An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

1. Morten Rasmussen¹,²,*,
2. Xiaosen Guo²,³,*,
3. Yong Wang⁴,*,
4. Kirk E. Lohmueller⁴,*,
5. Simon Rasmussen⁵,
6. Anders Albrechtsen⁶,
7. Line Skotte⁶,
8. Stinus Lindgreen¹,⁶,
9. Mait Metspalu⁷,
10. Thibaut Jombart⁸,
11. Toomas Kivisild⁹,
12. Weiwei Zhai¹⁰,
13. Anders Eriksson¹¹,
14. Andrea Manica¹¹,
15. Ludovic Orlando¹,
16. Francisco De La Vega¹²,
17. Silvana Tridico¹³,
18. Ene Metspalu⁷,
19. Kasper Nielsen⁵,
20. María C. Ávila-Arcos¹,
21. J. Víctor Moreno-Mayar¹,¹⁴,
22. Craig Muller¹⁵,
23. Joe Dortch¹⁶,
24. M. Thomas P. Gilbert¹,²,
25. Ole Lund⁵,
26. Agata Wesolowska⁵,
27. Monika Karmin⁷,
28. Lucy A. Weinert⁸,
29. Bo Wang³,
30. Jun Li³,
31. Shuaishuai Tai³,
32. Fei Xiao³,
33. Tsunehiko Hanihara¹⁷,
34. George van Driem¹⁸,
35. Aashish R. Jha¹⁹,
36. François-Xavier Ricaut²⁰,
37. Peter de Knijff²¹,
38. Andrea B Migliano⁹,²²,
39. Irene Gallego-Romero¹⁹,
40. Karsten Kristiansen²,³,⁶,
41. David M. Lambert²³,
42. Søren Brunak⁵,²⁴,
43. Peter Forster²⁵,²⁶,
44. Bernd Brinkmann²⁶,
45. Olaf Nehlich²⁷,
46. Michael Bunce¹³,
47. Michael Richards²⁷,²⁸,
48. Ramneek Gupta⁵,
49. Carlos D. Bustamante¹²,
50. Anders Krogh¹,⁶,
51. Robert A. Foley⁹,
52. Marta M. Lahr⁹,
53. Francois Balloux⁸,
54. Thomas Sicheritz-Pontén⁵,²⁹,
55. Richard Villems⁷,³⁰,
56. Rasmus Nielsen⁴,⁶,†,
57. Wang Jun²,³,⁶,³¹,†,
58. Eske Willerslev¹,²,†

+ Author Affiliations

1. ¹Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
2. ²Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark.
3. ³Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China.
4. ⁴Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720, USA.
5. ⁵Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark.
6. ⁶Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
7. ⁷Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia.
8. ⁸MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK.
9. ⁹Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK.
10. ¹⁰Beijing Institute of Genomics, Chinese Academy of Sciences, 7 Beitucheng West Road, Chaoyang District, Beijing 100029, China.
11. ¹¹Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
12. ¹²Department of Genetics, Stanford University, Stanford, CA 94305, USA.
13. ¹³Ancient DNA Lab, School of Biological Sciences and Biotechnology, Murdoch University, Western Australia 6150, Australia.
14. ¹⁴Undergraduate Program on Genomic Sciences, National Autonomous University of Mexico, Avenida Universidad s/n Chamilpa 62210, Cuernavaca, Morelos, Mexico.
15. ¹⁵Goldfields Land and Sea Council Aboriginal Corporation, 14 Throssell Street, Kalgoorlie, Western Australia 6430, Australia.
16. ¹⁶Department of Archaeology, University of Western Australia, Crawley, Western Australia 6009, Australia.
17. ¹⁷Department of Anatomy, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0374, Japan.
18. ¹⁸Institut für Sprachwissenschaft, Universität Bern, 3000 Bern 9, Switzerland.
19. ¹⁹Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
20. ²⁰Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Université de Toulouse (Paul Sabatier)–CNRS UMR 5288, 31073 Toulouse Cedex 3, France.
21. ²¹Department of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands.
22. ²²Department of Anthropology, University College London, London WC1E 6BT, UK.
23. ²³Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland 4111, Australia.
24. ²⁴Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
25. ²⁵Murray Edwards College, University of Cambridge, Cambridge CB3 0DF, UK.
26. ²⁶Institute for Forensic Genetics, D-48161 Münster, Germany.
27. ²⁷Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
28. ²⁸Department of Anthropology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
29. ²⁹Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark.
30. ³⁰Estonian Academy of Sciences, 6 Kohtu Street, 10130 Tallinn, Estonia.
31. ³¹Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark.

1. †To whom correspondence should be addressed. E-mail: ewillerslev@snm.ku.dk (E.W.); wangj@genomics.org.cn (W.J.); rasmus_nielsen@berkeley.edu (R.N.)

1. ↵* These authors contributed equally to this work.

Abstract

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

• Received for publication 14 July 2011.
• Accepted for publication 13 September 2011.