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.
European Nucleotide Archive
- Thermoluminescence dating of a 50,000-year-old human occupation site in northern Australia. Nature 345, 153–156 (1990) , &
- 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) &
- Post-glacial sea-level changes around the Australian margin: a review. Quat. Sci. Rev. 74, 115–138 (2013) , , , &
- Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations. Am. J. Hum. Genet. 65, 808–828 (1999) &
- An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334, 94–98 (2011) et al.
- A re-appraisal of the early Andean human remains from Lauricocha in Peru. PloS One. 10, e0127141 (2015) . et al.
- Deep roots for Aboriginal Australian Y chromosomes. Curr. Biol. 26, 809–813 (2016) et al.
- Antiquity and diversity of aboriginal Australian Y-chromosomes. Am. J. Phys. Anthropol. 159, 367–381 (2016) et al.
- Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc. Natl Acad. Sci. USA 104, 8726–8730 (2007) et al.
- Genetic evidence for the colonization of Australia. Quat. Int. 285, 44–56 (2013)
- Ancient mtDNA sequences from the First Australians revisited. Proc. Natl Acad. Sci. USA 113, 6892–6897 (2016) et al.
- A genomic history of Aboriginal Australia. Nature 538, 207–214 (2016) 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) et al.
- Late Quaternary palaeoenvironmental change in the Australian drylands. Quat. Sci. Rev. 74, 78–96 (2013) et al.
- Holocene demographic changes and the emergence of complex societies in prehistoric Australia. PLoS One 10, e0128661 (2015) , , , &
- ‘Complexity’ and the Australian continental narrative: themes in the archaeology of Holocene Australia. Quat. Int. 285, 182–192 (2013)
- Native title in Australia: an ethnographic perspective. (Cambridge Univ. Press, 2003)
- A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013) et al.
- IntCal13 and marine13 radiocarbon age calibration curves 0–50,000 years cal BP. Radiocarbon 55, 1869–1887 (2013) et al.
- Sunda and Sahul: Prehistoric Studies in Southeast Asia, Melanesia and Australia (eds , & ) 205–246 (Academic Press, 1977) in
- Humans, water, and the colonization of Australia. Proc. Natl Acad. Sci. USA 113, 11477–11482 (2016) , &
- Brief communication: the Australian Barrineans and their relationship to Southeast Asian negritos: an investigation using mitochondrial genomics. Hum. Biol. 85, 485–502 (2013) , &
- A Prehistory of Australia, New Guinea, and Sahul. (Academic Press, 1982) &
- Cultural innovation and megafauna interaction in the early settlement of arid Australia. Nature 539, 280–283 (2016) et al.
- Climate change not to blame for late Quaternary megafauna extinctions in Australia. Nat. Commun. 7, 10511 (2016) et al.
- New ages for the last Australian megafauna: continent-wide extinction about 46,000 years ago. Science 292, 1888–1892 (2001) et al.
- Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the last deglaciation. Sci. Adv. 2, e1501682 (2016) et al.
- 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) , , , &
- The Archaeology of Australia’s Deserts (Cambridge Univ. Press, 2013)
- Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. Sci. Adv. 2, e1501385 (2016) et al.
- BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007) &
- 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) et al.
- Time-dependent rates of molecular evolution. Mol. Ecol. 20, 3087–3101 (2011) et al.
- Inferences from tip-calibrated phylogenies: a review and a practical guide. Mol. Ecol. 25, 1911–1924 (2016) &
- Symbolic behaviour and the peopling of the southern arc route to Australia. Quat. Int. 202, 59–68 (2009) , , , &
- Paleontology. Did the Denisovans cross Wallace’s Line? Science 342, 321–323 (2013) &
- Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010) &
- Generating barcoded libraries for multiplex high-throughput sequencing. Methods Mol. Biol. 840, 155–170 (2012) , &
- Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B 370, 20130624 (2015) , , , &
- Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Protocols 9, 1056–1082 (2014) et al.
- AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012)
- A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet. 90, 675–684 (2012) et al.
- Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009) &
- mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013) , , , &
- Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012) et al.
- Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 30, E386–E394 (2009) &
- Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012) , , &
- mtDB: Human mitochondrial genome database, a resource for population genetics and medical sciences. Nucleic Acids Res. 34, D749–D751 (2006) &
- BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002)
- 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) , , , &
- Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 25, 1459–1471 (2008) , &
- Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88 (2006) , , &
- Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006) , &
- Encyclopedia of Measurement and Statistics (ed. ) 651–657 (Thousand Oaks, 2007) & in
- Correspondence Analysis in Practice. (CRC Press, 2007)
- FactoMineR: an R package for multivariate analysis. J. Stat. Softw. 25, 1–18 (2008) , &
- Least squares quantization in PCM. IEEE Trans. Inf. Theory 28, 129–137 (1982)
- Clustering by means of medoids. Statistical Data Analysis Based on the L 1-Norm and Related Methods. First International Conference 405–416416 (1987) &
- Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math. 20, 53–65 (1987)
- Cluster Analysis Basics and Extensions. R package version 2.0.4. CRAN (2016) , , , &
- 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)
- 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) &
- Algorithm AS 89: The upper tail probabilities of Spearman’s Rho. Appl. Stat. 24, 377–379 (1975) &
- VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003)
- Early human occupation at Devil’s Lair, southwestern Australia 50,000 years ago. Quat. Res. 55, 3–13 (2001) et al.
- Review of Devil’s Lair artefact classification and radiocarbon chronology. Aust. Archaeol. 43, 28–32 (1996) &
- Devil’s Lair, an example of prolonged cave use in South-Western Australia. World Archaeol. 10, 258–279 (1979)
- Recent and planned developments of the program OxCal. Radiocarbon 55, 720–730 (2013) &
- Dealing with outliers and offsets in radiocarbon dating. Radiocarbon 57, 1023–1045 (2009)
- SHCal13 Southern Hemisphere calibration, 0–50,000 years cal BP. Radiocarbon 55, 1889–1903 (2013) et al.
- New ΔR values for the southwest Pacific Ocean. Radiocarbon 46, 1005–1014 (2004) , &
- Pre-bomb marine reservoir variability in the Kimberley region, Western Australia. Radiocarbon 52, 1158–1165 (2010) , , , &
- Oceanic reservoir correction for marine radiocarbon dates from northwestern Australia. Aust. Archaeol. 20, 58–67 (1985)
- 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) 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) 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) et al.
- A 40,000 year-old human occupation site at Huon Peninsula, Papua New Guinea. Nature 324, 453–455 (1986) , , &
- Luminescence dating in archaeology: from origins to optical. Radiat. Meas. 27, 819–892 (1997)
Extended data figures and tables
Extended Data Figures
- 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).
- 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.
- Extended Data Figure 3: Sahul phylogenetic tree calibrated using mitogenome rate from ref. 32. (468 KB)
- 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).
- 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.
- 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.
- 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
- Supplementary Information (862 KB)
This file contains Supplementary Text, legends for Supplementary Tables 1-4 (see separate excel file) and additional references.
- Supplementary Tables (166 KB)
This file contains Supplementary Tables 1-4 (see Supplementary Information file for legends).