Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia

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

Subjects

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.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

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

Similar content being viewed by others

Accession codes

Primary accessions

European Nucleotide Archive

References

  1. Roberts, R. G., Jones, R. & Smith, M. A. Thermoluminescence dating of a 50,000-year-old human occupation site in northern Australia. Nature 345, 153–156 (1990)

    Article  ADS  Google Scholar 

  2. O’Connell, J. F. & Allen, J. The process, biotic impact, and global implications of the human colonization of Sahul about 47,000 years ago. J. Archaeol. Sci. 56, 73–84 (2015)

    Article  Google Scholar 

  3. Lewis, S. E., Sloss, C. R., Murray-Wallace, C. V., Woodroffe, C. D. & Smithers, S. G. Post-glacial sea-level changes around the Australian margin: a review. Quat. Sci. Rev. 74, 115–138 (2013)

    Article  ADS  Google Scholar 

  4. Redd, A. J. & Stoneking, M. Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations. Am. J. Hum. Genet. 65, 808–828 (1999)

    Article  CAS  Google Scholar 

  5. Rasmussen, M. et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334, 94–98 (2011)

    Article  ADS  CAS  Google Scholar 

  6. Fehren-Schmitz L . et al. A re-appraisal of the early Andean human remains from Lauricocha in Peru. PloS One. 10, e0127141 (2015)

    Article  Google Scholar 

  7. Bergström, A. et al. Deep roots for Aboriginal Australian Y chromosomes. Curr. Biol. 26, 809–813 (2016)

    Article  Google Scholar 

  8. Nagle, N. et al. Antiquity and diversity of aboriginal Australian Y-chromosomes. Am. J. Phys. Anthropol. 159, 367–381 (2016)

    Article  Google Scholar 

  9. Hudjashov, G. et al. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc. Natl Acad. Sci. USA 104, 8726–8730 (2007)

    Article  ADS  CAS  Google Scholar 

  10. van Holst Pellekaan, S. Genetic evidence for the colonization of Australia. Quat. Int. 285, 44–56 (2013)

    Article  Google Scholar 

  11. Heupink, T. H. et al. Ancient mtDNA sequences from the First Australians revisited. Proc. Natl Acad. Sci. USA 113, 6892–6897 (2016)

    Article  CAS  Google Scholar 

  12. Malaspinas, A.-S. et al. A genomic history of Aboriginal Australia. Nature 538, 207–214 (2016)

    Article  ADS  CAS  Google Scholar 

  13. Reeves, J. M. et al. Palaeoenvironmental change in tropical Australasia over the last 30,000 years—a synthesis by the OZ-INTIMATE group. Quat. Sci. Rev. 74, 97–114 (2013)

    Article  ADS  Google Scholar 

  14. Fitzsimmons, K. E. et al. Late Quaternary palaeoenvironmental change in the Australian drylands. Quat. Sci. Rev. 74, 78–96 (2013)

    Article  ADS  Google Scholar 

  15. Williams, A. N., Ulm, S., Turney, C. S. M., Rohde, D. & White, G. Holocene demographic changes and the emergence of complex societies in prehistoric Australia. PLoS One 10, e0128661 (2015)

    Article  Google Scholar 

  16. Ulm, S. ‘Complexity’ and the Australian continental narrative: themes in the archaeology of Holocene Australia. Quat. Int. 285, 182–192 (2013)

    Article  Google Scholar 

  17. Sutton, P. Native title in Australia: an ethnographic perspective. (Cambridge Univ. Press, 2003)

  18. Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013)

    Article  CAS  Google Scholar 

  19. Reimer, P. J. et al. IntCal13 and marine13 radiocarbon age calibration curves 0–50,000 years cal BP. Radiocarbon 55, 1869–1887 (2013)

    Article  CAS  Google Scholar 

  20. Bowdler, S. in Sunda and Sahul: Prehistoric Studies in Southeast Asia, Melanesia and Australia (eds Allen, J., Golson, J. & Jones, R. ) 205–246 (Academic Press, 1977)

  21. Bird, M. I., O’Grady, D. & Ulm, S. Humans, water, and the colonization of Australia. Proc. Natl Acad. Sci. USA 113, 11477–11482 (2016)

    Article  ADS  CAS  Google Scholar 

  22. Mcallister, P., Nagle, N. & Mitchell, R. J. Brief communication: the Australian Barrineans and their relationship to Southeast Asian negritos: an investigation using mitochondrial genomics. Hum. Biol. 85, 485–502 (2013)

    Article  Google Scholar 

  23. White, J. P. & O’Connell, J. F. A Prehistory of Australia, New Guinea, and Sahul. (Academic Press, 1982)

  24. Hamm, G. et al. Cultural innovation and megafauna interaction in the early settlement of arid Australia. Nature 539, 280–283 (2016)

    Article  ADS  Google Scholar 

  25. Saltré, F. et al. Climate change not to blame for late Quaternary megafauna extinctions in Australia. Nat. Commun. 7, 10511 (2016)

    Article  ADS  Google Scholar 

  26. Roberts, R. G. et al. New ages for the last Australian megafauna: continent-wide extinction about 46,000 years ago. Science 292, 1888–1892 (2001)

    Article  ADS  CAS  Google Scholar 

  27. Metcalf, J. L. et al. Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the last deglaciation. Sci. Adv. 2, e1501682 (2016)

    Article  ADS  Google Scholar 

  28. Williams, A. N., Ulm, S., Cook, A. R., Langley, M. C. & Collard, M. Human refugia in Australia during the Last Glacial Maximum and terminal Pleistocene: a geospatial analysis of the 25–12ka Australian archaeological record. J. Archaeol. Sci. 40, 4612–4625 (2013)

    Article  Google Scholar 

  29. Smith, M. The Archaeology of Australia’s Deserts (Cambridge Univ. Press, 2013)

  30. Llamas, B. et al. Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. Sci. Adv. 2, e1501385 (2016)

    Article  ADS  Google Scholar 

  31. Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007)

    Article  Google Scholar 

  32. Posth, C. et al. Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a late glacial population turnover in Europe. Curr. Biol. 26, 827–833 (2016)

    Article  CAS  Google Scholar 

  33. Ho, S. Y. W. et al. Time-dependent rates of molecular evolution. Mol. Ecol. 20, 3087–3101 (2011)

    Article  Google Scholar 

  34. Rieux, A. & Balloux, F. Inferences from tip-calibrated phylogenies: a review and a practical guide. Mol. Ecol. 25, 1911–1924 (2016)

    Article  Google Scholar 

  35. Balme, J., Davidson, I., McDonald, J., Stern, N. & Veth, P. Symbolic behaviour and the peopling of the southern arc route to Australia. Quat. Int. 202, 59–68 (2009)

    Article  Google Scholar 

  36. Cooper, A. & Stringer, C. B. Paleontology. Did the Denisovans cross Wallace’s Line? Science 342, 321–323 (2013)

    Article  ADS  CAS  Google Scholar 

  37. Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010)

    Article  Google Scholar 

  38. Knapp, M., Stiller, M. & Meyer, M. Generating barcoded libraries for multiplex high-throughput sequencing. Methods Mol. Biol. 840, 155–170 (2012)

    Article  CAS  Google Scholar 

  39. Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B 370, 20130624 (2015)

    Article  Google Scholar 

  40. Schubert, M. et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Protocols 9, 1056–1082 (2014)

    Article  CAS  Google Scholar 

  41. Lindgreen, S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012)

    Article  Google Scholar 

  42. Behar, D. M. et al. A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet. 90, 675–684 (2012)

    Article  CAS  Google Scholar 

  43. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009)

    Article  CAS  Google Scholar 

  44. Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013)

    Article  Google Scholar 

  45. Kearse, M. et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012)

    Article  Google Scholar 

  46. van Oven, M. & Kayser, M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 30, E386–E394 (2009)

    Article  Google Scholar 

  47. Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012)

    Article  CAS  Google Scholar 

  48. Ingman, M. & Gyllensten, U. mtDB: Human mitochondrial genome database, a resource for population genetics and medical sciences. Nucleic Acids Res. 34, D749–D751 (2006)

    Article  CAS  Google Scholar 

  49. Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)

    Article  CAS  Google Scholar 

  50. Keane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J. & Mclnerney, J. O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6, 29 (2006)

    Article  Google Scholar 

  51. Minin, V. N., Bloomquist, E. W. & Suchard, M. A. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 25, 1459–1471 (2008)

    Article  CAS  Google Scholar 

  52. Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006)

    Article  Google Scholar 

  53. Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006)

    Article  Google Scholar 

  54. Abdi, H. & Valentin, D. in Encyclopedia of Measurement and Statistics (ed. Salkind, N. ) 651–657 (Thousand Oaks, 2007)

  55. Greenacre, M. Correspondence Analysis in Practice. (CRC Press, 2007)

  56. Lê, S., Josse, J. & Husson, F. FactoMineR: an R package for multivariate analysis. J. Stat. Softw. 25, 1–18 (2008)

    Article  Google Scholar 

  57. Lloyd, S. P. Least squares quantization in PCM. IEEE Trans. Inf. Theory 28, 129–137 (1982)

    Article  Google Scholar 

  58. Kaufman, L. & Rousseeuw, P. J. Clustering by means of medoids. Statistical Data Analysis Based on the L 1-Norm and Related Methods. First International Conference 405–416416 (1987)

  59. Rousseeuw, P. J. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math. 20, 53–65 (1987)

    Article  Google Scholar 

  60. Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M. & Hornik, K. Cluster Analysis Basics and Extensions. R package version 2.0.4. CRAN (2016)

  61. R Development Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria http://www.R-project.org (2013)

  62. Legendre, P. & Fortin, M. J. Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol. Ecol. Resour. 10, 831–844 (2010)

    Article  Google Scholar 

  63. Best, D. J. & Roberts, D. E. Algorithm AS 89: The upper tail probabilities of Spearman’s Rho. Appl. Stat. 24, 377–379 (1975)

    Article  Google Scholar 

  64. Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003)

    Article  Google Scholar 

  65. Turney, C. S. M. et al. Early human occupation at Devil’s Lair, southwestern Australia 50,000 years ago. Quat. Res. 55, 3–13 (2001)

    Article  CAS  Google Scholar 

  66. Dortch, C. E. & Dortch, J. Review of Devil’s Lair artefact classification and radiocarbon chronology. Aust. Archaeol. 43, 28–32 (1996)

    Article  Google Scholar 

  67. Dortch, C. Devil’s Lair, an example of prolonged cave use in South-Western Australia. World Archaeol. 10, 258–279 (1979)

    Article  Google Scholar 

  68. Bronk Ramsey, C. & Lee, S. Recent and planned developments of the program OxCal. Radiocarbon 55, 720–730 (2013)

    Article  Google Scholar 

  69. Bronk Ramsey, C. Dealing with outliers and offsets in radiocarbon dating. Radiocarbon 57, 1023–1045 (2009)

    Article  Google Scholar 

  70. Hogg, A. et al. SHCal13 Southern Hemisphere calibration, 0–50,000 years cal BP. Radiocarbon 55, 1889–1903 (2013)

    Article  CAS  Google Scholar 

  71. Petchey, F., Phelan, M. & White, J. P. New ΔR values for the southwest Pacific Ocean. Radiocarbon 46, 1005–1014 (2004)

    Article  CAS  Google Scholar 

  72. O’Connor, S., Ulm, S., Fallon, S. J., Barham, A. & Loch, I. Pre-bomb marine reservoir variability in the Kimberley region, Western Australia. Radiocarbon 52, 1158–1165 (2010)

    Article  Google Scholar 

  73. Bowman, G. M. Oceanic reservoir correction for marine radiocarbon dates from northwestern Australia. Aust. Archaeol. 20, 58–67 (1985)

    Google Scholar 

  74. Roberts, R. G. et al. The human colonisation of Australia: optical dates of 53,000 and 60,000 years bracket human arrival at Deaf Adder Gorge, Northern Territory. Quat. Sci. Rev. 13, 575–583 (1994)

    Article  ADS  Google Scholar 

  75. Roberts, R. G. et al. Single-aliquot and single-grain optical dating confirm thermoluminescence age estimates at Malakunanja II rock shelter in northern Australia. Anc. TL 16, 19–24 (1998)

    CAS  Google Scholar 

  76. Bird, M. I. et al. Radiocarbon dating of organic- and carbonate-carbon in Genyornis and Dromaius eggshell using stepped combustion and stepped acidification. Quat. Sci. Rev. 22, 1805–1812 (2003)

    Article  ADS  Google Scholar 

  77. Groube, L., Chappell, J., Muke, J. & Price, D. A 40,000 year-old human occupation site at Huon Peninsula, Papua New Guinea. Nature 324, 453–455 (1986)

    Article  ADS  CAS  Google Scholar 

  78. Roberts, R. G. Luminescence dating in archaeology: from origins to optical. Radiat. Meas. 27, 819–892 (1997)

    Article  CAS  Google Scholar 

Download references

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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Adam Rohrlach
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Julien Soubrier
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Pere Bover
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Bastien Llamas
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jonathan Tuke
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Nigel Bean
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ali Abdullah-Highfold
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Shane Agius
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Amy O’Donoghue
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Isabel O’Loughlin
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Peter Sutton
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Fran Zilio
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Keryn Walshe
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Alan N. Williams
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Chris S. M. Turney
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Matthew Williams
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Stephen M. Richards
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Robert J. Mitchell
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Emma Kowal
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. John R. Stephen
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Lesley Williams
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Wolfgang Haak
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Alan Cooper
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Ethics declarations

Competing interests

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)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature21416

This article is cited by

Comments

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.

Search

Advanced search

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