruction of the two molars included in the maxillary and mandibular bones (right). All molars are positioned with the mesial surface towards the top and the distal surface towards the bottom. L (left); R (right); dm2 (second deciduous molar), M1 (permanent upper first molar), M1 (permanent lower first molar). b, bgPCA of the Procrustes shape coordinates of the PYS Ldm2 EDJ compared with those of Neanderthals (n = 6), fossil H. sapiens (n = 3) and modern humans (n = 5). c, bgPCA of the Procrustes shape coordinates of the PYS RM1 EDJ compared with those of Neanderthals (n = 6), fossil H. sapiens (n = 2) and modern humans (n = 12). d, bgPCA of the Procrustes shape coordinates of the PYS RM1 EDJ compared with those of Neanderthals (n = 12), fossil H. sapiens (n = 3) and modern humans (n = 12).

Extended Data Table 1 PYS faunal remains
Full size table
Extended Data Table 2 Diagenesis of identifiable and putative human bone in Mtoto’s section
Full size table

Supplementary information

Supplementary Information

This file contains Supplementary Sections A-J, including Supplementary Figures and Supplementary Tables 1-11 – see contents page for details.

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Martinón-Torres, M., d’Errico, F., Santos, E. et al. Earliest known human burial in Africa. Nature 593, 95–100 (2021). https://doi.org/10.1038/s41586-021-03457-8

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