Skip to main content

Thank you for visiting 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.

The dental proteome of Homo antecessor

An Author Correction to this article was published on 29 July 2020

This article has been updated


The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1,2,3,4,5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6,7,8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Phosphorylation of hominin enamel proteomes.
Fig. 2: Phylogenetic analysis of H. antecessor ATD6-92.
Fig. 3: Skeletal proteome preservation in the Middle and Early Pleistocene epoch (0.12–2.6 Ma).

Data availability

Mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium ( via the PRIDE partner repository with the dataset identifier PXD014342. Generated ancient protein consensus sequences used for phylogenetic analysis for H. antecessor (Atapuerca) and H. erectus (Dmanisi) hominins can be found in the Supplementary Data 2, which is formatted as a .fasta file. Full protein sequence alignments used during phylogenetic analysis can be accessed via Figshare ( Amino acid racemization data are available online through the NOAA database. The wiNNer model can be accessed on GitHub (

Change history


  1. Gabunia, L. et al. Earliest Pleistocene hominid cranial remains from Dmanisi, Republic of Georgia: taxonomy, geological setting, and age. Science 288, 1019–1025 (2000).

    Article  ADS  CAS  PubMed  Google Scholar 

  2. Zhu, Z. et al. Hominin occupation of the Chinese Loess Plateau since about 2.1 million years ago. Nature 559, 608–612 (2018).

    Article  ADS  CAS  PubMed  Google Scholar 

  3. Stringer, C. The origin and evolution of Homo sapiens. Phil. Trans. R. Soc. Lond. B 371, 20150237 (2016).

    Article  Google Scholar 

  4. Hublin, J. J. The origin of Neandertals. Proc. Natl Acad. Sci. USA 106, 16022–16027 (2009).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  5. Rightmire, G. Human evolution in the Middle Pleistocene: the role of Homo heidelbergensis. Evol. Anthropol. 6, 218–227 (1998).

    Article  Google Scholar 

  6. Cappellini, E. et al. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature 574, 103–107 (2019).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  7. Chen, F. et al. A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. Nature 569, 409–412 (2019).

    Article  ADS  CAS  PubMed  Google Scholar 

  8. Welker, F. et al. Enamel proteome shows that Gigantopithecus was an early diverging pongine. Nature 576, 262–265 (2019).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  9. Bermúdez de Castro, J. M. et al. A hominid from the lower Pleistocene of Atapuerca, Spain: possible ancestor to Neandertals and modern humans. Science 276, 1392–1395 (1997).

    Article  PubMed  Google Scholar 

  10. Carbonell, E. et al. Lower Pleistocene hominids and artifacts from Atapuerca-TD6 (Spain). Science 269, 826–830 (1995).

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Duval, M. et al. The first direct ESR dating of a hominin tooth from Atapuerca Gran Dolina TD-6 (Spain) supports the antiquity of Homo antecessor. Quat. Geochronol. 47, 120–137 (2018).

    Article  Google Scholar 

  12. Freidline, S. E., Gunz, P., Harvati, K. & Hublin, J.-J. Evaluating developmental shape changes in Homo antecessor subadult facial morphology. J. Hum. Evol. 65, 404–423 (2013).

    Article  PubMed  Google Scholar 

  13. Lacruz, R. S. et al. Facial morphogenesis of the earliest Europeans. PLoS One 8, e65199 (2013).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  14. Ferring, R. et al. Earliest human occupations at Dmanisi (Georgian Caucasus) dated to 1.85–1.78 Ma. Proc. Natl Acad. Sci. USA 108, 10432–10436 (2011).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lordkipanidze, D. et al. A complete skull from Dmanisi, Georgia, and the evolutionary biology of early Homo. Science 342, 326–331 (2013).

    Article  ADS  CAS  PubMed  Google Scholar 

  16. Stewart, N. A., Gerlach, R. F., Gowland, R. L., Gron, K. J. & Montgomery, J. Sex determination of human remains from peptides in tooth enamel. Proc. Natl Acad. Sci. USA 114, 13649–13654 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Tiwary, S. et al. High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis. Nat. Methods 16, 519–525 (2019).

    Article  CAS  PubMed  Google Scholar 

  18. Castiblanco, G. A. et al. Identification of proteins from human permanent erupted enamel. Eur. J. Oral Sci. 123, 390–395 (2015).

    Article  CAS  PubMed  Google Scholar 

  19. Asaka, T. et al. Type XVII collagen is a key player in tooth enamel formation. Am. J. Pathol. 174, 91–100 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Porto, I. M., Laure, H. J., de Sousa, F. B., Rosa, J. C. & Gerlach, R. F. New techniques for the recovery of small amounts of mature enamel proteins. J. Archaeol. Sci. 38, 3596–3604 (2011).

    Article  Google Scholar 

  21. Gasse, B., Chiari, Y., Silvent, J., Davit-Béal, T. & Sire, J.-Y. Amelotin: an enamel matrix protein that experienced distinct evolutionary histories in amphibians, sauropsids and mammals. BMC Evol. Biol. 15, 47 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Demarchi, B. et al. Protein sequences bound to mineral surfaces persist into deep time. eLife 5, e17092 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  23. Tagliabracci, V. S. et al. Secreted kinase phosphorylates extracellular proteins that regulate biomineralization. Science 336, 1150–1153 (2012).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  24. Hu, J. C. C., Yamakoshi, Y., Yamakoshi, F., Krebsbach, P. H. & Simmer, J. P. Proteomics and genetics of dental enamel. Cells Tissues Organs 181, 219–231 (2005).

    Article  CAS  PubMed  Google Scholar 

  25. Glimcher, M. J., Cohen-Solal, L., Kossiva, D. & de Ricqles, A. Biochemical analyses of fossil enamel and dentin. Paleobiology 16, 219–232 (1990).

    Article  Google Scholar 

  26. Wagner, G. A. et al. Radiometric dating of the type-site for Homo heidelbergensis at Mauer, Germany. Proc. Natl Acad. Sci. USA 107, 19726–19730 (2010).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  28. Bermúdez de Castro, J. M., Martinón-Torres, M., Arsuaga, J. L. & Carbonell, E. Twentieth anniversary of Homo antecessor (1997–2017): a review. Evol. Anthropol. 26, 157–171 (2017).

    Article  PubMed  Google Scholar 

  29. Gómez-Robles, A., Bermúdez de Castro, J. M., Arsuaga, J.-L., Carbonell, E. & Polly, P. D. No known hominin species matches the expected dental morphology of the last common ancestor of Neanderthals and modern humans. Proc. Natl Acad. Sci. USA 110, 18196–18201 (2013).

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  30. Meyer, M. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 531, 504–507 (2016).

    Article  ADS  CAS  PubMed  Google Scholar 

  31. Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).

    Article  ADS  PubMed  CAS  Google Scholar 

  32. Lacruz, R. S. et al. The evolutionary history of the human face. Nat. Ecol. Evol. 3, 726–736 (2019).

    Article  PubMed  Google Scholar 

  33. Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  34. The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).

    Article  CAS  Google Scholar 

  35. Welker, F. et al. Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae. PeerJ 5, e3033 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Hill, R. C. et al. Preserved proteins from extinct Bison latifrons identified by tandem mass spectrometry; hydroxylysine glycosides are a common feature of ancient collagen. Mol. Cell. Proteomics 14, 1946–1958 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Wadsworth, C. & Buckley, M. Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone. Rapid Commun. Mass Spectrom. 28, 605–615 (2014).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  38. Orlando, L. et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74–78 (2013).

    Article  ADS  CAS  PubMed  Google Scholar 

  39. Penkman, K. E. H., Kaufman, D. S., Maddy, D. & Collins, M. J. Closed-system behaviour of the intra-crystalline fraction of amino acids in mollusc shells. Quat. Geochronol. 3, 2–25 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Dickinson, M., Lister, A. M. & Penkman, K. E. H. A new method for enamel amino acid racemization dating: a closed system approach. Quat. Geochronol. 50, 29–46 (2019).

    Article  Google Scholar 

  41. Hill, R. L. Hydrolysis of proteins. Adv. Protein Chem. 20, 37–107 (1965).

    Article  CAS  PubMed  Google Scholar 

  42. Mackie, M. et al. Palaeoproteomic profiling of conservation layers on a 14th century italian wall painting. Angew. Chem. Int. Ed. Engl. 57, 7369–7374 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Castellano, S. et al. Patterns of coding variation in the complete exomes of three Neandertals. Proc. Natl Acad. Sci. USA 111, 6666–6671 (2014).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  44. de Manuel, M. et al. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354, 477–481 (2016).

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  45. Nater, A. et al. Morphometric, behavioral, and genomic evidence for a new orangutan species. Curr. Biol. 27, 3487–3498.e10 (2017).

    Article  CAS  PubMed  Google Scholar 

  46. Prado-Martinez, J. et al. Great ape genetic diversity and population history. Nature 499, 471–475 (2013).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  47. Hanson-Smith, V. & Johnson, A. PhyloBot: a web portal for automated phylogenetics, ancestral sequence reconstruction, and exploration of mutational trajectories. PLOS Comput. Biol. 12, e1004976 (2016).

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  48. Welker, F. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment. BMC Evol. Biol. 18, 23 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Hendy, J. et al. A guide to ancient protein studies. Nat. Ecol. Evol. 2, 791–799 (2018).

    Article  PubMed  Google Scholar 

  50. Zhang, J. et al. PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification. Mol. Cell. Proteomics 11, M111.010587 (2012).

    Article  PubMed  CAS  Google Scholar 

  51. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article  CAS  PubMed  Google Scholar 

  52. Chun, Y. H. P. et al. Cleavage site specificity of MMP-20 for secretory-stage ameloblastin. J. Dent. Res. 89, 785–790 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Yamakoshi, Y., Hu, J. C. C., Fukae, M., Yamakoshi, F. & Simmer, J. P. How do enamelysin and kallikrein 4 process the 32-kDa enamelin? Eur. J. Oral Sci. 114 (Suppl 1), 45–51, 93–95, 379–380 (2006).

    Google Scholar 

  54. Iwata, T. et al. Processing of ameloblastin by MMP-20. J. Dent. Res. 86, 153–157 (2007).

    Article  CAS  PubMed  Google Scholar 

  55. Nagano, T. et al. Mmp-20 and Klk4 cleavage site preferences for amelogenin sequences. J. Dent. Res. 88, 823–828 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Fukae, M. et al. Primary structure of the porcine 89-kDa enamelin. Adv. Dent. Res. 10, 111–118 (1996).

    Article  CAS  PubMed  Google Scholar 

  57. Colaert, N., Helsens, K., Martens, L., Vandekerckhove, J. & Gevaert, K. Improved visualization of protein consensus sequences by iceLogo. Nat. Methods 6, 786–787 (2009).

    Article  CAS  PubMed  Google Scholar 

  58. Prüfer, K. et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358, 655–658 (2017).

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

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

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  60. Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).

    Article  CAS  PubMed  Google Scholar 

  62. Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Bouckaert, R. et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS Comput. Biol. 15, e1006650 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Miller, M. A., Pfeiffer, W. & Schwartz, T. in Gateway Computing Environments Workshop (GCE) 1–8 (New Orleans, 2010).

  65. Besenbacher, S., Hvilsom, C., Marques-Bonet, T., Mailund, T. & Schierup, M. H. Direct estimation of mutations in great apes reconciles phylogenetic dating. Nat. Ecol. Evol. 3, 286–292 (2019).

    Article  PubMed  Google Scholar 

  66. Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references


F.W. is supported by a Marie Skłodowska Curie Individual Fellowship (no. 795569). E. Cappellini was supported by VILLUM FONDEN (no. 17649). E.W. is supported by the Lundbeck Foundation, the Danish National Research Foundation, the Novo Nordisk Foundation, the Carlsberg Foundation, KU2016 and the Wellcome Trust. Without the effort of the members of the Atapuerca research team during fieldwork, this work would have not been possible; we make a special mention of J. Rosell, who supervises the excavation of the TD6 level. The research of the Atapuerca project has been supported by the Dirección General de Investigación of the Ministerio de Ciencia, Innovación y Universidades (grant numbers PGC2018-093925-B-C31, C32, and C33); field seasons are supported by the Consejería de Cultura y Turismo of the Junta de Castilla y León and the Fundación Atapuerca. We acknowledge The Leakey Foundation through the personal support of G. Getty (2013) and D. Crook (2014–2016, 2018, and 2019) to M.M.-T., as well as F.W. (2017). Restoration and conservation work on the material have been carried out by P. Fernández-Colón and E. Lacasa from the Conservation and Restoration Area of CENIEH-ICTS and L. López-Polín from IPHES. The picture of the specimen ATD6-92 was made by M. Modesto-Mata. E. Cappellini, J.C., J.V.O. and P. Gutenbrunner are supported by the Marie Skłodowska-Curie European Training Network (ETN) TEMPERA, a project funded by the European Union’s Framework Program for Research and Innovation Horizon 2020 (grant agreement no. 722606). Amino acid analyses were undertaken thanks to the Leverhulme Trust (PLP-2012-116) and NERC (NE/K500987/1). T.M.-B. is supported by BFU2017-86471-P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social ‘La Caixa’ and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). C.L.-F. is supported by a FEDER-MINECO grant (PGC2018-095931-B-100). M.K. was supported by the Postdoctoral Junior Leader Fellowship Programme from ‘la Caixa’ Banking Foundation (LCF/BQ/PR19/11700002). M.M. is supported by the Danish National Research Foundation award PROTEIOS (DNRF128). Work at the Novo Nordisk Foundation Center for Protein Research is funded in part by a donation from the Novo Nordisk Foundation (grant number NNF14CC0001). The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech) and it is a member of the ProteoRed PRB3 consortium, which is supported by grant PT17/0019 of the PE I+D+i 2013-2016 from the Instituto de Salud Carlos III (ISCIII) and ERDF. We acknowledge support from the Spanish Ministry of Science, Innovation and Universities, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208, and ‘Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya’ (2017SGR595). D.L. and A.M. are supported by the John Templeton Foundation (no. 52935) and by the Shota Rustaveli National Science Foundation of Georgia (no. FR-18-27262). We thank M. L. Schjellerup Jørkov for providing specimen Ø1952.

Author information

Authors and Affiliations



E. Cappellini, E.W., J.M.B.d.C., D.L., C.L.-F. and F.W. designed the study. E. Cappellini, M.M., F.W., J.R.-M., R.R.J.-C., M.R.D., C.C. and M.d.M. performed experiments. E. Cappellini, A.M., J.L.A., E. Carbonell, P. Gelabert, E.S., J.C., J.V.O., T.M.-B. and D.L. provided material, reagents or research infrastructure. F.W., J.R.-M., P. Gutenbrunner, S.T., E. Cappellini, F.R., M.M.-T., J.M.B.d.C., M.K., M.R.D., C.L.-F. and K.P. analysed data. F.W., E. Cappellini and J.M.B.d.C. wrote the manuscript with input from all other authors.

Corresponding authors

Correspondence to Frido Welker, José María Bermúdez de Castro, Eske Willerslev or Enrico Cappellini.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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 Location and stratigraphy of the hominin fossils studied.

a, Geographic location of Gran Dolina and Dmanisi. Base map was generated using public domain data from b, Summarized stratigraphic profile of Gran Dolina, including the location of hominin fossils in layers ‘Pep’ and ‘Jordi’ of sublevel TD6.2.

Extended Data Fig. 2 Hominin specimens studied.

a, ATD6-92 in buccal view. The fragment represents a portion of a permanent lower left first or second molar. b, D4163 in occlusal view. The specimen is a fragmented right upper first molar. Scale bar differs between a and b.

Extended Data Fig. 3 Amino acid racemization of D4163.

a, b, The extent of intracrystalline racemization in enamel for the free amino acid (FAA) (x axis) fraction and the total hydrolysable amino acids (THAA) (y axis) fraction for aspartic acid plus asparagine (here denoted Asx) (a), and glutamic acid plus glutamine (here denoted Glx) (b), demonstrates endogenous amino acids breaking down within a closed system. The hominin value is displayed in relation to values for enamel samples from other fauna from Dmanisi6 (blue squares) and a range of previously obtained Pleistocene and Pliocene Proboscidea from the UK40 (grey diamonds). Fauna are shown for comparison, but different rates in their protein breakdown mean that they will show different extents of racemization. The x and y axis are on different scales.

Extended Data Fig. 4 Sequence coverage for five enamel-specific proteins across Pleistocene samples and recent human controls.

For each protein, the bars span protein positions covered, with positions remapped to the human reference proteome. The top row indicates the position of a selection of known MMP20 and KLK4 cleavage products of the enamel-specific proteins AMELX55, AMBN52 and ENAM56. Several in vivo proteolytic degradation fragments of ENAM share the same N terminus, but have unknown C termini53. Dotted line for AMBN indicates a putative cleavage product based on known MMP20 (squares) and KLK4 (circles) in vivo cleavage positions. For AMTN, serines (S) at positions 115 and 116 (indicated by asterisks) are conserved among vertebrates and involved in mineral-binding21. Additional cleavage products as well as MMP20 and KLK4 cleavage sites are known in all enamel-specific proteins. SK33916 and Ø1952 are two recent human control samples (Methods). AA, amino acids; Steph., Stephanorhinus6; TRAP, tyrosine-rich amelogenin polypeptide.

Extended Data Fig. 5 Homo antecessor specimen ATD6-92 represents a male hominin.

a, Mass spectrum of an AMELY-specific peptide from the recent human control Ø1952. b, Mass spectrum of the same AMELY-specific peptide from H. antecessor. c, Alignment of a selection of AMELY- and AMELX-specific peptide fragment ion series deriving from H. antecessor. The alignment stretches along human AMELX isoform 1, positions 37 to 52 only (Uniprot accession numbers Q99217 (AMELX), Q99218 (AMELY)). See Supplementary Fig. 5 for another example of an AMELY-specific MS2 spectrum.

Extended Data Fig. 6 Enamel proteome damage.

a, b, Glutamine (Q) and asparagine (N) deamidation of enamel-specific proteins from H. antecessor (Atapuerca) (a), and H. erectus (Dmanisi) (b). Values are based on 1,000 bootstrap replications of protein deamidation. c, Relationship between mean asparagine (N) and glutamine (Q) deamidation for all proteins in both the Atapuerca and Dmanisi hominin datasets. Error bars represent 95% confidence interval window of 1,000 bootstrap replications of protein deamidation. Dashed line is x = y. d, Peptide length distribution of H. antecessor (Atapuerca), H. erectus (Dmanisi), four previously published enamel proteomes6,8,16 and one additional human Medieval control sample (Ø1952). For a, b and d, the number of peptides (n) is given for each violin plot. The box plots within the violin plots define the range of the data (whiskers extend to 1.5× the interquartile range), outliers (black dots, beyond 1.5× the interquartile range), 25th and 75th percentiles (boxes), and medians (centre lines). P values of two-sided t-tests conducted between sample pairs are indicated. No independent replication of these experiments was performed.

Extended Data Fig. 7 Survival of in vivo MMP20 and KLK4 cleavage sites in the Atapuerca enamel proteome.

a, Experimentally observed cleavage matrices for ameloblastin (AMBN), enamelin (ENAM) and amelogenin (AMELX and AMELY) (Methods). Fold differences are colour-coded by comparing observed PSM cleavage frequencies to a random cleavage matrix for each protein separately7. b, Fold differences for all observed cleavage pairs per protein. Red filled circles represent MMP20, KLK4 and signal peptide cleavage sites mentioned in the literature53,54,55,56. Red open circles indicate cleavage sites located up to two amino acid positions away from such sites. c, PSM coverage for each protein. The signal peptide (thick horizontal bar labelled ‘sig’), known MMP20 and KLK4 cleavage sites (vertical bars), and O- and N-linked glycosylation sites (asterisks) are also indicated. For AMELX, peptide positions for all three known isoforms were remapped to the coordinates of isoform 3, which represents the longest isoform (UniProt accession Q99217-3). The x and y axes differ between the three panels of c.

Extended Data Fig. 8 Phylogenetic position of D4163 through Bayesian analysis.

Nomascus leucogenys and M. mulatta were used as outgroups.

Extended Data Table 1 Extraction and mass spectrometry details of analyses conducted on both ancient hominin specimens
Extended Data Table 2 Ancient hominin enamel proteome composition and coverage

Supplementary information

Supplementary Information

Supplementary Information containing supplementary information on the archaeological sites of Gran Dolina, Atapuerca, and Dmanisi, amino acid racemization, proteomic data extraction, data generation, and data analysis, as well as phylogenetic analysis of recovered ancient hominin proteomes. The Supplementary Information contains 11 SI tables and 16 SI figures.

Reporting Summary

Supplementary Data

Supplementary information file containing annotated MS/MS spectra of phylogenetic interest.

Supplementary Data

File in .fasta format containing recovered Homo antecessor (Atapuerca) and Homo erectus (Dmanisi) protein sequences. Sequence coverage obtained after MaxQuant and PEAKS analysis is combined.

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Welker, F., Ramos-Madrigal, J., Gutenbrunner, P. et al. The dental proteome of Homo antecessor. Nature 580, 235–238 (2020).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing