Enamel proteins reveal biological sex and genetic variability in southern African Paranthropus

peer-reviewed · Science · 2025

peer-reviewed · Science · 2025. Palesa P. Madupe et al. Paranthropus robustus is a morphologically well-documented Early Pleistocene hominin species from southern…
Date 2025-05-29
Type peer-reviewed
Venue Science
Publisher American Association for the Advancement of Science (AAAS)
Contribution downstream-application
DOI 10.1126/science.adt9539
Citations (OpenAlex) 25

Abstract

Paranthropus robustus is a morphologically well-documented Early Pleistocene hominin species from southern Africa with no genetic evidence reported so far. In this work, we describe the mass spectrometric sequencing of enamel peptides from four ~2 million-year-old dental specimens attributed morphologically to P. robustus from the site of Swartkrans in South Africa. The identification of AMELY-specific peptides enabled us to assign two specimens to male individuals, whereas semiquantitative mass spectrometric data analysis attributed the other two to females. A single amino acid polymorphism and the enamel-dentine junction shape variation indicated potential subgroups present within southern African Paranthropus . This study demonstrates how palaeoproteomics can help distinguish sexual dimorphism from other sources of variation in African Early Pleistocene hominins.

Authors

  1. Palesa P. Madupe · University of Cape Town, University of Copenhagen
  2. Claire Koenig · Novo Nordisk Foundation, University of Copenhagen
  3. Ioannis Patramanis · Novo Nordisk Foundation, University of Copenhagen
  4. Patrick L. Rüther · Novo Nordisk Foundation, University of Cape Town, University of Copenhagen
  5. Nomawethu Hlazo · Novo Nordisk Foundation, University of Cape Town, University of Copenhagen
  6. Meaghan Mackie · National Heritage Council, Novo Nordisk Foundation, University College Dublin, University of Cape Town, University of Copenhagen, University of Turin
  7. Mirriam Tawane · Consejo Superior de Investigaciones Científicas, Institut de Biologia Evolutiva, National Heritage Council, University of Cape Town
  8. Johanna Krueger · Consejo Superior de Investigaciones Científicas, Institut de Biologia Evolutiva, University of Copenhagen
  9. Alberto J. Taurozzi · Novo Nordisk Foundation, University of Copenhagen
  10. Gaudry Troché · Novo Nordisk Foundation, University of Copenhagen
  11. Job Kibii · University of Cape Town
  12. Robyn Pickering · University of Cape Town, University of York
  13. Marc R. Dickinson · University of Cape Town, University of York
  14. Yonatan Sahle · University of Cape Town, University of Johannesburg
  15. Dipuo Kgotleng · Duke University, University of Cape Town, University of Johannesburg
  16. Charles Musiba · Duke University, National Museums of Kenya, University of Cape Town
  17. Fredrick Manthi · National Museums of Kenya, University of Cape Town
  18. Liam Bell
  19. Michelle DuPlessis · Bordeaux Proteome, Centre National de la Recherche Scientifique, Chimie et Biologie des Membranes et des Nanoobjects, Université de Bordeaux
  20. Catherine Gilbert · Bordeaux Proteome, Centre National de la Recherche Scientifique, Chimie et Biologie des Membranes et des Nanoobjects, University of the Witwatersrand, Université de Bordeaux
  21. Bernhard Zipfel · Consejo Superior de Investigaciones Científicas, Institut de Biologia Evolutiva, University of the Witwatersrand
  22. Lukas F. K. Kuderna · Consejo Superior de Investigaciones Científicas, Institut Català de Paleontologia Miquel Crusafont, Institut de Biologia Evolutiva, Universitat Autònoma de Barcelona, Universitat Pompeu Fabra
  23. Esther Lizano · Consejo Superior de Investigaciones Científicas, Institut Català de Paleontologia Miquel Crusafont, Institut de Biologia Evolutiva, Universitat Autònoma de Barcelona, Universitat Pompeu Fabra, University of Copenhagen
  24. Frido Welker · Max Planck Institute for Evolutionary Anthropology, Max Planck Institute of Biochemistry, University of Copenhagen
  25. Pelagia Kyriakidou · Consejo Superior de Investigaciones Científicas, Institut Català de Paleontologia Miquel Crusafont, Institut de Biologia Evolutiva, Max Planck Institute of Biochemistry, Universitat Pompeu Fabra
  26. Jürgen Cox · Centre de Recherches sur la Cognition Animale, Consejo Superior de Investigaciones Científicas, Institut Català de Paleontologia Miquel Crusafont, Institut de Biologia Evolutiva, Max Planck Institute of Biochemistry, Universitat Pompeu Fabra, University of Bergen, Université de Toulouse
  27. Catherine Mollereau · Bordeaux Proteome, Centre National de la Recherche Scientifique, Centre de Recherches sur la Cognition Animale, Chimie et Biologie des Membranes et des Nanoobjects, Université de Bordeaux, Université de Toulouse
  28. Caroline Tokarski · Bordeaux Proteome, Centre National de la Recherche Scientifique, Chimie et Biologie des Membranes et des Nanoobjects, Institute of Infectious Disease and Molecular Medicine, Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, University of Cape Town, Université de Bordeaux, Université de Lille
  29. Jonathan M. Blackburn · Institute of Infectious Disease and Molecular Medicine, University of Cape Town, University of Copenhagen
  30. Jazmín Ramos-Madrigal · Centro Nacional de Análisis Genómico, Consejo Superior de Investigaciones Científicas, Institució Catalana de Recerca i Estudis Avançats, Institut Català de Paleontologia Miquel Crusafont, Institut de Biologia Evolutiva, Universitat Autònoma de Barcelona, University of Copenhagen
  31. Tomas Marques-Bonet · Barcelona Institute of Science and Technology, Centro Nacional de Análisis Genómico, Consejo Superior de Investigaciones Científicas, Institució Catalana de Recerca i Estudis Avançats, Institució Catalana de Recerca i Estudis Avançats (ICREA), Institut Català de Paleontologia Miquel Crusafont, Institut de Biologia Evolutiva, Universitat Autònoma de Barcelona, Universitat Pompeu Fabra, University Pompeu Fabra, University of York
  32. Kirsty Penkman · Centre National de la Recherche Scientifique, De la Préhistoire à l’Actuel : Culture, Environnement et Anthropologie, University of York, University of the Witwatersrand, Université de Bordeaux
  33. Clément Zanolli · Centre National de la Recherche Scientifique, De la Préhistoire à l’Actuel : Culture, Environnement et Anthropologie, University of Cape Town, University of Toronto, University of the Witwatersrand, Université de Bordeaux
  34. Lauren Schroeder · University of Cape Town, University of Copenhagen, University of Toronto
  35. Fernando Racimo · Novo Nordisk Foundation, University of Copenhagen
  36. Jesper V. Olsen · Novo Nordisk Foundation, University of California San Diego, University of Cape Town, University of Copenhagen
  37. Rebecca R. Ackermann · University of Cape Town, University of Copenhagen
  38. Enrico Cappellini · University of Copenhagen

Methods and tools

  • Paranthropus robustus enamel proteome: Palaeoproteomic sequencing of enamel peptides from four Paranthropus robustus teeth at Swartkrans, assigning sex from AMELY peptides and detecting a polymorphism that hints at subgroups.

Methods it uses

  • PEAKS: Commercial DP-based de novo

Data deposited

  • Enamel proteins reveal biological sex and intrataxon variability within Paranthropus robustus — as deposited · PXD040221

Cites (5)

Cited by (3)

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