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Proteomic evidence of dietary sources in ancient dental calculus

Hendy, Jessica, Warinner, Christina, Bouwman, Abigail, Collins, Matthew J., Fiddyment, Sarah, Fischer, Roman, Hagan, Richard, Hofman, Courtney A., Holst, Malin, Chaves, Eros, Klaus, Lauren, Larson, Greger, Mackie, Meaghan, McGrath, Krista, Mundorff, Amy Z., Radini, Anita, Rao, Huiyun, Trachsel, Christian, Velsko, Irina M., Speller, Camilla F.·2018·Proceedings of the Royal Society B: Biological Sciences
DOI 10.1098/rspb.2018.0977PMC PMC6083251
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Abstract

Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.

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  • The dental calculus proteomic approach may not capture the diversity of foods consumed by an individual, and there is a bias toward certain food groups.

    “While informative on the consumption of particular foodstuffs, it is clear that this approach may not capture the diversity of foods consumed by that individual, and there is a bias toward certain food groups (107).”

    From Ancient protein analysis in archaeology (2021) · cites this paper as [107]

  • Hendy et al. reported that in samples of ancient dental calculus there appears to be a bias toward detection of milk proteins over other foods.

    “For example, Hendy et al. (107) reported that in samples of ancient dental calculus there appears to be a bias toward the detection of milk proteins over other foods.”

    From Ancient protein analysis in archaeology (2021) · cites this paper as [107]

  • Whether seemingly rapid shifts in ancestry detected in aDNA data were result of sudden massive population replacements and/or long-term individual human mobility due to institutions such as patrilocality has been a matter of discussion and debate.

    “Whether seemingly rapid shifts in ancestry detected in aDNA data were the result of sudden massive population replacements and/or long-term individual human mobility due to institutions such as patrilocality has also been a matter of discussion and debate 333,334 .”

    From Ancient DNA analysis (2021) · cites this paper as [334]

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Research works printed but not linked: 49

  1. 10.1038/ng.2536 · DOI · Paper page
  2. 10.1038/ng.2906 · DOI · Paper page
  3. 10.1038/srep07104 · DOI · Paper page
  4. Velsko IM et al. 2017 The dental calculus metabolome in modern and historic samples. bioRxiv. 136176. (doi:10.1101/136176) · DOI
  5. 10.1002/ajpa.23147 · DOI
  6. 10.1002/oa.1173 · DOI
  7. 10.1016/j.jas.2007.12.005 · DOI
  8. 10.1073/pnas.1016868108 · DOI
  9. 10.1016/j.jas.2012.02.020 · DOI
  10. 10.1371/journal.pone.0100808 · DOI
  11. 10.1016/j.jas.2014.11.024 · DOI
  12. 10.1098/rstb.2013.0376 · DOI
  13. 10.1126/science.1249274 · DOI
  14. 10.7554/eLife.17092 · DOI · Paper page
  15. 10.1038/s41598-017-06390-x · DOI · Paper page
  16. 10.1021/ac800515v · DOI · Paper page
  17. 10.1016/j.quaint.2016.04.015 · DOI · Paper page
  18. 10.1038/srep31053 · DOI
  19. 10.1016/j.jprot.2013.11.016 · DOI · Paper page
  20. 10.1016/j.jas.2014.02.005 · DOI · Paper page
  21. 10.1002/rcm.6481 · DOI
  22. 10.1371/journal.pone.0158636 · DOI
  23. 10.1038/nature21674 · DOI
  24. 10.1002/pmic.201400436 · DOI
  25. Mackie M, Hendy J, Lowe AD, Sperduti A, Holst M, Collins MJ, Speller CF. 2017 Preservation of the metaproteome: variability of protein preservation in ancient dental calculus. Sci. Technol. Archaeol. Res. 3, 74–86. (doi:10.1080/20548923.2017.1361629) · DOI · Paper page
  26. Leonard C, Vashro L, O'Connell JF, Henry AG. 2015 Plant microremains in dental calculus as a record of plant consumption: a test with Twe forager-horticulturalists. J. Archaeol. Sci. Rep. 2, 449–457. (doi:10.1016/j.jasrep.2015.03.009) · DOI
  27. 10.1016/j.jas.2015.04.003 · DOI
  28. 10.1021/jf00082a015 · DOI
  29. 10.1016/S0958-6946(02)00140-1 · DOI
  30. 10.1016/j.fm.2008.01.007 · DOI
  31. 10.1042/bj2550113 · DOI
  32. 10.4324/9781315001906 · DOI
  33. 10.1104/pp.97.1.165 · DOI
  34. 10.1016/0016-7037(92)90223-6 · DOI
  35. 10.1126/science.278.5337.432 · DOI
  36. 10.1073/pnas.1603477113 · DOI
  37. 10.1073/pnas.0808752105 · DOI
  38. 10.1007/s00114-016-1420-x · DOI
  39. 10.1038/ng2123 · DOI
  40. 10.1371/journal.pone.0013352 · DOI
  41. 10.1074/mcp.R500012-MCP200 · DOI · Paper page
  42. 10.1186/1471-2105-13-S16-S4 · DOI
  43. 10.1093/bioinformatics/btm545 · DOI
  44. 10.1016/j.aca.2008.03.032 · DOI
  45. 10.1021/pr301139y · DOI
  46. 10.1002/pmic.200500856 · DOI
  47. 10.1074/mcp.T400006-MCP200 · DOI
  48. 10.1002/pmic.201500170 · DOI
  49. Vizcaíno JA et al. 2013 The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41 D1063–D1069. (doi:10.1093/nar/gks1262) · DOI · Paper page

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Metadata

Authors
Hendy, J., Warinner, C., Bouwman, A., Collins, M. J., Fiddyment, S., Fischer, R., Hagan, R., Hofman, C. A., Holst, M., Chaves, E., Klaus, L., Larson, G., Mackie, M., McGrath, K., Mundorff, A. Z., Radini, A., Rao, H., Trachsel, C., Velsko, I. M., & Speller, C. F.
Affiliations
  • Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
  • Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
  • Institute for Evolutionary Medicine, ETH-Zürich, University of Zürich, Zürich, Switzerland
  • BioArCh, Department of Archaeology, University of York, York, UK
  • Discovery Proteomics Facility, Target Discovery Institute, University of Oxford, Oxford, UK
  • Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
  • Department of Periodontology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
  • The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
  • EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
  • Department of Anthropology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
  • Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, People's Republic of China
  • Functional Genomics Center, ETH-Zürich, University of Zürich, Zürich, Switzerland
ORCID
Venue
Proceedings of the Royal Society B: Biological Sciences
Publisher
The Royal Society
Published
2018-07-18
Volume
285
Issue
1883
ISSN
  • 0962-8452
  • 1471-2954
DOI
10.1098/rspb.2018.0977
PMC
PMC6083251
Cited by
104
References
5
Language
en
Licence
Funders
  • Wellcome Trust (108375/Z/15/Z)
  • Kennedy Trust Fund
  • White Rose University Consortium Collaboration Fund
  • The Max Planck Society
  • National Science Foundation (BCS-1516633, BCS-1523264, BCS-1643318)
  • DNRF Niels Bohr Professorship (DNRF128)
  • University of York C2D2 Research Priming Fund (097829/Z/11/A)
  • Oxford University Fell Fund (EBD-10130)

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