Exploring the potential of dental calculus to shed light on past human migrations in Oceania

Irina M Velsko; Zandra Fagernäs; Monica Tromp; Stuart Bedford; Hallie R Buckley; Geoffrey Clark; John Dudgeon; James Flexner; Jean-Christophe Galipaud; Rebecca Kinaston; Cecil M Lewis Jr; Elizabeth Matisoo-Smith; Kathrin Nägele; Andrew T Ozga; Cosimo Posth; Adam B Rohrlach; Richard Shing; Truman Simanjuntak; Matthew Spriggs; Anatauarii Tamarii; Frédérique Valentin; Edson Willie; Christina Warinner

doi:10.1038/s41467-024-53920-z

Exploring the potential of dental calculus to shed light on past human migrations in Oceania

Nat Commun. 2024 Nov 24;15(1):10191. doi: 10.1038/s41467-024-53920-z.

Authors

Irina M Velsko¹, Zandra Fagernäs^{1

2}, Monica Tromp^{3

4

5}, Stuart Bedford^{6

7}, Hallie R Buckley⁵, Geoffrey Clark⁶, John Dudgeon⁸, James Flexner⁹, Jean-Christophe Galipaud¹⁰, Rebecca Kinaston¹¹, Cecil M Lewis Jr¹², Elizabeth Matisoo-Smith⁵, Kathrin Nägele¹, Andrew T Ozga¹³, Cosimo Posth^{1

14

15}, Adam B Rohrlach^{1

16}, Richard Shing¹⁷, Truman Simanjuntak¹⁸, Matthew Spriggs^{17

19}, Anatauarii Tamarii²⁰, Frédérique Valentin²¹, Edson Willie¹⁷, Christina Warinner^{22

23

24

25}

Affiliations

¹ Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
² University of Copenhagen, Globe Institute, Copenhagen, Denmark.
³ Department of Archaeology, Max Planck Institute for Geoanthropology, Jena, Germany.
⁴ Southern Pacific Archaeological Research, Archaeology Programme, University of Otago, Dunedin, New Zealand.
⁵ Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
⁶ Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Canberra, Australia.
⁷ Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
⁸ Department of Anthropology, Idaho State University, Pocatello, ID, USA.
⁹ Archaeology, School of Humanities, University of Sydney, Sydney, Australia.
¹⁰ Research Institute for Development and National Museum of Natural History, Paris, France.
¹¹ BioArch South, Waitati, New Zealand.
¹² Department of Anthropology, University of Oklahoma, Norman, OK, USA.
¹³ Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.
¹⁴ Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
¹⁵ Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany.
¹⁶ School of Biological Sciences, The University of Adelaide, Adelaide, Australia.
¹⁷ Vanuatu Cultural Centre, Port-Vila, Vanuatu.
¹⁸ National Research and Development Centre for Archaeology, Jakarta, Indonesia.
¹⁹ School of Archaeology and Anthropology, College of Arts & Social Sciences, The Australian National University, Canberra, Australia.
²⁰ Direction de la Culture et du Patrimoine, Puna'auia, French Polynesia.
²¹ CNRS UMR 8068, MSH Mondes, Nanterre, France.
²² Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. warinner@fas.harvard.edu.
²³ Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany. warinner@fas.harvard.edu.
²⁴ Archaeogenetics Unit, Leibniz Institute for Infection Biology and Natural Products Research Hans Knoll Institute, Jena, Germany. warinner@fas.harvard.edu.
²⁵ Department of Anthropology, Harvard University, Cambridge, MA, USA. warinner@fas.harvard.edu.

Abstract

The Pacific islands and Island Southeast Asia have experienced multiple waves of human migrations, providing a case study for exploring the potential of ancient microbiomes to study human migration. We perform a metagenomic study of archaeological dental calculus from 102 individuals, originating from 10 Pacific islands and 1 island in Island Southeast Asia spanning ~3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone, and comparable to that of calculus from temperate regions. Oral microbial community composition is minimally driven by time period and geography in Pacific and Island Southeast Asia calculus, but is found to be distinctive compared to calculus from Europe, Africa, and Asia. Phylogenies of individual bacterial species in Pacific and Island Southeast Asia calculus reflect geography. Archaeological dental calculus shows good preservation in tropical regions and the potential to yield information about past human migrations, complementing studies of the human genome.

MeSH terms

Archaeology
Asia, Southeastern
Bacteria / classification
Bacteria / genetics
Bacteria / isolation & purification
DNA, Ancient / analysis
Dental Calculus* / history
Dental Calculus* / microbiology
History, Ancient
Human Migration* / history
Humans
Metagenomics / methods
Microbiota* / genetics
Oceania
Pacific Islands
Phylogeny

Substances

DNA, Ancient

Abstract

MeSH terms

Substances

Grants and funding