Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia

Journal name:
Nature
Volume:
544,
Pages:
180–184
Date published:
DOI:
doi:10.1038/nature21416
Received
Accepted
Published online

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.

At a glance

Figures

  1. Australian mtDNA phylogeny.
    Figure 1: Australian mtDNA phylogeny.

    Phylogenetic analysis of Aboriginal Australian and Melanesian (dashed grey lines) mitogenomes using BEAST31, showing the four major haplogroups detected in Australia (in colour), along with other Aboriginal Australian lineages not used in dating analyses (solid black lines). The age of the most recent common ancestor (TMRCA) and 95% highest posterior density intervals were calculated for each Aboriginal-Australian-only clade (red dots) using human mitochondrial evolutionary rates calibrated with Palaeolithic European and Asian mitogenomes18, 32 to minimize the effects of rate temporal dependency33, 34 (see Methods). The posterior distributions for each TMRCA are shown behind the phylogeny, in matching colours. The dark grey box represents the initial colonization of Australia indicated by archaeological evidence at 48.8 ± 1.3 ka (see Methods). The light grey box indicates the period when mitochondrial lineages were still sorting into Australia or New Guinea/Melanesia, which occurred during the initial colonization of Sahul. Genetic divergences during this time (for example, between M16 and M42, or O and N) might have occurred outside Australia, and were excluded from TMRCA calculations. The short branch length of an ancient S2 sequence14 reflects the radiocarbon-dated age of the specimen. The early Holocene diversification of lineages within haplogroup O2 is indicated with an asterisk. LGM, Last Glacial Maximum.

  2. Australian mtDNA phylogeography.
    Figure 2: Australian mtDNA phylogeography.

    Phylogeographic distributions of Aboriginal Australian mitogenome haplotypes, grouped into the four major haplogroups O, S, P and M with timescales calculated using an ancient-DNA-calibrated molecular clock (see Methods). Lineages from samples in the current study (circles) are shown at the location of the oldest known maternal ancestor recorded in genealogical and geographic data, generally before the effects of European colonization. Triangles represent data from modern samples reported in previous studies. The size of the symbols reflects the number of identical haplotypes as indicated in the figure. Identical sequences from the same location were pruned, whereas those from multiple locations were only used where they could not be explained through genealogical records. Coloured circles and lines represent haplotypes with known geographical provenance, with colours matching the cluster assignments of the multiple correspondence analysis (Supplementary Table 3), whereas grey (empty) circles represent the geographic distribution of samples not falling within each specific haplogroup. Previously published haplotypes that lack detailed geographic data histories are shown with yellow triangles (and black lines) for each haplogroup, whereas those with no associated locations are shown on the tree as black branches alone. 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).

  3. The peopling of Australia.
    Figure 3: The peopling of Australia.

    Model of the peopling of Australia combining genetic and archaeological data, showing approximate, and stylised, coastal movements of haplogroups O and R (west) and P, S, and M (east). The inferred movement of S into the interior is influenced by the path of a recent study on water sources and human movement21. Data from other studies where pre-European distributions are unclear are indicated with a dagger (†), and include a potential late-glacial movement into the western central desert region (blue dashed arrows; see Methods). Early archaeological sites in Australia and New Guinea (black dots) are given with mean ages for earliest occupation of sites in each region (Supplementary Table 4). Insufficient data were available for sites with white dots, which were not used in the age model for the initial Sahul colonization date but provide independent age controls. Ages in southwestern and south central Australia, at Devil’s Lair (49–46 ka) and Warratyi rock shelter (49–45 ka), suggest that the overall population movements were rapid and that the coastal regions of Australia were colonized within a few thousand years. Approximate late Pleistocene vegetation reconstructions are shown (from ref. 35). The map was adapted from the figure in ref. 36, originally constructed by J.S.

  4. The geographical distribution of the oldest recorded maternal ancestors for the hair sample donors.
    Extended Data Fig. 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).

  5. Sahul phylogenetic tree calibrated using the mitogenome rate from ref.
    Extended Data Fig. 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.

  6. Sahul phylogenetic tree calibrated using mitogenome rate from ref. 32.
    Extended Data Fig. 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.

  7. Australian phylogeography incorporating mtDNA lineage information from modern samples reported in ref. 12.
    Extended Data Fig. 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).

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

  9. Locations of the early occupation sites used to estimate the timing of the colonization of Sahul.
    Extended Data Fig. 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.

  10. Palaeodemography of Australian mitogenomes.
    Extended Data Fig. 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.

Tables

  1. Complete Australian phylogeography test results
    Extended Data Table 1: Complete Australian phylogeography test results

Accession codes

Primary accessions

European Nucleotide Archive

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Author information

  1. These authors contributed equally to this work.

    • Ray Tobler &
    • Adam Rohrlach
  2. These authors jointly supervised this work.

    • Wolfgang Haak &
    • Alan Cooper

Affiliations

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

    • Adam Rohrlach,
    • Jonathan Tuke &
    • Nigel Bean
  3. ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia 5005, Australia

    • Adam Rohrlach,
    • Jonathan Tuke &
    • Nigel Bean
  4. Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia 5000, Australia

    • Julien Soubrier
  5. South Australian Museum, Adelaide, South Australia 5005, 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, South Australia 5005, 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, New South Wales 2052, Australia

    • Alan N. Williams &
    • Chris S. M. Turney
  8. School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, Australian Capital Territory 0200, Australia

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

    • Robert J. Mitchell
  10. Alfred Deakin Institute, Deakin University, Melbourne, Victoria 3125, Australia

    • Emma Kowal
  11. Australian Genome Research Facility, The Waite Research Precinct, Adelaide, South Australia 5064, 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, 07745 Jena, Germany

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

    • Alan Cooper

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.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to:

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.

Author details

Extended data figures and tables

Extended Data Figures

  1. Extended Data Figure 1: The geographical distribution of the oldest recorded maternal ancestors for the hair sample donors. (135 KB)

    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).

  2. Extended Data Figure 2: Sahul phylogenetic tree calibrated using the mitogenome rate from ref. (443 KB)

    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.

  3. Extended Data Figure 3: Sahul phylogenetic tree calibrated using mitogenome rate from ref. 32. (468 KB)

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

  4. Extended Data Figure 4: Australian phylogeography incorporating mtDNA lineage information from modern samples reported in ref. 12. (384 KB)

    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).

  5. Extended Data Figure 5: Age-depth model for Devil’s Lair, south-western Australia. (408 KB)

    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.

  6. Extended Data Figure 6: Locations of the early occupation sites used to estimate the timing of the colonization of Sahul. (362 KB)

    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.

  7. Extended Data Figure 7: Palaeodemography of Australian mitogenomes. (67 KB)

    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 Tables

  1. Extended Data Table 1: Complete Australian phylogeography test results (244 KB)

Supplementary information

PDF files

  1. Supplementary Information (862 KB)

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

Excel files

  1. Supplementary Tables (166 KB)

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

Additional data