November 08, 2012

Deep structure in Y-chromosome phylogeny (Scozzari et al. 2012)

The following two figures summarize the new phylogenetic information:



The discovery of new haplogroup C7 in Italian is potentially important, since it may mean that haplogroup C --for which region-specific clades covering East Asia (with an American twig), South Asia, Australasia are known-- may have also been present natively in Europe. It will certainly be interesting to resolve occasional C chromosomes that have been occasionally found in West Eurasia at a finer level, and do some whole-Y sequencing on the different C clades to figure out exactly how they are phylogenetically related.

It is also interesting to note that the geographical origin of the human Y-chromosome phylogeny (NW Africa) is discordant with that of mtDNA (apparently in the Khoe-San of South Africa). This underscores the futility of trying to determine "where" modern humans originated in a geographically circumscribed area.

PLoS ONE 7(11): e49170. doi:10.1371/journal.pone.0049170

Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree

Rosaria Scozzari et al.

One hundred and forty-six previously detected mutations were more precisely positioned in the human Y chromosome phylogeny by the analysis of 51 representative Y chromosome haplogroups and the use of 59 mutations from literature. Twenty-two new mutations were also described and incorporated in the revised phylogeny. This analysis made it possible to identify new haplogroups and to resolve a deep trifurcation within haplogroup B2. Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.

Link

12 comments:

andrew said...

NW quadrant is surprising. I would have expected NE or East Central or even Southern Africa before NW quadrant at the most basal level.

eurologist said...

Yeah, C desperately needs some high-resolution work - so do F*GH and MS.

Also, A1b and A1a should really receive their own letter (e.g., "Z" and "y").

Ponto said...

In the phylogenetic tree Haplogroup K is unlabelled but descendent haplogroup R, Q, M and so on are labelled. I find that rather odd considering haplogroup K still exists.

mooreisbetter said...

Can you post more on this new branch of C in Italy? I would speculate that it is a legacy of Hunnic or Avar invasions. Wouldn't that be most likely? Haven't we already shown that the Asian steppe nomadic invaders were Hap C? Italy was invaded by Huns several times, and Huns also served in late Roman armies.

Ezr said...

"Asian steppe nomadic invaders were Hap C"

No. Ancient DNA from the Xiongnu and other nomads from the area showed they were almost exclusively "Q". "C" expanding west is probably from much later, at the time of the Mongol expansion.

Also, I think the branching of C7 makes an eastern Asian origin less likely.

Onur said...

No. Ancient DNA from the Xiongnu and other nomads from the area showed they were almost exclusively "Q". "C" expanding west is probably from much later, at the time of the Mongol expansion.

That is not true. We do not have enough ancient DNA samples from the Xiongnu and the other nomads from the area whose Y-chromosome haplogroup we know, but despite that we have some ancient DNA samples from the Xiongnu and the other nomads from the area whose Y-chromosome haplogroup we know to be haplogroup C (those whose sub-haplogroup we know belong to the C3 sub-haplogroup). In fact, from the extant evidence it seems the Xiongnu and the other nomads from the area possessed more Y-chromosome haplogroup C than Q. Even Andronovans possessed some Y-chromosome haplogroup C, but none of them have been shown to possess Y-chromosome haplogroup Q.

Ezr said...

@Onur
Still most samples from the area, including Xiongnu, have at least some Q, often in the majority, and crucially the Pengyang remains (which are OLDER than most "Xiongnu" samples) were exclusively Q.

Onur said...

Still most samples from the area, including Xiongnu, have at least some Q, often in the majority, and crucially the Pengyang remains (which are OLDER than most "Xiongnu" samples) were exclusively Q.

I was referring to the ancient DNA samples mainly from what is now Mongolia, eastern Kazakhstan and Inner Mongolia, which are either from the Xiongnu or from similar nomadic cultures (but I also reffered to the ancient DNA samples from Andronovans, who were living much to the west in Central Asia and Siberia). Pengyang, which is in the north-central part of the historical Han/Hui Chinese lands, is too peripheral for nomadic cultures and was home to both sedentary and nomadic cultures historically.

terryt said...

" I would speculate that it is a legacy of Hunnic or Avar invasions. Wouldn't that be most likely? Haven't we already shown that the Asian steppe nomadic invaders were Hap C?"

East Asian C is virtually all C3 although I understand that C*(xC3) has been found there. C7 is a totally different haplogroup so cannot have been part of the invasions you suggest. A remote possibility is that it came in as C* and coalesced after that in Italy.

"It is also interesting to note that the geographical origin of the human Y-chromosome phylogeny (NW Africa) is discordant with that of mtDNA (apparently in the Khoe-San of South Africa). This underscores the futility of trying to determine 'where' modern humans originated in a geographically circumscribed area".

As you have been suggesting for some time, a 'single' place of origin is so unlikely to be the case that we may as well rule it out completely.

NW quadrant is surprising. I would have expected NE or East Central or even Southern Africa before NW quadrant at the most basal level".

For mt-DNA 'NE or East Central or even Southern Africa' is extremely likely. However there is no reason at all why both mt-DNA and Y-DNA should have arisen in the same region as each other, or even at the same time.

eurologist said...

"NW quadrant is surprising. I would have expected NE or East Central or even Southern Africa before NW quadrant at the most basal level."

Andrew,

That's only surprising if you insist that the most basal lineages are associated with AMHs.

Onur said...

I was referring to the ancient DNA samples mainly from what is now Mongolia, eastern Kazakhstan and Inner Mongolia, which are either from the Xiongnu or from similar nomadic cultures

all of them from at least about 2000 years before present

eurologist said...

Uhm, I guess my comment above just received more relevance:

http://dienekes.blogspot.com/2012/11/a00-at-ftdna2012-history-in-making.html