September 22, 2011

First aboriginal Australian genome published

Aboriginal Australians (AA) have been somewhat of a black hole in population genetics research. So, it's great news that after today's Reich et al. paper on Denisova admixture, there is another new paper that presents the first full genome sequence of an aboriginal Australian.

I don't know why it has been so difficult to study AAs so far; my guess is that some type of politics has prevented it, similar to those that have hindered population genetics research in some Amerindian groups. Unfortunately, the current publication does not seem to represent the beginning of a new era in AA research, as the genome does not belong to a living AA, but rather to a 100-year old hair sample.

On one hand this makes sense: old DNA is preferable to fresh one when one deals with populations that have undergone admixture in recent times. I don't know how many AA have European admixture, but my guess is that, surely, pure-blooded living AA still exist, so, one could in principle obtain DNA from them.

Nonetheless, we should be thankful for the new data which provide a much needed new data point of mankind's diversity. Also, given recent developments, even a single genome may prove to be invaluable.

The supplementary material (pdf) has, as usual, most of the interesting details of the paper.

Coverage in the Australian.

(to be continued)

UPDATE: I will take the age estimates in the paper with a grain of salt, because they are not independent estimates, but rely on a calibration of the European-East Asian split (fixed at 2,000 generations), and the Out-of-Africa event (fixed at 3,500 generations). Hence, from the supplement:
Based on how our model was set up, the European-Aboriginal Australian and African-Aboriginal Australian split times that we presented above could be no less than 2,000 and 3,500 generations ago, respectively.
So, at most the data shows that Europeans are closer related to East Asians than either of them is to Australian aboriginals. The actual ages in years are conditioned on the timing of the aforementioned events, which, in turn, have been estimated in the past using various assumptions (see my recent post on Gronau et al. 2011).

Science DOI: 10.1126/science.1211177

An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia

Morten Rasmussen et al.

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.

Link

8 comments:

Onur said...

I will take the age estimates in the paper with a grain of salt, because they are not independent estimates, but rely on a calibration of the European-East Asian split (fixed at 2,000 generations), and the Out-of-Africa event (fixed at 3,500 generations).

Does the invalidity of the age estimates invalidate or weaken the conclusions that at least two dispersal waves occurred into eastern Eurasia and that the ancestors of Mongoloids and Australoids admixed after the divergence of the ancestors of Caucasoids and Mongoloids and prior to the divergence between Asian Mongoloids and American Mongoloids (=Native Americans)? I guess not. Of course, those who have access to the full paper can know better.

Xaver said...

If the conclusion is right and there were two dispersal waves which were 25-50 kya apart, it raises one interesting question:
How did the Neanderthal genes enter both waves in almost the same amount?

DocG said...

I'm puzzled. First, as I understand it, they weren't able to extract DNA from the roots of the hairs, but only from the strands themselves. Since such strands contain only mtDNA, how were they able to derive a complete genome?

Second, as this was reported in the NY Times, their evidence is considered especially important since contemporary Australian aborigines have refused to cooperate with pop. geneticists. But this is untrue. Earlier studies of aboriginal mtDNA and Y DNA do exist, and since they represent a much larger sample than the one reported here (only a single person, whose DNA is hardly "ancient"), I fail to see the significance of this study, or why it should take precedence over far more representative earlier ones.

For references, see Chapter 14 of my book, Sounding the Depths: http://soundingthedepths.blogspot.com/2011/03/chapter-fourteen-mysteries-of-sahul.html, where I discuss some of the problems associated with the early history of Sahul in some detail.

terryt said...

"Does the invalidity of the age estimates invalidate or weaken the conclusions that at least two dispersal waves occurred into eastern Eurasia and that the ancestors of Mongoloids and Australoids admixed after the divergence of the ancestors of Caucasoids and Mongoloids and prior to the divergence between Asian Mongoloids and American Mongoloids (=Native Americans)? I guess not".

I, for one, would think not.

"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".

I would guess that the first dispersal is of Y-hap C and mtDNA N. The second is of Y-hap K and mtDNA M.

"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".

That makes sense because Native Americans contain haplogroups from both branches of both haplogroups.

M said...

With the background of poor treatment towards Aboriginals I'm not surprised there haven't been other studies done. That said, there does seem to be interesting information about visual cortex in Aborigenes:

"For example, Professor Clive Harper, a neuropathologist at the of the University of Sydney Hospital, claims to have found that among Aborigines, the area of the brain responsible for visual processing is 25 percent larger than average. Harper’s studies, the last of which was published in the Journal of Hirnforschung (Brain Research), indicates that Aboriginal children have near photographic memories, an evolutionary gift from their ancestors, who "had to master the vast landscape to survive."

http://www.jonentine.com/reviews/straw_man_of_race.htm

bmdriver said...

does that mean the second dispersal was from south asia?

DocG said...

"With the background of poor treatment towards Aboriginals I'm not surprised there haven't been other studies done."

But there HAVE been other studies: "Peopling of the Sahul: mtDNA Variation in Aboriginal Australian and Papua New Guinean Populations," American Journal of Human Genetics, 65, 1999;
Max Ingman and Ulf Gyllensten, "Mitochondrial Genome Variation and Evolutionary History of Australian and New Guinean Aborigines," Genome Res. 2003 13: 1600-1606; "Gene Flow from the Indian Subcontinent to Australia: Evidence from the Y Chromosome," by Alan Redd et al., Curr Biol. 2002 Apr 16;12(8):673-7.

German Dziebel said...

@Xaver

"If the conclusion is right and there were two dispersal waves which were 25-50 kya apart, it raises one interesting question:
How did the Neanderthal genes enter both waves in almost the same amount?"

Especially so, since American Indians often show elevated frequencies of those "Neanderthal" alleles compared to Old World populations, as in blood groups (type O), in HLA (A*002, C*07:02) and in X chromosome (B006). I think this question hits out of Africa right on the button. All the matches between Eurasian hominids and non-African humans must be due to common descent, not admixture, and hence it's Africa that was colonized by modern humans, not the regions outside of Africa were colonized from Africa.