February 03, 2012

Y-chromosome admixture in self-identified Australian Aboriginals

Forensic Sci Int Genet. 2012 Jan 30. [Epub ahead of print]

An investigation of admixture in an Australian Aboriginal Y-chromosome STR database.

Taylor D, Nagle N, Ballantyne KN, van Oorschot RA, Wilcox S, Henry J, Turakulov R, Mitchell RJ.

Abstract

Y-chromosome specific STR profiling is increasingly used in forensic casework. However, the strong geographic clustering of Y haplogroups can lead to large differences in Y-STR haplotype frequencies between different ethnicities, which may have an impact on database composition in admixed populations. Aboriginal people have inhabited Australia for over 40,000 years and until ∼300 years ago they lived in almost complete isolation. Since the late 18th century Australia has experienced massive immigration, mainly from Europe, although in recent times from more widespread origins. This colonisation resulted in highly asymmetrical admixture between the immigrants and the indigenes. A State jurisdiction within Australia has created an Aboriginal Y-STR database in which assignment of ethnicity was by self-declaration. This criterion means that some males who identify culturally as members of a particular ethnic group may have a Y haplogroup characteristic of another ethnic group, as a result of admixture in their paternal line. As this may be frequent in Australia, an examination of the extent of genetic admixture within the database was performed. A Y haplogroup predictor program was first used to identify Y haplotypes that could be assigned to a European haplogroup. Of the 757 males (589 unique haplotypes), 445 (58.8%) were identified as European (354 haplotypes). The 312 non-assigned males (235 haplotypes) were then typed, in a hierarchical fashion, with a Y-SNP panel that detected the major Y haplogroups, C-S, as well as the Aboriginal subgroup of C, C4. Among these 96 males were found to have non-Aboriginal haplogroups. In total, ∼70% of Y chromosomes in the Aboriginal database could be classed as non-indigenous, with only 169 (129 unique haplotypes) or 22% of the total being associated with haplogroups denoting Aboriginal ancestry, C4 and K* or more correctly K(xL,M,N,O,P,Q,R,S). The relative frequencies of these indigenous haplogroups in South Australia (S.A.) were significantly different to those seen in samples from the Northern Territory and Western Australia. In S.A., K* (∼60%) has a much higher frequency than C4 (∼40%), and the subgroup of C4, C4(DYS390.1del), comprised only 17%. Clearly admixture in the paternal line is at high levels among males who identify themselves as Australian Aboriginals and this knowledge may have implications for the compilation and use of Y-STR databases in frequency estimates.

Link

9 comments:

Easy772 said...

I think Y-DNA C4 would be the truly indigenous marker. From what I gathered, Y-DNA K carriers are from the 2nd wave out of Africa, probably settled in Australia and intermixed with the C carriers. This also explains why K carriers and their descendants usually don't have the Denisovan admixture. Denisovan admixture from what I can tell is highly correlated with presence of Y-DNA C in Polynesia and Australia.

Andrew Oh-Willeke said...

Why do a study like this that gets published in 2012 without simultaneously doing autosomal and mtDNA? Once you've got that many people agreeing to be subject for a very special and small population, it can't be materially more expensive to do all three at once and the statistical power you gain from being able to corrolate all three sets of data with each other would make the study more valuable than three separate studies (Y-DNA, mtDNA and autosomal DNA) with the same number of subjects each.

Annie Mouse said...

In Australia it looks like the gracile Homo sapiens came first followed by the robusts (from the skulls).

And South Australia is a lot deeper into the continent than the Northern Territory which is on the doorstep to the continent so more likely to feel the impact of later immigration. WA is sort of in between. But I suppose the location of these haplogroups could be more due to the Y chromosome swamping effects we see in Europe than original arrival.

Where do you see a correlation of archaics with C rather than K? So far it has looked like to me Homo sapiens arrived in Australia and the archaic admixed (robust) folk arrived or manifested afterwards. But we are talking about just a handful of skulls. I had been leaning towards thinking that the admixture with the Denisovans took place on the mainland en route to Australia and Papua on a second wave.

bloggybee said...

Matt Ridley on Early Humans Leaving Africa

http://online.wsj.com/article/SB10001424052970204740904577192960294508268.html?mod=lifestyle_newsreel

terryt said...

"This also explains why K carriers and their descendants usually don't have the Denisovan admixture. Denisovan admixture from what I can tell is highly correlated with presence of Y-DNA C in Polynesia and Australia".

Actually the latest paper on the subject has the 'Denisova' genes concentrated in New Guinea/Melanesia, and only reaching as far into the Pacific as does Y-DNA K. That tends to indicate that the gene is more associated with K than with C2/C4.

"So far it has looked like to me Homo sapiens arrived in Australia and the archaic admixed (robust) folk arrived or manifested afterwards".

There have been some claims that the apparently later 'robusts' are just variations within a single population in Australia. But I tend to agree with you. They are a later arrival. Presumably from a population bypassed by the earlier Australians.

"I had been leaning towards thinking that the admixture with the Denisovans took place on the mainland en route to Australia and Papua on a second wave".

That is my best guess too.

"I suppose the location of these haplogroups could be more due to the Y chromosome swamping effects we see in Europe than original arrival".

That could be the explanation for how K is commonest in South Australia.

Easy772 said...

Possibly, but there is still a strong Y-DNA C presence in Melanesia and Papua New Guinea. Why do populations with presence of Y-DNA K for instance from ISEA not have Denisovan admixture while Eastern Indonesians with presences of both certain subclades of "C" and Y-DNA "K" do?

Looking at the map from Dienekes earlier post regarding Denisovan admixture still leaves me to believe that the parallel between populations with Denisovan admixture is the presence of certain subclades of Y-DNA C.

http://en.wikipedia.org/wiki/Y-DNA_haplogroups_in_Oceanian_populations

http://2.bp.blogspot.com/-zrkpOtEdlVU/TntvaCK8OtI/AAAAAAAAEJc/RlAacxjxKWo/s1600/denisova3.png

I could very well be wrong, but I'm here to learn. :)

terryt said...

"Possibly, but there is still a strong Y-DNA C presence in Melanesia and Papua New Guinea".

But C reaches far out into Eastern Polynesia where the 'Denisova' genes are absent. K and M are later arrivals in the wider Pacific and the Denisova mix is confined to regions thay made it to.

"Why do populations with presence of Y-DNA K for instance from ISEA not have Denisovan admixture"

They do, don't they? But K is a very minor component of Indonesian haplogroups so the DFenisova is much reduced.

"Eastern Indonesians with presences of both certain subclades of 'C' and Y-DNA 'K' do?"

The O 'Mongoloid' haplogroups are a smaller proportion overall in Eastern Indonesia. The Denisova has been less diluted there.

"Looking at the map from Dienekes earlier post regarding Denisovan admixture still leaves me to believe that the parallel between populations with Denisovan admixture is the presence of certain subclades of Y-DNA C".

Perhaps by admixture with K/M haplogroups. Denisova is certainly not associated with C2 in Eastern Polynesia.

Easy772 said...

Certain populations in ISEA and mainland Asia have significant presences of K, yet have slim to nil Denisovan admixture. Asian populations such as Tibetans, Burmese, various Chinese minorities, non-negrito Filipinos and Western Indonesians have significant frequency of K yet have near 0% Denisovan admixture.(To my knowledge) Actually East Indonesia only showed 10.5% K frequency, Borneo showed 10.0%.


"Stoneking says that this pattern hints at at least two waves of human migration into Asia: an early trek that included the ancestors of contemporary Aboriginal Australians, New Guineans and some other Oceanians, followed by a second wave that gave rise to the present residents of mainland Asia. Some members of the first wave (though not all of them) interbred with Denisovans. However, the Denisovans may have vanished by the time the second Asian migrants arrived. This also suggests that the Denisovan's range, so far linked only to a cave in southern Siberia, once extended to Southeast Asia and perhaps Oceania.

Given that the Denisova hominin is about 41ka old, that would imply that East Asian ancestors moved through their territory after that date, when the Denisovans were already extinct, partially absorbed by first-wave "Australasian-like" people."

The first wave C and D. The second wave K and descendants.

I wouldn't write off the theory that certain K carriers didn't mate with the Denisovans and that's why there's little to no trace of their genes in present day Southeast Asian populations with significant presence of K.

I've heard it said that Denisovans are merely a mix of Neanderthal and Homo Erectus and that further confuses things. In any case it's pretty complicated.

terryt said...

"Certain populations in ISEA and mainland Asia have significant presences of K, yet have slim to nil Denisovan admixture".

True. But they lie mainly to the north of Java which is the most liklely region for humans to have mixed with SE Asian H. erectus. And K does not comprise a particularly high proportion of Y-DNA in most of SE Asia. Besides which K1 is found in small numbers in India, as is the Denisova admixture.

"Asian populations such as Tibetans, Burmese, various Chinese minorities, non-negrito Filipinos and Western Indonesians have significant frequency of K"

Are you sure? They have MNOPS haplogroups but not much 'K' as far as I know.

"Given that the Denisova hominin is about 41ka old, that would imply that East Asian ancestors moved through their territory after that date"

No. The 'Denisova hominin' is that age but the paper says:

"This also suggests that the Denisovan's range, so far linked only to a cave in southern Siberia, once extended to Southeast Asia and perhaps Oceania".

The Denisova admixture in Papuans appears to be from SE Asia, not the Altai. And most likely from SE Asian H. erectus, which had been isolated in the region for one and a half million years. The admixture could have happened at any time since then. Most likely, of course, when modern humans first entered the region.

"I've heard it said that Denisovans are merely a mix of Neanderthal and Homo Erectus and that further confuses things. In any case it's pretty complicated".

I'll admit it's far from simple. For example mt-DNA shows Denisovans split from the line that led to modern humans before the Neandwerthals did so. The paper even suggests the coriginal carriers of the denisovan genes split from the others as much as 3 million years ago.