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Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia

Nature volume 544, pages 180–184 (2017)Cite this article

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Abstract

Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49–45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.

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Figure 1: Australian mtDNA phylogeny.
Figure 2: Australian mtDNA phylogeography.
Figure 3: The peopling of Australia.

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Acknowledgements

We acknowledge the support and involvement of the Point Pearce, Cherbourg and Koonibba communities and the individual families. We also acknowledge the work of N. Tindale, J. Birdsell and members of the original Board for Archaeological Research expeditions collecting the specimens. We thank the South Australian Museum, Australian Research Council, University of Adelaide Environment Institute, the Genographic Project and Bioplatforms Australia for support, and S. Ulm, G. Gower, I. Mathieson, L. O’Brien, S. Easteal, M. Vilar, C. Stringer and ACAD colleagues for helpful comments and advice. The Aboriginal Heritage Project webpage is https://www.adelaide.edu.au/acad/ahp/, and this work was carried out under the auspices of the University of Adelaide Human Research Ethics Committee, project approval H-2014-252.

Author information

Author notes

  1. Ray Tobler and Adam Rohrlach: These authors contributed equally to this work.

  2. Wolfgang Haak and Alan Cooper: These authors jointly supervised this work.

Authors and Affiliations

  1. Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, 5005, South Australia, Australia

    Ray Tobler, Julien Soubrier, Pere Bover, Bastien Llamas, Matthew Williams, Stephen M. Richards, Wolfgang Haak & Alan Cooper

  2. School of Mathematical Sciences, The University of Adelaide, Adelaide, 5005, South Australia, Australia

    Adam Rohrlach, Jonathan Tuke & Nigel Bean

  3. ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, 5005, South Australia, Australia

    Adam Rohrlach, Jonathan Tuke & Nigel Bean

  4. Genetics and Molecular Pathology, SA Pathology, Adelaide, 5000, South Australia, Australia

    Julien Soubrier

  5. South Australian Museum, Adelaide, 5005, South Australia, Australia

    Ali Abdullah-Highfold, Shane Agius, Amy O’Donoghue, Isabel O’Loughlin, Peter Sutton, Fran Zilio & Keryn Walshe

  6. School of Biological Sciences, The University of Adelaide, Adelaide, 5005, South Australia, Australia

    Peter Sutton

  7. Palaeontology, Geobiology and Earth Archives Research Centre, and Climate Change Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, New South Wales, Australia

    Alan N. Williams & Chris S. M. Turney

  8. School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, 0200, Australian Capital Territory, Australia

    Matthew Williams

  9. Department of Biochemistry and Genetics, La Trobe University, Melbourne, 3086, Victoria, Australia

    Robert J. Mitchell

  10. Alfred Deakin Institute, Deakin University, Melbourne, 3125, Victoria, Australia

    Emma Kowal

  11. Australian Genome Research Facility, The Waite Research Precinct, Adelaide, 5064, South Australia, Australia

    John R. Stephen

  12. Community Elder and Cultural Advisor, Cherbourg, Queensland, Australia

    Lesley Williams

  13. Department of Archeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany

    Wolfgang Haak

  14. Environment Institute, The University of Adelaide, Adelaide, 5005, South Australia, Australia

    Alan Cooper

Authors
  1. Ray Tobler
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Contributions

The project was conceived by A.C., W.H. and P.S. and directed by A.C. and W.H. Archival research and community outreach was led by I.O., A.A-H., S.A., A.O., F.Z. and L.W. with A.C., W.H., R.T. and R.J.M. The genetic sequencing was performed and coordinated by W.H., P.B., M.W., S.R. and J.R.S., and the genetic analysis by W.H., R.T., A.R., J.S., J.T., N.B., B.L. and A.C. Archaeological and anthropological interpretations were provided by P.S., C.T., A.N.W. and K.W. The manuscript was written by A.C. and R.T., with critical input from P.S., C.T., A.N.W., A.R., J.S., W.H. and all other co-authors. R.T., J.S., A.N.W. and A.R. compiled the Supplementary Information.

Corresponding author

Correspondence to Alan Cooper.

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The authors declare no competing financial interests.

Additional information

Reviewer Information Nature thanks P. Bellwood, C. Lalueza-Fox and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Figure 1 The geographical distribution of the oldest recorded maternal ancestors for the hair sample donors.

Despite being collected from three different historical locations—Cherbourg (Queensland), Point Pearce and Koonibba (both South Australia)—the broad distribution of the maternal ancestors of the hair sample donors demonstrates the massive displacement experienced by Aboriginal Australians after European colonization. This pattern illustrates why the accurate reconstruction of Aboriginal Australian genetic history ultimately relies upon samples or genealogical records that capture patterns prior to this displacement. Map data was sourced from the Oak Ridge National Laboratory Distributed Active Archive Center (https://webmap.ornl.gov/wcsdown/wcsdown.jsp?dg_id=10003_1).

Extended Data Figure 2 Sahul phylogenetic tree calibrated using the mitogenome rate from ref.

18. BEAST31 phylogenetic tree of 123 Australian and Melanesian mtDNA lineages, which was calibrated using the ancient mitogenome rate in ref. 18 to minimize the impacts of temporal dependency33,34 and improve estimation of the timing of the founding migrations. The major mitogenome haplogroups are shown at the base of each clade, and posterior support values are provided for all nodes.

Extended Data Figure 3 Sahul phylogenetic tree calibrated using mitogenome rate from ref. 32.

As for Extended Data Fig. 2, except that rate calibration used the mitogenome rate from ref. 32.

Extended Data Figure 4 Australian phylogeography incorporating mtDNA lineage information from modern samples reported in ref. 12.

The additional samples from ref. 12 are shown as stars and are distributed according to their reported locations of collection, all other sample information is presented in an identical manner to Fig. 2. The mtDNA haplogroups from ref. 12 are coloured according to the system used in Fig. 2, with haplogroups not previously shown (that is, R, R12, M42, P3b and S5) indicated with new colours that are described beneath the relevant haplogroup map (we have added the two R haplogroups on the P haplogroup map, as this is the closest sister clade). As in Fig. 2, mtDNA samples from other studies are shown in yellow, with the samples from ref. 12 having a yellow dot to indicate this status. Map data was sourced from the Oak Ridge National Laboratory Distributed Active Archive Center (https://webmap.ornl.gov/wcsdown/wcsdown.jsp?dg_id=10003_1).

Extended Data Figure 5 Age-depth model for Devil’s Lair, south-western Australia.

The age-depth model was generated with OxCal v.4.2.4 (ref. 68) using the Poisson process (outlier) deposition model. Original ages with 68% uncertainty (prior to modeling) with laboratory codes shown on left hand side. Prior (light grey) and posterior (dark grey) probability distributions are plotted. The blue and green envelopes describe the 68% confidence interval for the sedimentary units below and above layer 30 (lower) respectively.

Extended Data Figure 6 Locations of the early occupation sites used to estimate the timing of the colonization of Sahul.

Sites used for colonization time estimation are shown as black dots, with white dots indicating sites that were used to provide independent age controls. Sites names: 1, Buang Merabak; 2, Matenkupkum; 3, Huon Peninsula; 4, Ivane; 5, Kupona na Dari; 6, Yombon; 7, Nawarla Gabarnmang; 8, Malakunanja II; 9, Nauwalabila I; 10, Carpenter’s Gap; 11, Riwi; 12, Djadjiling; 13, Ganga Mara; 14, Jansz; 15, Mandu Mandu; 16, Upper Swan; 17, Devil’s Lair; 18, Allen’s Cave; 19, GRE8; 20, Ngarrabullgan; 21, Menindee; 22, Cooper’s Dune (PACD H1); 23, Lake Mungo; and 24, Warreen Cave. Additional information for these sites including phase calibrated age ranges for initial occupation is provided in Supplementary Table 4. Phase calibrations were performed using OxCal v.4.2.4 (ref. 68) and resulted in an estimate of the initial colonization of Sahul at 48.8 ± 1.3 ka. The map was adapted from the figure in ref. 36, originally constructed by J.S.

Extended Data Figure 7 Palaeodemography of Australian mitogenomes.

GMRF Skyride51 analysis of the 98 Australian-only mtDNA lineages showing the estimated effective maternal population size since the initial colonization of Sahul around 50 ka (see Methods). Owing to the lack of available calibration points, the palaeodemographic curve should be considered relatively approximate. Nonetheless, there is no obvious indication of a major population bottleneck during the Last Glacial Maximum (around 21–18 ka). Line, median and grey shading, 95% highest posterior densities.

Extended Data Table 1 Complete Australian phylogeography test results
Full size table

Supplementary information

Supplementary Information

This file contains Supplementary Text, legends for Supplementary Tables 1-4 (see separate excel file) and additional references. (PDF 862 kb)

Supplementary Tables

This file contains Supplementary Tables 1-4 (see Supplementary Information file for legends). (XLSX 166 kb)

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Tobler, R., Rohrlach, A., Soubrier, J. et al. Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. Nature 544, 180–184 (2017). https://doi.org/10.1038/nature21416

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