Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Earliest known human burial in Africa

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.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

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.

Data availability

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

References

  1. 1.

    Mcbrearty, S. & Brooks, A. S. The revolution that wasn’t: a new interpretation of the origin of modern human behavior. J. Hum. Evol. 39, 453–563 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2.

    Mounier, A. & Mirazón Lahr, M. Deciphering African late middle Pleistocene hominin diversity and the origin of our species. Nat. Commun. 10, 3406 (2019).

    ADS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Scerri, E. M. L. et al. Did our species evolve in subdivided populations across Africa, and why does it matter? Trends Ecol. Evol. 33, 582–594 (2018).

    PubMed  PubMed Central  Google Scholar 

  4. 4.

    Carbonell, E. & Mosquera, M. The emergence of a symbolic behaviour: the sepulchral pit of Sima de los Huesos, Sierra de Atapuerca, Burgos, Spain. C. R. Palevol 5, 155–160 (2006).

    Google Scholar 

  5. 5.

    Pettitt, P. The Palaeolithic Origins of Human Burial (Routledge, 2011).

  6. 6.

    Zilhão, J. in Death Rituals and Social Order in the Ancient World: Death Shall Have No Dominion (eds Renfrew, C. et al.) 27–44 (Cambridge Univ. Press, 2016).

  7. 7.

    Roberts, P. et al. Late Pleistocene to Holocene human palaeoecology in the tropical environments of coastal eastern Africa. Palaeogeogr. Palaeoclimatol. Palaeoecol. 537, 109438 (2020).

    Google Scholar 

  8. 8.

    Shipton, C. et al. 78,000-year-old record of Middle and Later stone age innovation in an East African tropical forest. Nat. Commun. 9, 1832 (2018).

    ADS  PubMed  PubMed Central  Google Scholar 

  9. 9.

    d’Errico, F. et al. Trajectories of cultural innovation from the Middle to Later Stone Age in Eastern Africa: personal ornaments, bone artifacts, and ocher from Panga ya Saidi, Kenya. J. Hum. Evol. 141, 102737 (2020).

    PubMed  PubMed Central  Google Scholar 

  10. 10.

    Prendergast, M. E. et al. Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets. PLoS ONE 12, e0182565 (2017).

    PubMed  PubMed Central  Google Scholar 

  11. 11.

    Skoglund, P. et al. Reconstructing prehistoric African population structure. Cell 171, 59–71.e21 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Grove, M. & Blinkhorn, J. Neural networks differentiate between Middle and Later Stone Age lithic assemblages in eastern Africa. PLoS ONE 15, e0237528 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Duday, A. in Social Archaeology of Funerary Remains (eds Gowland, R. L. & Knüsel, C. J.) 30–56 (Oxbow Books, 2006).

  14. 14.

    Knüsel, C. J. Crouching in fear: terms of engagement for funerary remains. J. Soc. Archaeol. 14, 26–58 (2014).

    Google Scholar 

  15. 15.

    Blaizot, F. Les Espaces Funéraires de l’Habitat Groupé des Ruelles à Serris du VIIe au XIe Siècles Seine et Marne, Île-de-France: Taphonomie du Squelette, Modes d’Inhumation, Organisation et Dynamique (Univ. Bordeaux, 2011).

  16. 16.

    Kapandii, I. A. Physiologie Articulaire: Schémas Comment Mécanique Humaine Vol. 3 (Maloine, 1972).

  17. 17.

    Defleur, A. Les Sépultures Moustériennes (Editions de CNRS, 1993).

  18. 18.

    Backwell, L., Huchet, J.-B., Jashashvili, T., Dirks, P. H. G. M. & Berger, L. R. Termites and necrophagous insects associated with early Pleistocene (Gelasian) Australopithecus sediba at Malapa, South Africa. Palaeogeogr. Palaeoclimatol. Palaeoecol. 560, 109989 (2020).

    Google Scholar 

  19. 19.

    Ghiorse, W. C. in Manganese in Soils and Plants (eds Graham, R. D. et al.) 75–85 (Springer, 1988).

  20. 20.

    Thompson, I. A., Huber, D. M., Guest, C. A. & Schulze, D. G. Fungal manganese oxidation in a reduced soil. Environ. Microbiol. 7, 1480–1487 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Gargett, R. H. Middle Palaeolithic burial is not a dead issue: the view from Qafzeh, Saint-Césaire, Kebara, Amud, and Dederiyeh. J. Hum. Evol. 37, 27–90 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Bailey, S. E. & Hublin, J.-J. in Neanderthals Revisited: New Approaches and Perspectives (eds Hublin, J.-J. et al.) 191–209 (Springer, 2006).

  23. 23.

    Grine, F. E. Middle Stone Age human fossils from Die Kelders Cave 1, Western Cape Province, South Africa. J. Hum. Evol. 38, 129–145 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Liu, W. et al. The earliest unequivocally modern humans in southern China. Nature 526, 696–699 (2015).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Martín-Albaladejo, M., Martinón-Torres, M., García-González, R., Arsuaga, J. L. & Bermúdez de Castro, J. M. Morphometric analysis of Atapuerca-Sima de los Huesos lower first molars. Quat. Int. 433, 156–162 (2017).

    Google Scholar 

  26. 26.

    Henshilwood, C. S. & Marean, C. W. The origin of modern human behavior: critique of the models and their test implications. Curr. Anthropol. 44, 627–651 (2003).

    Google Scholar 

  27. 27.

    Vermeersch, P. M., Paulissen, E., Gijselings, G. & Janssen, J. Middle Palaeolithic chert exploitation pits near Qena (Upper Egypt). Paéorient 12, 61–65 (1986).

    Google Scholar 

  28. 28.

    Van Peer, P., Vermeersch, P. M. & Paulissen, E. Chert Quarrying, Lithic Technology and Human Burial at the Palaeolithic Site of Taramsa 1, Upper Egypt Vol. 5 (Leuven Univ. Press, 2010).

  29. 29.

    Vermeersch, P. M. et al. A Middle Palaeolithic burial of a modern human at Taramsa Hill, Egypt. Antiquity 72, 475–484 (1998).

    Google Scholar 

  30. 30.

    d’Errico, F. & Backwell, L. Earliest evidence of personal ornaments associated with burial: the Conus shells from Border Cave. J. Hum. Evol. 93, 91–108 (2016).

    Google Scholar 

  31. 31.

    Beaumont, P. B., de Villiers, H. & Vogel, J. C. Modern man in sub-Saharan Africa prior to 49000 years BP: a review and evaluation with particular reference to Border Cave. S. Afr. J. Sci. 74, 409–419 (1978).

    Google Scholar 

  32. 32.

    Cooke, H. B. S., Malan, B. D. & Wells, L. H. Fossil man in the Lebombo Mountains, South Africa: the ‘Border Cave,’ Ingwavuma District, Zululand. Man 45, 6–13 (1945).

    Google Scholar 

  33. 33.

    d’Errico, F. et al. Additional evidence on the use of personal ornaments in the Middle Paleolithic of North Africa. Proc. Natl Acad. Sci. USA 106, 16051–16056 (2009).

    ADS  Google Scholar 

  34. 34.

    Henshilwood, C. S., d’Errico, F. & Watts, I. Engraved ochres from the Middle Stone Age levels at Blombos Cave, South Africa. J. Hum. Evol. 57, 27–47 (2009).

    Google Scholar 

  35. 35.

    Henshilwood, C. S. et al. An abstract drawing from the 73,000-year-old levels at Blombos Cave, South Africa. Nature 562, 115–118 (2018).

    ADS  CAS  Google Scholar 

  36. 36.

    Steele, T. E., Alvarez-Fernandez, E. & Hallet-Desguez, E. A review of shells as personal ornamentation during the African Middle Stone Age. Paleoanthropology 24, 24–51 (2019).

    Google Scholar 

  37. 37.

    White, T. D. Cut marks on the Bodo cranium: a case of prehistoric defleshing. Am. J. Phys. Anthropol. 69, 503–509 (1986).

    CAS  Google Scholar 

  38. 38.

    Clark, J. D. et al. Stratigraphic, chronological and behavioural contexts of Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature 423, 747–752 (2003).

    ADS  CAS  Google Scholar 

  39. 39.

    Dirks, P. H. G. M. et al. Geological and taphonomic evidence for deliberate body disposal by the primitive hominin species Homo naledi from the Dinaledi Chamber. eLife 4, e09561 (2015).

    PubMed  PubMed Central  Google Scholar 

  40. 40.

    Stiner, M. C. Love and death in the Stone Age: what constitutes first evidence of mortuary treatment of the human body? Biol. Theory 12, 248–261 (2017).

    Google Scholar 

  41. 41.

    Scerri, E. M. L., Chikhi, L. & Thomas, M. G. Beyond multiregional and simple out-of-Africa models of human evolution. Nat. Ecol. Evol. 3, 1370–1372 (2019).

    PubMed  PubMed Central  Google Scholar 

  42. 42.

    Brooks, A. S. et al. Long-distance stone transport and pigment use in the earliest Middle Stone Age. Science 360, 90–94 (2018).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Henshilwood, C. S. et al. A 100,000-year-old ochre-processing workshop at Blombos Cave, South Africa. Science 334, 219–222 (2011).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Wadley, L. in The Oxford Handbook of African Archaeology (eds Mitchell, P. & Lane, P.) 15 (Oxford Univ. Press, 2020).

  45. 45.

    Richter, D. et al. The age of the hominin fossils from Jebel Irhoud, Morocco, and the origins of the Middle Stone Age. Nature 546, 293–296 (2017).

    ADS  CAS  Google Scholar 

  46. 46.

    Guo, Y.-J. et al. New ages for the Upper Palaeolithic site of Xibaimaying in the Nihewan Basin, northern China: implications for small-tool and microblade industries in north-east Asia during Marine Isotope Stages 2 and 3. J. Quat. Sci. 32, 540–552 (2017).

    Google Scholar 

  47. 47.

    Li, B., Jacobs, Z. & Roberts, R. G. Validation of the LnTn method for De determination in optical dating of K-feldspar and quartz. Quat. Geochronol. 58, 101066 (2020).

    Google Scholar 

  48. 48.

    Blegen, N. et al. Distal tephras of the eastern Lake Victoria basin, equatorial East Africa: correlations, chronology and a context for early modern humans. Quat. Sci. Rev. 122, 89–111 (2015).

    ADS  Google Scholar 

  49. 49.

    Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).

    Google Scholar 

  50. 50.

    Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Rohland, N., Glocke, I., Aximu-Petri, A. & Meyer, M. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nat. Protocols 13, 2447–2461 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. 52.

    Gansauge, M.-T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, e79 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. 54.

    Korlević, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 59, 87–93 (2015).

    PubMed  PubMed Central  Google Scholar 

  55. 55.

    Glocke, I. & Meyer, M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth. Genome Res. 27, 1230–1237 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. 56.

    Slon, V. et al. Mammalian mitochondrial capture, a tool for rapid screening of DNA preservation in faunal and undiagnostic remains, and its application to Middle Pleistocene specimens from Qesem Cave (Israel). Quat. Int. 398, 210–218 (2016).

    Google Scholar 

  57. 57.

    Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  58. 58.

    Maricic, T., Whitten, M. & Pääbo, S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE 5, e14004 (2010).

    ADS  PubMed  PubMed Central  Google Scholar 

  59. 59.

    Renaud, G., Stenzel, U. & Kelso, J. leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. 42, e141 (2014).

    PubMed  PubMed Central  Google Scholar 

  60. 60.

    Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61.

    Huson, D. H., Auch, A. F., Qi, J. & Schuster, S. C. MEGAN analysis of metagenomic data. Genome Res. 17, 377–386 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Slon, V. et al. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356, 605–608 (2017).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  63. 63.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. 64.

    Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Scheuer, L. & Black, S. in Human Osteology: In Archeology and Forensic Science (eds. Cox, M. & Mays, S.) 9–22 (Cambridge Univ. Press, 2000).

  66. 66.

    Bullock, P. et al. Handbook for Soil Thin Section Description (Waine Research, 1985).

  67. 67.

    Stoops, G. Guidelines for Analysis and Description of Soil and Regolith Thin Sections. (Soil Science Soc. Am., 2003).

  68. 68.

    Stoops, G., Marcelino, V. & Mees, F. (eds.) Interpretation of Micromorphological Features of Soils and Regoliths (Elsevier, 2018).

  69. 69.

    Hollund, H. I. et al. What happened here? Bone histology as a tool in decoding the postmortem histories of archaeological bone from Castricum, the Netherlands. Int. J. Osteoarchaeol. 22, 537–548 (2012).

    Google Scholar 

  70. 70.

    Hedges, R. E. M., Millard, A. R. & Pike, A. W. G. Measurements and relationships of diagenetic alteration of bone from three archaeological sites. J. Archaeol. Sci. 22, 201–209 (1995).

    Google Scholar 

  71. 71.

    Millard, A. R. in Handbook of Archaeological Sciences (eds. Brothwell, D. R. & Pollard, A. M.) 637–674 (Wiley, 2001).

  72. 72.

    Hackett, C. J. Microscopical focal destruction (tunnels) in exhumed human bones. Med. Sci. Law 21, 243–265 (1981).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. 73.

    Jans, M. M. E. in Current Developments in Bioerosion (eds. Wisshak, M. & Tapanila, L.) 397–404 (Springer, 2008).

  74. 74.

    Carlsen, O. Dental Morphology (Munksgaard, 1987).

  75. 75.

    Tobias, P. V. The Skulls, Endocasts and Teeth of Homo habilis Vol. 4 (Cambridge Univ. Press, 1991).

  76. 76.

    Turner, C. G., Nichol, C. R. & Scott, G. R. in Advances in Dental Anthropology (eds. Kelley, M. & Larsen, C.) 13–31 (Wiley-Liss, 1991).

  77. 77.

    Scott, G. R. & Turner, C. G. The Anthropology of Modern Human Teeth: Dental Morphology and Its Variation in Recent Human Populations. (Cambridge Univ. Press, 1997).

  78. 78.

    Martinón-Torres, M. et al. Dental evidence on the hominin dispersals during the Pleistocene. Proc. Natl Acad. Sci. USA 104, 13279–13282 (2007).

    ADS  Google Scholar 

  79. 79.

    Martinón-Torres, M. et al. Dental remains from Dmanisi (Republic of Georgia): morphological analysis and comparative study. J. Hum. Evol. 55, 249–273 (2008).

    Google Scholar 

  80. 80.

    Martínez de Pinillos, M., Martinón-Torres, M., Martín-Francés, L., Arsuaga, J. L. & Bermúdez de Castro, J. M. Comparative analysis of the trigonid crests patterns in Homo antecessor molars at the enamel and dentine surfaces. Quat. Int. 433, 189–198 (2017).

    Google Scholar 

  81. 81.

    Martinón-Torres, M., Bermúdez de Castro, J. M., Gómez-Robles, A., Prado-Simón, L. & Arsuaga, J. L. Morphological description and comparison of the dental remains from Atapuerca-Sima de los Huesos site (Spain). J. Hum. Evol. 62, 7–58 (2012).

    PubMed  PubMed Central  Google Scholar 

  82. 82.

    Molnar, S. Human tooth wear, tooth function and cultural variability. Am. J. Phys. Anthropol. 34, 175–189 (1971).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. 83.

    Lefèvre, J. Etude odontologique des hommes de Muge. Bull. Mem. Soc. Anthropol. Paris 10, 301–333 (1973).

    Google Scholar 

  84. 84.

    Bermúdez de Castro, J. M., Sarmiento, S., Cunha, E., Rosas, A. & Bastir, M. Dental size variation in the Atapuerca-SH Middle Pleistocene hominids. J. Hum. Evol. 41, 195–209 (2001).

    PubMed  PubMed Central  Google Scholar 

  85. 85.

    Bailey, S. E. A morphometric analysis of maxillary molar crowns of Middle-Late Pleistocene hominins. J. Hum. Evol. 47, 183–198 (2004).

    PubMed  PubMed Central  Google Scholar 

  86. 86.

    Olejniczak, A. J. et al. Dental tissue proportions and enamel thickness in Neandertal and modern human molars. J. Hum. Evol. 55, 12–23 (2008).

    PubMed  PubMed Central  Google Scholar 

  87. 87.

    Martin, L. Significance of enamel thickness in hominoid evolution. Nature 314, 260–263 (1985).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  88. 88.

    Kono, R. T. Molar enamel thickness and distribution patterns in extant great apes and humans: new insights based on a 3-dimensional whole crown perspective. Anthropol. Sci. 112, 121–146 (2004).

    Google Scholar 

  89. 89.

    Toussaint, M. et al. The Neandertal lower right deciduous second molar from Trou de l’Abîme at Couvin, Belgium. J. Hum. Evol. 58, 56–67 (2010).

    PubMed  PubMed Central  Google Scholar 

  90. 90.

    Zanolli, C. et al. Is the deciduous/permanent molar enamel thickness ratio a taxon-specific indicator in extant and extinct hominids? C. R. Palevol 16, 702–714 (2017).

    Google Scholar 

  91. 91.

    Olejniczak, A. J. & Grine, F. E. High-resolution measurement of Neandertal tooth enamel thickness by microfocal computed-tomography. S. Afr. J. Sci. 101, 219–220 (2005).

    Google Scholar 

  92. 92.

    Maureille, B., Rougier, H., Houët, F. & Vandermeersch, B. Les dents inférieures du Néandertalien Regourdou 1 (site de Regourdou, commune de Montignac, Dordogne): analyses métriques et comparatives. Paleo 13, 183–200 (2001).

    Google Scholar 

  93. 93.

    Scolan, H., Santos, F., Tillier, A.-M., Maureille, B. & Quintard, A. Des nouveaus vestiges Néanderthaliens à Las Pélénos (Monsempron-Libos, Lot-et-Garonne, France). Bull. Mem. Soc. Anthropol. Paris 24, 69–95 (2012).

    Google Scholar 

  94. 94.

    Bayle, P. et al. in Pleistocene Databases: Acquisition, Storing, Sharing (eds. Macchiarelli, R. & Weniger, G. C.) 29–46 (Mettmann: Wissenschaftliche Schriften des Neanderthal Museums 4, 2011).

  95. 95.

    Macchiarelli, R., Bondioli, L., Mazurier, A. & Zanolli, C. in Technique and Application in Dental Anthropology (eds. Irish, J. D. & Nelson, G. C.) 425–448 (Cambridge Univ. Press, 2008).

  96. 96.

    Mitteroecker, P. & Bookstein, F. Linear discrimination, ordination, and the visualization of selection gradients in modern morphometrics. Evol. Biol. 38, 100–114 (2011).

    Google Scholar 

  97. 97.

    Bookstein, F. Morphometric Tools for Landmark Data Geometric and Biology (Cambridge Univ. Press, 1991).

  98. 98.

    Mitteroecker, P., Gunz, P., Windhager, S. & Schaefer, K. A brief review of shape, form, and allometry in geometric morphometrics, with applications to human facial morphology. Hystrix 24, 59–66 (2013).

    Google Scholar 

  99. 99.

    ISO. Particle Size Analysis — Laser Diffraction Methods https://www.iso.org/obp/ui/#iso:std:iso:13320:ed-1:v2:en (ISO, 2009).

  100. 100.

    Jones, R. M. Particle size analysis by laser diffraction: ISO 13320, standard operating procedures, and mie theory. Am. Lab. 35, 44–47 (2003).

    CAS  Google Scholar 

  101. 101.

    Macdonald, P. & Du, J. Mixdist: Finite Mixture Distribution Models https://cran.r-project.org/package=mixdist (2012).

  102. 102.

    Konert, M. & Vandenberghe, J. Comparison of laser grain size analysis with pipette and sieve analysis: A solution for the underestimation of the clay fraction. Sedimentology 44, 523–535 (1997).

    ADS  CAS  Google Scholar 

  103. 103.

    Sitzia, L., Gayo, E. M. & de Pol-Holz, R. A perched, high-elevation wetland complex in the Atacama Desert (northern Chile) and its implications for past human settlement. Quat. Res. 92, 33–52 (2019).

    Google Scholar 

  104. 104.

    Aitchison, J. The Statistical Analysis of Compositional Data (Chapman and Hall, 1986).

  105. 105.

    Martín-Fernández, J. A., Barcelo-Vidal, C. & Pawlowsky-Glahn, V. Dealing with zeros and missing values in compositional data sets using nonparametric imputation. Math. Geol. 35, 253–278 (2003).

    MATH  Google Scholar 

  106. 106.

    Dray, S. & Dufour, A.-B. The ade4 package: implementing the duality diagram for ecologists. J. Stat. Soft. 22, 4 (2007).

    Google Scholar 

  107. 107.

    Pitarch Martí, A., Wei, Y., Gao, X., Chen, F. & d’Errico, F. The earliest evidence of coloured ornaments in China: the ochred ostrich eggshell beads from Shuidonggou Locality 2. J. Anthropol. Archaeol. 48, 102–113 (2017).

    Google Scholar 

  108. 108.

    Downs, R. T. The RRUFF project: An integrated study of the chemistry, crystallography, raman and infrared spectroscopy of minerals. Prog. Abstr. 19th Gen. Meeting Intl Mineralog. Assoc. O03-13 (2006).

  109. 109.

    Julien, C. M., Massot, M. & Poinsignon, C. Lattice vibrations of manganese oxides. Part I. Periodic structures. Spectrochim. Acta A Mol. Biomol. Spectrosc. 60, 689–700 (2004).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  110. 110.

    Bellot-Gurlet, L. et al. Raman studies of corrosion layers formed on archaeological irons in various media. J. Nano Res. 8, 147–156 (2009).

    CAS  Google Scholar 

  111. 111.

    Hanesch, M. Raman spectroscopy of iron oxides and (oxy) hydroxides at low laser power and possible applications in environmental magnetic studies. Geophys. 177, 941–948 (2009).

    CAS  Google Scholar 

  112. 112.

    Babay, S., Mhiri, T. & Toumi, M. Synthesis, structural and spectroscopic characterizations of maghemite γ-Fe2o3 prepared by one-step coprecipitation route. J. Mol. Struct. 1085, 286–293 (2015).

    ADS  CAS  Google Scholar 

Download references

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.

Author information

Affiliations

Authors

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.

ac, 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.

ah, Polarizing microscopy (a, cf) 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
Extended Data Table 2 Diagenesis of identifiable and putative human bone in Mtoto’s section

Supplementary information

Supplementary Information

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

Reporting Summary

Peer Review File

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links