A Change in Research Paradigm RE R1b?

[Humanist]

European Journal of Human Genetics 20, 313-320 (March 2012) | doi:10.1038/ejhg.2011.192
Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists
Kristian J Herrera, Robert K Lowery, Laura Hadden, Silvia Calderon,Carolina Chiou, Levon Yepiskoposyan, Maria Regueiro, Peter A Underhill and Rene J Herrera
However, we detect very restricted genetic affinities with Europe that suggest any later cultural diffusions from Armenia to Europe were not associated with substantial amounts of paternal gene flow, despite the presence of closely related Indo-European languages in both Armenia and Southeast Europe.

Populations inhabiting regions in closer proximity to the European continent need to be examined as well. 

Here are two minority Levantine coast populations.   

Druze (Shlush et al.):

Druze Modal
13   24   14   11   x   x   12   12   ?   13   13   29

2 identical Druze haplotypes compared to the supposed Tut haplotype
DRZ   13   24   14   11   xx   xx   12   12   ?   13   13   30
DRZ   13   24   14   11   xx   xx   12   12   ?   13   13   30
TUT   13   24   14   11   11   14   XX   XX   10   13   13    30

Other Druze haplotypes
13   24   14   11   x   x   12   12   ?   14   13   30
13   24   14   11   x   x   12   12   ?   14   13   30
13   25   14   11   x   x   12   12   ?   14   13   30
14   24   14   10   x   x   12   12   ?   14   13   30
14   24   14   10   x   x   12   12   ?   14   13   30
14   24   14   10   x   x   12   12   ?   14   13   30
14   24   14   10   x   x   12   12   ?   14   13   30
14   24   14   13   x   x   12   12   ?   14   13   30
14   24   14   10   x   x   12   12   ?   14   13   32
12   24   14   11   x   x   12   12   ?   13   14   28
12   25   14   10   x   x   11   12   ?   13   13   29
12   24   14   11   x   x   12   12   ?   13   13   29
12   24   14   11   x   x   12   12   ?   13   13   29
12   24   14   11   x   x   12   12   ?   13   13   29
12   24   14   11   x   x   12   12   ?   13   13   29
12   24   14   11   x   x   12   12   ?   13   13   29
12   25   14   10   x   x   11   12   ?   13   13   29
12   24   14   11   x   x   12   12   ?   13   13   29
12   24   14   11   x   x   12   12   ?   13   13   29


Alawite haplotypes (Dönbak et al.)
n=12 13   24   14   11   11   15   XX   XX   XX   14   13   30
n=5   13   24   14   11   11   15   XX   XX   XX   13   13   29
n=3   12   25   14   11   11   14   XX   XX   XX   13   13   29
n=2   12   24   14   12   11   14   XX   XX   XX   14   13   30
n=2   13   24   14   11   11   15   XX   XX   XX   12   13   28
n=1   12   23   14   10   11   14   XX   XX   XX   14   13   30
n=1   12   24   14   10   10   14   XX   XX   XX   12   13   29
n=1   12   24   14   10   11   14   XX   XX   XX   13   13   29
n=1   12   24   14   11   11   14   XX   XX   XX   14   13   30
n=1   12   24   14   12   11   14   XX   XX   XX   13   13   29
n=1   12   25   14   12   11   14   XX   XX   XX   14   13   30
n=1   13   24   14   10   11   15   XX   XX   XX   14   13   30
n=1   13   24   14   11   11   15   XX   XX   XX   15   13   31
n=1   13   24   14   11   10   15   XX   XX   XX   15   13   31

The value reported for DYS439 in the Druze paper appeared unusually high.  Possibly an error in the order presented in the supplementary sheet, or a conversion is necessary.

[Maliclavelli]

On DNA-Rootsweb Steven Perkins asks:

“What is so unusual about this 25 Marker Y DNA haplotype that he has no matches in the FTDNA database?
13 25 16 10 10-16 12 10 10 14 11 31 15 9-10 11 11 24
14 19 32 12-15-15-16”
 
and Anatole Klyosov answers:

“The haplotype which you have shown is quite usual in a sense that it has
only four mutations from the (deduced) ancestral haplotype (aka base
haplotype). Mutations are random, and those DYS385a = 11 --> 10 and DYS385b
= 14 --> 16 (compared with the initial ancestral alleles) are quite trivial
statistically. Those four mutations (one more is DYS389-1 = 13 -->14) can
easily occur in the course of those 5-7 thousand years. In that sense there
is nothing unexpected in that haplotype, and that is what I meant. On the
other hand, you can call it unusual because those DYS385a,b mutations are
relatively rare, compared with other Tenths. Statistics, though, is silly,
and it does not care which allele to mutate.
It all boils down that the haplotype is quite common from the viewpoint of
mutational statistics, but it is rather uncommon compared with the typical
alleles in R1a haplotypes. From this point of view DYS388=10 is also rather
unusual allele in R1a haplogroup”.

But these are just the mutations I called for the tangent and not around the modal, which of course there are too, and not considering them falsifies all the calculations.
I’d like that Klyosov explained this Indian haplotype of R1a1a.

[Maliclavelli]

Humanist, I’ll study your data, but, as you have said, they are “minorities”, then not representative of all Middle East (the same I could say for the massive presence of mt K1a amongst Druzes) and why not to consider DYS439? Results are probably reliable and, being this a fast mutating marker, probably it has had some mutations for the tangent and not around the modal and may be the witness of a different story; above all a larger ancientness of this haplogroup and that it may have come to Middle East from elsewhere. Middle East, as I have said ad abundantiam, lacks the path of R1b1* and above all of the knots of this path: R-L150-, R-L51+ etc.

[Mark Jost]

I think by seeing where R1a1a might have been at a given time, will help us better understand what was happening with R1b.  Based on the R1a1a project site, the pre-M417 R1a looks like a post-younger dryas or neolithic expansion from SW Asia.  However, they went on to become more prolific once in Europe, unlike known neolithic groups E, F, and G.  There is also the east-west split with R1b.  All of this suggests  R1a arrived at a different time and place than the others.  I think a mesolithic movement out of central Asia from its' R1 root up to the Urals, then west to Europe might be an option that explains the differences.   The L664 branch has a NW/Baltic-Scandinavian affinity which might put the European R1a homeland near there among early forest cultures.  I noticed there is now a Russian in the project who is M417-.

The branch of R1a1a that seems to be associated with IE is Z645+, mainly in the form of Z283 and Z93.  However, I don't think they were predominant among the early PIE steppe people.  The Sredny Stog and Yamnaya physical types are different than the Corded R1a people.   They were more Cro-magnon like which suggest upper paleolithic origins unlike the more gracile Cordeds.

The Z283 branches are mostly confined to the regions east of Germany and north of the Balkans.  In other words, the old Corded-Ware territories that later gave rise to the Balts and Slavs.  The lesser amounts of R1a outside of this area can be explained by historical movements.  The regions to the south and west were probably full of R1b's and other former neolithic groups by 2500 (my Z645 interclade midpoint) and most likely by 2000 (Z283+ intraclade midpoint).   This, imo, is when the R1a-R1b east west split forms. R1b probably brought centum languages to the west, but the how, why, and what the relationship with R1a's can be debated.

EuroGenes Autosome DNA project ran by Davidski posted a blog two days ago titled "
Northwest Eurasians + Southwest Eurasians + Mesolithic survivors = modern Europeans"

Here is the his newest take on the point that "North Atlantic is essentially the remnant of the pre-Baltic Northwest Eurasians, and appears to have found refuge in far Western and Northwestern Europe, in the valleys of the Caucasus Mountains, and in South Asia. "

One of his members created a nice Heat map "shows the relative spread of three key genetic clusters, from the (Davidski - EuroGenes) K=13, in a wide range of populations from Europe, North Africa, and West, Central and South Asia"

http://bga101.blogspot.com/2012/03/northwest-eurasians-southwest-eurasians.html

Comments?

MJost

[rms2]

As already mentioned, the Northwest Eurasians can be reliably split into two clusters, marked on the map in cyan and magenta. I call the cyan cluster North Atlantic, because it peaks in the Irish and other Atlantic fringe groups, and the magenta Baltic, because it shows the highest frequencies in Lithuanians and nearby populations. The story suggested by the map is pretty awesome, with the Baltic cluster seemingly exploding from somewhere in the middle of the Northwest Eurasian range, and pushing its close relatives to the peripheries of that range. Thus, under such a dramatic model, the North Atlantic is essentially the remnant of the pre-Baltic Northwest Eurasians, and appears to have found refuge in far Western and Northwestern Europe, in the valleys of the Caucasus Mountains, and in South Asia.

I'm not sure I get this guy, since he is using autosomal dna and yet makes a reference to his "Northwest Eurasians" as belonging to y haplogroups R1a and R1b.

But it sounds as if he is cheerleading for R1a as the Indo-Europeans and R1b as "the remnant of the pre-Baltic Northwest Eurasians". Of course, that doesn't make sense, because there isn't all that much R1a in the West and loads of R1b. In fact, there is still a pretty fair amount of R1b pretty far east in Europe and into Scandinavia.

So maybe he means something else.

But if his "Baltic cluster" is supposed to be represented by R1a, then there was hardly an explosion, at least where Western Europe is concerned (more like a small, rather inconsequential fart, but that's about it).

[Mark Jost]

A fart maybe but another reader ran Dieneke's' admixture formula on the EuroGenes data and posted this (and read some of Davidski's latestest comments after this one):

Eduardo PintoMar 8, 2012 04:33 AM
I've used this equation to estimate the time of divergence of the K=13 components and it actually makes your point stronger.

http://dienekes.blogspot.com/2012/02/timeline-of-human-prehistory.html


It seems that at one point the West Central Asian, the North Atlantic and Caucasus comprised one of the major neolithic groups, most definitely your Northwest Eurasian group. And then around 11 ky BP it started spliting into those three groups, first the WCA, then the caucasus, followed lastly by the NA.
As for the Baltic it only came to be around 4 ky BP.

SWA vs. WCA
23*log(1-0.060)/log(1-1/(2*8465))=24.09ky

M vs. WCA
23*log(1-0.059)/log(1-1/(2*7276))=20.35Ky

SWA vs. CA
23*log(1-0.047)/log(1-1/(2*7851))=17.39ky

SWA vs. M
23*log(1-0.046)/log(1-1/(2*7813))=16.92ky

M vs. CA
23*log(1-0.043)/log(1-1/(2*6662))=13.47ky

M vs. NA
23*log(1-0.047)/log(1-1/(2*6002))=13.23ky

M vs. BA
23*log(1-0.040)/log(1-1/(2*6829))=12.84ky

WCA vs. CA
23*log(1-0.035)/log(1-1/(2*7313))=11.98ky

BA vs. CA
23*log(1-0.036)/log(1-1/(2*6867))=11.58ky

NA vs. CA
23*log(1-0.036)/log(1-1/(2*6039))=10.18ky

NA vs. BA
23*log(1-0.014)/log(1-1/(2*6207))=4.02ky