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Author Topic: Let's reconsider the Cantabrian Refugium  (Read 1485 times)
Maliclavelli
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« on: December 25, 2009, 06:04:01 AM »

The paper “Remarkably little variation in proteins encoded by the Y chromosome’s single-copy genes, implying effective purifying selection” (AJHG, 2009, 85) by Rozen et al., posted by Steven Perkins on “Genealogy-dna”, and which has had the attention of Thomas Krahn, is very interesting also for us. Not only it demonstrates that our Y isn’t going to die soon, but also that perhaps we must reconsider the Cantabrian Refugium as that of R1b. Even though the authors haven’t tested all the subclades of Y, the paper demonstrates that  there is a link between R1b1b2(M269) and R1b1b2(M167), but not with R1b1b2(M222), then R-L21. Of course we need a deep test, but I think we can conclude that R-S116, from which derived R-M167, was already formed in the Cantabrian Refugium and the other subclades arose elsewhere. It would be interesting to test an R-U106 re: this coding region.      
« Last Edit: December 25, 2009, 10:48:27 AM by Maliclavelli » Logged

Maliclavelli


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Maliclavelli
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« Reply #1 on: December 25, 2009, 11:46:58 AM »

Probably there is more in these results: only R1b1b2* is from Western Europe and the ancestor of R-M167 and R-L21 ( and of all other subclades). The other R1b1b2 (KDM5D+3291 and KALP-239) are from other parts of the world and have nothing to do with this Western European haplogroup.
We don’t know where the authors have kept these donors, but certainly from different regions of the world, and R1b1b2* is the Western European one. The other ones aren’t of any subclade of Karafet 2008, otherwise the authors would have said it.
« Last Edit: December 25, 2009, 11:48:42 AM by Maliclavelli » Logged

Maliclavelli


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Maliclavelli
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« Reply #2 on: December 25, 2009, 12:44:52 PM »

Thomas Krahn has said he would have looked for the primers after these holidays, but we already know their locations:


R1b1b2- Kalp is 14508659 C to G

and

R1b1b2-KDM5D is 20329316 T to C.

Unfortunately neither deCODEme nor 23andME have tested these SNPs.
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Maliclavelli


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rms2
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« Reply #3 on: December 25, 2009, 02:45:27 PM »

Can you post a link to this paper?

My initial comment is that what you wrote doesn't seem to make sense (sorry). A link between M269 and M167 but not between M269 and M222? What does that mean?

There are lots of reasons to discard the idea of a Cantabrian Ice Age Refuge for R1b.
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Maliclavelli
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« Reply #4 on: December 25, 2009, 05:03:06 PM »

Rich, the answer to your question is very simple. These R1b1b2 are all R-M269, but only from the European one are derived all the subclades we find now in Europe, not having they the mutation the other two R1b1b2s have. We can do two hypotheses: or R1b1b2-M269 was diffused  from the Caucasus to the Pyrenees, or the Eastern R1b1b2 comes from Western Europe.  Anyway the Eastern ones aren’t the  fathers of the European subclades, not having they their mutations.
A few days ago, Damon Chitsaz from Iran, who is on the Adriano’s spreadsheet and is an R1b1b2a like me, by my invite, posted his V3 of 23andMe to Adriano. He has a back mutation that nobody of Western Europeans has.
I think that these are the decisive proofs about the origin of European R1b1b2 and subclades.

P.S. I found the link to the supplements of the paper (not the paper which isn't free) on "Genealogy-dna".
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Maliclavelli


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« Reply #5 on: December 25, 2009, 05:09:37 PM »

http://www.cell.com/AJHG/supplemental/S0002-9297%2809%2900526-6
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Maliclavelli


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rms2
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« Reply #6 on: December 25, 2009, 08:14:02 PM »

Rich, the answer to your question is very simple. These R1b1b2 are all R-M269, but only from the European one are derived all the subclades we find now in Europe, not having they the mutation the other two R1b1b2s have. We can do two hypotheses: or R1b1b2-M269 was diffused  from the Caucasus to the Pyrenees, or the Eastern R1b1b2 comes from Western Europe.  Anyway the Eastern ones aren’t the  fathers of the European subclades, not having they their mutations.
A few days ago, Damon Chitsaz from Iran, who is on the Adriano’s spreadsheet and is an R1b1b2a like me, by my invite, posted his V3 of 23andMe to Adriano. He has a back mutation that nobody of Western Europeans has.
I think that these are the decisive proofs about the origin of European R1b1b2 and subclades.

P.S. I found the link to the supplements of the paper (not the paper which isn't free) on "Genealogy-dna".


That still doesn't make sense. The eastern R-M269 doesn't have the downstream western mutations precisely because it is OLDER than the western stuff. R1b1b2 entered Europe in the older form. Its descendants in Western Europe have changes their grandfathers (figuratively speaking) didn't have. That seems pretty simple to me.

The alternative, that the older form of R1b1b2 migrated eastward out of Iberia leaving behind brothers who mutated while it went to Eastern Europe and did not, seems more than a bit of a stretch.
« Last Edit: December 25, 2009, 08:14:58 PM by rms2 » Logged

Maliclavelli
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« Reply #7 on: December 26, 2009, 01:48:10 AM »

Rich, again, if your theory is true, anyway all subclades downstreem R1b1b2 in Western Europe are born here, then they are “Western European” ones, you and Vizachero are thinking from a few thousands of years, I think many. But… for demonstrating this you must find in Western Asia many R1b1b2 without these mutations the two samples have, as I am always waiting that someone does find there some R1b1b2/L23+/L150- like the Italian Romitti. Vizachero are saying that this is a back mutation. I have said that this is very unlikely.
By what I have said, I think it is clear that from R1b1b2-M269 in Western Europe arose an R1b1b2-S116+ without the mutation R-L21 has, which generated R-M167 and another R-S116 which has the mutation which generated R-L21. Of course we need more test for understanding when this mutation occurred. Anyway I think that this is a matter of we Europeans. Western Asians have had another story. The back mutation of the Iranian Chitsaz is another proof.
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Maliclavelli


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« Reply #8 on: December 26, 2009, 02:25:01 AM »

....
A few days ago, Damon Chitsaz from Iran, who is on the Adriano’s spreadsheet and is an R1b1b2a like me, by my invite, posted his V3 of 23andMe to Adriano. He has a back mutation that nobody of Western Europeans has....
What is the back mutation that Damon has?
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R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
Maliclavelli
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« Reply #9 on: December 26, 2009, 04:23:27 AM »

See Adriano's spreadsheet: everybody under hg. P is 2172/rs9786602 CC, Chitsaz is AA. Then a backmutation happened downstream of P.

This backmutation is likable, that supposed by Vizachero of L150 not. It is a question of time and probabilities.
« Last Edit: December 26, 2009, 04:24:40 AM by Maliclavelli » Logged

Maliclavelli


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« Reply #10 on: December 26, 2009, 06:57:19 AM »

Of course the mutation USP9Y3636/M222 belongs only to this subclade of R-L21, then R-L21, like R-M167, derived from an R-116 without mutations like its Western-European ancestor R1b1b2-M269.
If, as I suppose, the two R1b1b2 with different mutations in the coding region are from Western Asia, my hypothesis is always worth. Perhaps it is less valid the hypotheis of a Cantabrian Refugium, but I strengthen my theory of the Italian origin of R1b1b2/L23- till R1b1b2/L23+/L150- and L150+.
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Maliclavelli


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rms2
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« Reply #11 on: December 26, 2009, 11:08:17 AM »

I'm not seeing it. I don't see that Chitsaz's mutation is anything more than a private one (we all possess those), and of course M167 is a different branch off P312 than L21 is.

On the other hand, we see an SNP trail from east to west (or SE to NW), with by far most of those who branched off closest to M269* in the east, and those with the downstream mutations we know about farther west. That there are exceptions here and there doesn't change the overall picture of east to west movement.

R1b1b2 does not appear to be old enough to have even been in existence during the last Ice Age, so it is an anachronism to refer to refugia with regard to R1b1b2.

« Last Edit: December 26, 2009, 11:08:42 AM by rms2 » Logged

Maliclavelli
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« Reply #12 on: December 26, 2009, 11:53:59 AM »

Dear Rich, mine of course were only hypotheses to be verified. This morning I have written to Professor Steve Rozen, the author of the paper. He has been so kind to answer me within a few tens of minutes. I have thanked him saying that “the more one is ‘great’ the more is ‘helpful’”. It seems unbelievable that a great scientist like him has been so quick to answer (and to answer)!
Unfortunately I have only the supplemental data and not the paper, which isn’t free, and, of course, I have misunderstood something. The samples come from NIH/NHGRI and of course the origin isn’t known. GM02294 has been described in Hirschhorn R. et al., “Erythrocyte Adenosine Deaminase Deficiency without Immunodeficiensy”, in J. Clin. Invest., 1979, 64, 1130-1139. Probably is a Kung!, i.e. a Bushman, and it is interesting to find an hg. R1* among them. Then the mutation in a code region has caused a great disease, but that evidently doesn’t prevent to survive (also R-M222 don’t seem to be badly off!).
Probably it is misleading the tree of the haplogroups at page 5 of the supplemental data. The R* is probably “M207/UTY+325+18” and the mutations aren’t cumulative.
We need to wait that Thomas Krahn tests some samples for these two mutations to know whether my hypotheses are reliable.
« Last Edit: December 26, 2009, 04:52:03 PM by Maliclavelli » Logged

Maliclavelli


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« Reply #13 on: December 27, 2009, 01:01:47 PM »

The authors of the paper write that there is remarkably little variation in X-degenerate protein sequences: two chromosomes drawn at random differ on average by a single amino acid, with half of these differences arising from a single, conservative Asp-›Glu mutation that occurred approximately 50,000 years ago. Further analysis showed that nucleotide diversity and the proportion of variant sites are significantly lower for  nonsynonymous sites than for synonymous sites, introns, or pseudogenes. These differences imply that natural selection has operated effectively in preserving the amino acid sequences of the Y chromosome’s X-degenerate proteins during the last approximately 100,000 years of human history.
This does mean that nonsynonymous mutations, like that of M207/UTY+325+18, and fixed in some populations like  the !Kung for some advantage we don’t know, are very rare.
The mutations of R1b1b2/-KALP-239 and of R1b1b2/-KDM5D+3291 are of an intron, then don’t have any consequence on the coding work and we can think that they aren’t rare, but, if the samples were chosen at random , really very diffused, on average  33% each one.
Then all my hypotheses, waiting for  Krahn’s tests I suppose he is always doing, maintain all their power.
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Maliclavelli


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rms2
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« Reply #14 on: December 27, 2009, 01:39:48 PM »

Not being able to read the paper for myself, I'm not seeing anything that would cause me to reconsider the idea that R1b spent the Ice Age anywhere near Western Europe. It seems to me the evidence is too strongly against such an idea.
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Maliclavelli
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« Reply #15 on: December 27, 2009, 03:10:20 PM »

The question is a little bit more complex, but the meaning of my words doesn’t change. Also the mutation of M207 is an intron, the mutation of KDM5+3291 hasn’t  consequences because in a “four-fold degenerate site” etc.

Rich, nor I have the paper, only the supplemental data, and I am trying to understand what I can. You know that my idea isn't (and never was) of a Refugium of R1b in Western Europe during LGM, but the presence in Italy during the Younger Dryas of an R1b1* from which derived the subclades from M269 to L23+/L150+. Whether R1b1* came from West or from East I don't know for sure, but in the past I thought that the R1b1* which generated  P297 and M269 was that we now find in the Spanish Peninsula and in the British Isles.
« Last Edit: December 28, 2009, 02:49:32 AM by Maliclavelli » Logged

Maliclavelli


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« Reply #16 on: December 28, 2009, 02:48:49 AM »

Rich, finally I have understood. That of the paper is a true genealogical tree. We all Hg. R have the mutation M207 which isn't dangerous. The child of the sample had many diseases for other mutations. Probably only the !kung have many R*, very rare among other peoples.

This confirms once more my first hypothesis.
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Maliclavelli


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