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Monday, May 3, 2010

Finally some good research on R1b1b2!

This is a most important paper for those interested in Y-DNA R1b and specifically European and West Asian R1b1b2:

Laura Morelli et al., A Comparison of Y-Chromosome Variation in Sardinia and Anatolia Is More Consistent with Cultural Rather than Demic Diffusion of Agriculture. PLoS ONE 2010. Open access.

An excellent critique of Balaresque 2009, totally in the line I was favoring myself.

Most important is maybe fig. 2A, where the use of (novel?) STR marker DYSA7.2, in addition to the usual ones, unveils a clear structure within R1b1b2-M269. I have annotated it for easier visualization:


Click to enlarge


Duality


The already quite obvious Europe-Anatolia (A-B) duality of this haplogroup becomes terribly apparent: two different star-like structures connected by a less clear group (C) centered at the Balcans.


I imagine that sooner than later, someone will come up with a defining SNP for the more than likely Anatolian haplogroup. If I'm correct, with the current nomenclature it should be something like R1b1b2a2. However the root of the whole R1b1b2 haplogroup might also be in that cluster (or is it in C?).

It is surely important to notice that this presumptive R1b1b2a2 haplogroup (at least a clear haplotype star-like structure) also experienced quite apparently a rapid expansion of its own, mostly in West Asia and the Balcans, which is in turn surely related to the expansion of R1b as such through the Mediterranean, Africa (R1b1a) and Central Asia (R1b1b1).


R1b expansion pattern

We may well say that R1b expanded quite dynamically but not with total simple continuity but in colonization "bouts". The first bout is probably best represented by R1b1a scatter in the NE Mediterranean arch (two subclades) and around Central Africa (maybe with a Sudan origin, two subclades too). The second bout is surely a minor one towards Central Asia represented by R1b1b1 (typical of Uyghurs, an odd Chalcolithic founder effect in a previously desert area). The third bout is the spread of R1b1b2-M269 in West Asia and Europe, which represents the bulk of the R1b worldwide in raw numbers.

This third bout is actually two, as is evident in this paper (but was also evident before for those who can "read between lines" at least) but they may have happened in parallel (in which case my annotation above is more strictly correct) or they may have happened sequentially (in which case, lineage B would be R1b1b2a*, except for one of the branches that is actually the root: R1b1b2*).

A quite plausible reconstruction of the spread of R1b (c. 50-30 Ka ago?)
Click to expand


Synthesis

Whatever the case, two things are clear:

1. There is a neat distinction between R1b1b2(xR1b1b2a1) and R1b1b2a1.

2. R1b1b2a1 had its own distinct and fundamentally unique expansion in West Europe, sensu lato.

Also notice that, as happens in previous versions, there are many branches hanging from the R1b1b2a1 central node (modal haplotype also), which appears to contradict the known subhaplogroup structure that only recognizes two branches and which seems to be quite imperfect as of now.


Tempo

As you know I am not any fan of the molecular clock but it's worth mentioning the estimates of this paper for they totally contradict the Neolithic model: the pool of Sardinian and Anatolian R1b1b2 gets an estimate age of 32.6 Ka, the Sardinian one has an age of 27.0 Ka and the Anatolian of 19.6. But the regional ages may be misleading because they include members of both clades, however the overall age should be roughly correct within the molecular clock paradigm.

This would fit with a Gravettian expansion but could also fit with an even older Aurignacian one. It makes some good sense, specially as we are talking of a single expansion that replaced all what was there before, which could only happen at very low population densities, and also because it is a single expansion and not two. It also makes good sense with the likely pattern of expansion of its likely mtDNA companion haplogroup H (also V probably).

As the authors admit, the Magdalenian late glacial recolonization (and noticeable demic expansion) is also within the scope. However I find difficult to explain R1b1b2a1 in Italy within this context, as Italy remained Epigravettian until the very Neolithic. It is also much easier to replace all when there's almost nothing to replace, as was surely the case after the Campanian Ignimbrite supervolcano eruption of c. 40 Ka ago.


Other lineages

The paper is also of interest for other haplogroups such as E, G and J. However I fail to see anything clear surely because of the excessive emphasis in exploring Sardinian-Anatolian connections without a wider scope.


See also: for a completely opposite editorial opinion and likely heated discussion at Dienekes'.


4 comments:

Natsuya said...

Hey Maju, you may be interested in this upcoming paper:

Increased Resolution Within Y-Chromosome Haplogroup R1b M269
Sheds Light On The Neolithic Transition In Europe

George Busby et al.

Early studies on classical polymorphisms have largely been vindicated by the growing tome of information on the genetic structure of European populations, with mtDNA, Y-Chromosome and autosomal markers all combining to give a fundamental pattern of migration from the East. The processes behind this pattern are however, less clear, particularly with regard to uniparental markers. Much debate still rages about how best to use Y and mtDNA to date particular historical movements, or indeed if it is appropriate at all. For example, whilst some progress has been made recently in calibrating the mtDNA clock, the selection of a mutation rate with which to date the Y-Chromosome is contentious, as the two most favoured values can give dates that differ by a factor of three.

In order to address this we have investigated the sub-lineages of the common European haplogroup R1b-M269. This haplogroup has been shown to be clinal in Europe, and more recently has been posited to be the result of the Neolithic expansion from the Near East. Here, we use newly characterised SNPs downstream of M269 to produce a refined picture of the haplogroup in Europe, and further show that the diversity of this lineage cannot be entirely attributed to Neolithic migration out of Anatolia. We use simple coalescent simulations to estimate an absolute lower bound for the age of the sub-haplogoups. Rather than originating with the farmers from the East, we suggest that the sub-structure of R1b-M269 visible in Europe today, and thus the great majority of European paternal ancestry, is the result of the interaction between the Neolithic wave of expansion and populations of early Europeans already present in the path of the wave.

http://www.yhrd.org/files/7th_y_user_workshop_programme_abstracts.pdf

Maju said...

Hi, Natsuya. Thanks for the notice. Sadly it doesn't seem that the paper is published yet.

I found that Dienekes had already commented on it a couple of weeks ago.

McG said...

Maju: I've talked to you before. My Ysearch is z5hg3. I am SNP tested for R-L21* and am negative for any other extended deep ancestry test provided by FtDNA.

I know that VV has said this article is "fatally flawed", which means he doesn't agree with it. Before I was SNP tested I was told I was Eastern European/Asian, mostly because of my 12 @ 393 and 13 @ 388, 23 at 390. I also have a 14 at 557 which is almost unique to me. I have run into a brick wall using pedigreed mutation rates, I think they compress time. I know the MC is not your cup of tea, but Zhivotovsky makes more sense to me for longer tMRCA estimates. My heritage is scottish and I have a direct line back to scotland in about 1650. How would you approach evaluating the haplotype I have?

Maju said...

"I am SNP tested for R-L21* and am negative for any other extended deep ancestry test provided by FtDNA".

L21 or S21?

Because L21 is a marker for R1b1b2a1a2f, which, following Wikipedia, "is common in Britain, Ireland and possibly Northern France".

S21 instead defines R1b1b2a1a1, a couple of steps upstream.

Anyhow, I made a quick check of haplotypes listed in the Balaresque paper (the data is good, not so much the analysis) and I did a find possible match in Turkey and quasi-matches in the Netherlands (1), England (1), Germany(1), Turkey (quite common)... 1 step apart in DYS 388 (she does not use DYS 557) from what you mention. There is also a quasi-match which changes in the DYS 393 (England).

But I am just comparing three STR markers. :(

I would trust the SNP test and, if in great doubt, do it again. What SNP markers say is the truth within the phylogeny, as far as we can tell, STR haplotypes are only proxies and occasionally at least may be misleading.

"I have run into a brick wall using pedigreed mutation rates, I think they compress time".

They do, of course. That's their virtue or vice, depending on your point of view.