The genetic history of Aboriginal Australians – University of Copenhagen

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21 September 2016

The genetic history of Aboriginal Australians

ORIGINS

It remains debated how Australia was initially populated and how changes in language and culture in the continent happened. Australia contains some of the oldest archaeological evidence of modern humans outside Africa dating back to about 50,000 years. Still about 90% of Aboriginal Australians speak languages belonging to a single linguistic family that dates back no more than a few thousand years. The first population genomic studies on Aboriginal Australians published in this week’s Nature provide some of the answers.

Early peopling of Australia and the continent’s subsequent population history has remained a matter of scientific debate for decades. To address these questions an international team of scientists have, in collaboration with Aboriginal Australian co-authors, sequenced 83 modern Aboriginal Australian and 25 modern Papuan genomes – the Australians’ northern neighbours – covering most of the Australian continent and the New Guinea Highlands.

The new data reveals a number of interesting findings. On the grand scale and going as far back in time as to shortly after modern humans migrated out of Africa the DNA-sequences show that together the Aboriginal Australians and Papuans split from Europeans and Asians about 58,000 years ago.

Approximately 8,000 years later, at the time when the first people arrived in Sahul (the New Guinean/Australian continent), the size of the population decreased. Aboriginal Australians and Papuans later diverged c. 37,000 years ago, long before the physical separation of Australia and New Guinea, some 10,000 years ago. These people, coming from mainland Asia and travelling into Australia, were the ancestors of most if not all modern day Australians. Subsequently, the ancestral Australian population differentiated c. 31,000 years ago into subgroups with the formation of the central desert likely acting as a barrier to migrations.

First author on the paper Assistant Professor Anna-Sapfo Malaspinas from the Centre for GeoGenetics at the Natural History Museum at the University of Copenhagen, the SIB Swiss Institute of Bioinformatics and the University of Bern says about the findings:

“The genetic diversity among Aboriginal Australians is amazing. Perhaps because the continent has been inhabited for such a long time we find that groups from southwestern desert Australia are more genetically different from groups of northeastern Australia than are for example Native Americans and Siberians, and this is within a single continent”.

Biological anthropologist Dr Michael Westaway from Griffith University obtains a saliva sample from Thanakwith Elder Mr Thomas Wales, Cape York, Australia. (Photo credit: Tom Cebula, Wall to Wall Media).

Biological anthropologist Dr Michael Westaway from Griffith University obtains a saliva sample from Thanakwith Elder Mr Thomas Wales, Cape York, Australia. (Photo credit: Tom Cebula, Wall to Wall Media).

Some 90% of present-day Australian Aboriginals belong to the Pama-Nyungan linguistic family. This family originated only around 6,000 years ago, but according to the new study the people who speak the Pama-Nyungan languages today started to become genetically differentiated in Australia as early as 31,000 years ago. How this fits together has puzzled scientists for decades. Lundbeck Foundation Professor Eske Willerslev from the Copenhagen-based Centre for GeoGenetics, Cambridge University and the Sanger Welcome Institute is senior author on the paper and initiated and led the study. He explains:

“Initially this difference in ages between the genetic results and the linguistic understanding was puzzling. We first thought that the languages had to be much older than previously hypothesized. But then we found evidence for a population increase and expansion from north eastern Australia to the rest of the continent around 10,000 years ago. Likely, this population increase is what brought linguistic and cultural changes with it”.

The results also show that all Pama-Nyungan speakers´ sequences derive from the same founding population in Australia that diversified from Papuans c. 37,000 years ago despite the landmasses being physically connected until just 10,000 years ago. The Aboriginal Australians appear to have been isolated from other groups until just a few thousand years ago when first Asians and later Europeans made contact. The only exception to this is northeastern Australia where there has been continuous gene flow between Papuans and Australians. David Lambert who initiated and led the study with Eske Willerslev explains:

“It’s surprising that the genetic structure in Australia and New Guinea dates back as far as 37,000 years and that contact seems to have been established to most of the continent only recently. It provides Australia with a truly unique history not seen anywhere else in the World. What will be important in the future is including samples from non-Pama-Nyungan speakers to reveal if they share the same history with the populations of this study”.

It has been heavily debated whether anatomically modern humans left the African continent in one or several waves. The authors found that Australians are mostly the result of a single wave out of Africa, in line with a study appearing in the same issue of Nature and led by Harvard Professor David Reich. This does not exclude more complex scenarios where for example earlier waves of anatomically modern humans would have contributed very little to the modern Australian and Papuan' genomic landscape. This latter scenario is put forward by a paper also co-authored by Professor Eske Willerslev in the same issue of Nature and led by Prof. Mait Metspalu from the Estonian Biocentre in Tartu.

Preliminary discussions between Aboriginal elders and scientists about the project. (Photo: Preben Hjort).

Preliminary discussions between Aboriginal elders and scientists about the project. (Photo credit: Preben Hjort, Magus Film).

Professor Laurent Excoffier of the University of Bern and SIB Swiss Institute of Bioinformatics who led several key analyses in the Australian paper explains:

“Discussions have been intense as to what extent Aboriginal Australians represent a separate Out-of-Africa exit to those of Asians and Europeans. We find that, once we take into account admixture with archaic humans, the vast majority of the Aboriginal Australian genetic makeup comes from the same African exit as other non-Africans”.

Genetics among Aboriginal Australian peoples is a sensitive issue. The scientists have worked with the local Aboriginal Australian organisations as well as with elders and the ethical board of Griffith University. Many groups were interested in participating in the study while a few refused. Dr. Craig Muller from the Centre for GeoGenetics who did much of the sampling explains:

“During the course of this project we have developed close relationships with many individuals. We have collaborated closely with Aboriginal elders in each language group who provided important cultural information and guided us to the appropriate people to participate. We were pleased that a number of these elders agreed to be co-authors of the study. I think this study sets standards marking the start of a new era where scientists and the traditional owners of the land work closely together to the benefit of both”.

Mr. Aubrey Lynch, elder from the Wongatha Aboriginal language group, who participated in the study. (Photo credit: Preben Hjort, Mayday Film).

Mr. Aubrey Lynch, elder from the Wongatha Aboriginal language group, who participated in the study. (Photo credit: Preben Hjort, Magus Film).

Mr Aubrey Lynch, a senior Wongatha Traditional Owner and co-author of this study, adds,

“The result from this study confirms our beliefs that we have ancient connections to our lands and have been here far longer than anyone else. It also shows something of the depth and extent of our kinship connections across our land.”

The paper 'A Genomic History of Aboriginal Australia' is published online in the journal Nature on 21. September 2016.

Contact

Lundbeck Foundation Professor Eske Willerslev
Centre for GeoGenetics
Natural History Museum of Denmark
Mail. ewillerslev@snm.ku.dk
Tel. +45 2875 1309
University of Cambridge 
Department of Zoology
Downing St.
Cambridge CB2 3EJ (UK)
Phone: +45 28751309 
Email: ew482@cam.ac.uk

Assistant Professor Anna-Sapfo Malaspinas
Centre for GeoGenetics, Natural History Museum of Denmark,
University of Copenhagen, Denmark
Institute for Ecology and Evolution and SIB Swiss Institute of Bioinformatics, University of Bern, Switzerland
Mail. anna-sapfo.malaspinas@iee.unibe.ch
Tel. +30 698 290 7492

Professor Laurent Excoffier
Institute of Ecology and Evolution, University of Bern, Switzerland
SIB Swiss Institute of Bioinformatics
Mail. Laurent.excoffier@iee.unibe.ch
Tel. +41 31 631 30 31 or +41 76 389 52 70

Professor David Lambert FRSNZ FQA
Professor of Evolutionary Biology
Environmental Futures Research Institute
Griffith Sciences
Griffith University
Australia
Tel. +61 7 373 55298
Mail: d.lambert@griffith.edu.au

Dr. Craig Muller
Centre for GeoGenetics
Natural History Museum of Denmark
Mail: craig.muller@iinet.net.au
Tel. +61 0420 304 001

Mr. Aubrey Lynch
Elder, Wongatha Aboriginal language group
Tel. +61 0428 919 124

Communications Officer Uffe Wilken
Centre for GeoGenetics
Natural History Museum of Denmark,
University of Copenhagen, Denmark
Mail: ugwilken@snm.ku.dk
Tel. +45 3177 2016; +45 4018 5992

Communications Officer Martin Bertelsen
Natural History Museum of Denmark,
University of Copenhagen, Denmark
1350 København K
Mail: mlbertelsen@snm.ku.dk
Tel. +45 24 48 21 47

 

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