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Author Topic: History of haplogroup R1b1 and subclades  (Read 2280 times)
Maliclavelli
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« on: June 06, 2012, 01:38:47 PM »

These are the 22 markers of Klyosov:

R-M269:       11,12,13,11,11,12,11,9,15,16,8,10,8,12,10,12,12,8,12,11,11,12
Mangino:      12,13,13,11,11,12,11,8,15,16,8,10,8,  0,10,12,12,8,11,11,11,12
R1b1*          12,13,13,11,11,11,11,8,15,16,8,10,8,12,10,12,12,8,11,11,11,12
R-M73          12,12,13,11,11,10,11,8,16,16,8,10,8,12,10,12,12,8,12,11,11,12
R-M335        12,12,13,11,12,11,11,8,15,16,8,10,8,12,10,12,12,8,12,11,12,11

Mangino has 1 mutation as to R1b1* (we have to not consider DYS425): DYS438 and has 4 mutation as to R-M269: DYS426, DYS388, DYS478, DYS617, then he belongs to a R-M269, but of a clade separated from R1b1 about 4000 years after its constitution and 16000 before the survived clade of M-269.

R-M73 has 4 mutations as to R1b1: DYS388, DYS438, DYS395S1a, DYS617 and belongs to a clade separated from R1b1 from 16000 years.

R-M335 has 5 mutations as to R1b1: DYS388, DYS454, DYS617, DYS640, DYS492 and belongs to a clade separated by R1b1 from 20000 years.

« Last Edit: June 08, 2012, 02:00:59 PM by Maliclavelli » Logged

Maliclavelli


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Richard Rocca
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« Reply #1 on: June 06, 2012, 02:26:51 PM »

Gioiello, can you please add the DYS numbers as a header to the above?
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ironroad41
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« Reply #2 on: June 06, 2012, 02:52:39 PM »

This is the 22 dys loci sequence:  426, 388, 392, 455,454, 438, 531,578,395S1a, 395S1b, 590, 641, 472, 425, 594, 436, 490, 450, 617, 568, 640, 492.
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ironroad41
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« Reply #3 on: June 06, 2012, 03:49:33 PM »

These are the 22 markers of Klyosov:

R-M269:       11,12,13,11,11,12,11,9,15,16,8,10,8,12,10,12,12,8,12,11,11,12
Mangino:      12,13,13,11,11,12,11,8,15,16,8,10,8,  0,10,12,12,8,11,11,11,12
R1b1*          12,13,13,11,11,11,11,8,15,16,8,10,8,12,10,12,12,8,11,11,11,12
R-M73          12,12,13,11,11,10,11,8,16,16,8,10,8,12,10,12,12,8,12,11,11,12
R-M335        12,12,13,11,12,11,11,8,15,16,8,10,8,12,10,12,12,8,12,11,12,11

Mangino has 1 mutation respect to R1b1* (we have to not consider DYS425): DYS438 and has 4 mutation respect to R-M269: DYS426, DYS388, DYS478, DYS617, then he belongs to a R-M269, but of a clade separated from R1b1 about 4000 years after its constitution and 16000 before the survived clade of M-269.

R-M73 has 4 mutations respect to R1b1: DYS388, DYS438, DYS395S1a, DYS617 and belongs to a clade separated from R1b1 from 16000 years.

R-M335 has 5 mutations respect to R1b1: DYS388, DYS454, DYS617, DYS640, DYS492 and belongs to a clade separated by R1b1 from 20000 years.


I did some math using A. Klyosovs set of 22 mutators, R1b1 and my haplotype and I get 40K years separation.  There are 8 mutations in the set with three of them at 392: 10 vs 13 which I counted as 3 mutations?  I do not have any idea how correct this is, but it is an interesting result to ponder.  Note I used a fudge factor of 1.2 to account for any back mutations.

p.s. the calculation was made using Klyosovs equations.
« Last Edit: June 06, 2012, 04:44:47 PM by ironroad41 » Logged
Maliclavelli
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« Reply #4 on: June 06, 2012, 04:13:27 PM »

I have done a rough calculation based upon the previous one I did for the Sicilian U152 Cucina, i.e. about 4000 years for mutation. I'd be glad if Anatole Klyosov did the calculation. He has written a great work about the origin of mankind, and I think he is right, as I have written elsewhere, and some doubt about Africa, hg. E etc., I have expressed also in the past.
About our hg. R1b1 it was important to me to say that its ancientness is greater than it is usually thought. At this point, if the times were these or about them, given the presence of R1b1 in Iberia and in the Isles, I think that the idea of the Cantabrian Refugium before the LGM should be revisited.
Of course Italy may have had some R1b1 before the Younger Dryas and my theory about DeMao, Toniolo, Mangino, R-M269=YCAII=17-23, R-L51 could maintain all its importance.
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Maliclavelli


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Arch Y.
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« Reply #5 on: June 10, 2012, 07:20:58 PM »

I have done a rough calculation based upon the previous one I did for the Sicilian U152 Cucina, i.e. about 4000 years for mutation. I'd be glad if Anatole Klyosov did the calculation. He has written a great work about the origin of mankind, and I think he is right, as I have written elsewhere, and some doubt about Africa, hg. E etc., I have expressed also in the past.
About our hg. R1b1 it was important to me to say that its ancientness is greater than it is usually thought. At this point, if the times were these or about them, given the presence of R1b1 in Iberia and in the Isles, I think that the idea of the Cantabrian Refugium before the LGM should be revisited.
Of course Italy may have had some R1b1 before the Younger Dryas and my theory about DeMao, Toniolo, Mangino, R-M269=YCAII=17-23, R-L51 could maintain all its importance.

I think the idea of R1b's ancientness has been revisited several times by academia and every single time successfully refuted.  R1b is no older than 18kya and origins are southwestern Asia. R1b was most likely not in Iberia before the Younger Dryas and the idea that we will find R1b in the Upper Paleolithic is pretty much absurd. I think those in HG I have been experiencing difficulties to find some continuity that just doesn't exist from this time frame in Western Europe, or even elsewhere for that matter. So far, the late and early Neolithic is the best we get. Mesolithic finds have not yielded R1b anywhere in Western Europe. Not to say R1b couldn't have been in Western Europe at this time, I just don't think it emerged from this region prior to the Younger Dryas. I just have a hard time understanding why it would be so difficult for a band of R1b people to travel across the stretches of the vast Eurasian plains into Western Europe during the Mesolithic. That's like saying early settlers couldn't discover Alaska because they didn't have planes. I'm sure a few R1b people wandered into the far west of Europe, but doesn't necessarily mean their "ancestry" emerged there.

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JeanL
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« Reply #6 on: June 10, 2012, 08:11:30 PM »

I think the idea of R1b's ancientness has been revisited several times by academia and every single time successfully refuted.  R1b is no older than 18kya and origins are southwestern Asia. R1b was most likely not in Iberia before the Younger Dryas and the idea that we will find R1b in the Upper Paleolithic is pretty much absurd. I think those in HG I have been experiencing difficulties to find some continuity that just doesn't exist from this time frame in Western Europe, or even elsewhere for that matter. So far, the late and early Neolithic is the best we get. Mesolithic finds have not yielded R1b anywhere in Western Europe. Not to say R1b couldn't have been in Western Europe at this time, I just don't think it emerged from this region prior to the Younger Dryas. I just have a hard time understanding why it would be so difficult for a band of R1b people to travel across the stretches of the vast Eurasian plains into Western Europe during the Mesolithic. That's like saying early settlers couldn't discover Alaska because they didn't have planes. I'm sure a few R1b people wandered into the far west of Europe, but doesn't necessarily mean their "ancestry" emerged there.

Arch

I’m sorry to bug you, but do you know of any Mesolithic finds in Western Europe that have yielded any Y-DNA haplogroups?
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ironroad41
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« Reply #7 on: June 11, 2012, 07:07:15 AM »

I've said elsewhere that it is pretty farfetched to expect any remains from settlements in Europe pre 6K or so.  The glaciers erased anything they covered which was most of northern europe and then the subsequent 60 m. rise of the ocean destroyed most of the extant coastal settlements.   The landscape of the mesolithic differed from the subsequent coastlines.  I expect that we will continue to find settlements in the near East which, apparently, wasn't bothered by these natural events. The work at the U. of Birmingham to map the landscape of Doggerland may identify underwater sites of high probability of recovering pre-deluge artifacts?
« Last Edit: June 11, 2012, 07:10:43 AM by ironroad41 » Logged
rms2
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« Reply #8 on: June 11, 2012, 07:20:28 AM »

I've said elsewhere that it is pretty farfetched to expect any remains from settlements in Europe pre 6K or so.  The glaciers erased anything they covered which was most of northern europe and then the subsequent 60 m. rise of the ocean destroyed most of the extant coastal settlements.   The landscape of the mesolithic differed from the subsequent coastlines.  I expect that we will continue to find settlements in the near East which, apparently, wasn't bothered by these natural events. The work at the U. of Birmingham to map the landscape of Doggerland may identify underwater sites of high probability of recovering pre-deluge artifacts?

I believe there are quite a number of very old skeletons or parts of skeletons from Europe in various collections. I don't know how suitable any one of them is for dna testing, but they are available.

It is really difficult to get dna from very very old remains, especially y-dna, but scientists have extracted dna from 38,000-year-old Neanderthal femurs, so it's not impossible.

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Mike Walsh
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« Reply #9 on: June 11, 2012, 08:26:39 AM »

I've said elsewhere that it is pretty farfetched to expect any remains from settlements in Europe pre 6K or so. The glaciers erased anything they covered which was most of northern europe and then the subsequent 60 m. rise of the ocean destroyed most of the extant coastal settlements.  

I don't understand your logic. You seem to string disconnected information together to make a point.  The Last Glacial Maximum was about 20K years ago, not 6K. Thy Younger Dryas did not impose glaciers through out Europe and the Younger Dryas was about 10K.   I'm not sure how you define settlements but there are artifacts found in Europe from well before 6K years ago that indicate groups of people living together.

  The landscape of the mesolithic differed from the subsequent coastlines.  I expect that we will continue to find settlements in the near East which, apparently, wasn't bothered by these natural events. The work at the U. of Birmingham to map the landscape of Doggerland may identify underwater sites of high probability of recovering pre-deluge artifacts?

I think your own words from the Ukraine thread can best describe your thinking on some of these things.
I could imagineer all kinds of scenarios, but what would be the use?
« Last Edit: June 11, 2012, 08:27:39 AM by Mikewww » Logged

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ironroad41
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« Reply #10 on: June 11, 2012, 08:42:52 AM »

From what I've read, most settlements, pre flood, were probably within the flood plain?Thats where a lot of the food was.  Whether the LGm was 20K or 18K BP is argumentative.  My point is that a lot of usable land available 10K years BP is not now available.  I still think that the amount of usable material for analysis from N. Eur. is small compared to the near East.
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Richard Rocca
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« Reply #11 on: June 11, 2012, 09:28:56 AM »

We may never get a good Y-DNA sample from the Mesolithic, but with every non-R1b Neolithic sample that turns up, the chances that R1b was in Western Europe during the Mesolithic gets reduced. I mean, what are the odds that R1b was hiding out in some corner of Western Europe and did not mix with a single Neolithic group during a span of thousands of years?
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Jean M
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« Reply #12 on: June 11, 2012, 09:31:15 AM »

I've said elsewhere that it is pretty farfetched to expect any remains from settlements in Europe pre 6K or so.

You are not aware then of all the evidence of Palaeolothic and Mesolithic settlements in Europe? Or are you claiming a lack of human remains from them?

Teeth from Grotta del Cavallo, southern Italy, have been recently reclassified as belonging to anatomically modern humans some 45,000–43,000 years old, while an anatomically modern human jaw from Kent's Cavern, UK has been recently re-dated to between 44,200 and 41,500 years old. The first complete skull discovered was 35,000 years old and from Peştera cu Oase, Romania. There are human remains from all subsequent periods. The earliest European DNA so far extracted is 30,000 years old mtDNA U2 from Markina Gora, Russia.
 

« Last Edit: June 11, 2012, 09:47:34 AM by Jean M » Logged
JeanL
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« Reply #13 on: June 11, 2012, 09:41:12 AM »

We may never get a good Y-DNA sample from the Mesolithic, but with every non-R1b Neolithic sample that turns up, the chances that R1b was in Western Europe during the Mesolithic gets reduced. I mean, what are the odds that R1b was hiding out in some corner of Western Europe and did not mix with a single Neolithic group during a span of thousands of years?

Under the model I'm proposing, very high, just as the odds that I1 was hiding out in some corner in NW Europe and did not mix with a single Neolithic group during a span of thousands of years.
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ironroad41
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« Reply #14 on: June 11, 2012, 09:45:51 AM »

I am aware of the cro-magnon caves in France, et.al.  also of the caves in England where the drawings are of fauna indigineous to Africa I believe.

The issue with bone samples is one of contamination, especially in caves where sites were occupied for thousands of years.

If there is so much material available, why is there no presented analysis of these sites?

The point is that the sparsity of remains suggests one of several scenarios:  a.  Nobody lived there, or doggone few.  b. There have been natural occurrances which swept any data away. c. We haven't found it yet.

I live in the northeast of the USA.  The soils are highly acidic and eroded.  There were literally millions of indians in this country in the early 1600's. It is hard to reconstruct much of the early life from remains/artifacts.  Most of them except primarily for stoneware are gone.  My son has an MS in anthropology and studied the northeast and the shell cultures of northern mexico.

p.s. my goodness, red doesn't become you.
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Jean M
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« Reply #15 on: June 11, 2012, 09:51:18 AM »

If there is so much material available, why is there no presented analysis of these sites?

If you mean Y-DNA, it is only fairly recently that techniques have been good enough to extract it. Initially tests were for mtDNA, as there is much more of that in the body. The chances of getting autosomal DNA are lower. However under good conditions of preservation, it can be done, as we can see from the results so far.  

A major consideration is cost. It is still very expensive to extract ancient DNA of any type. But big projects are currently under way.

« Last Edit: June 11, 2012, 09:55:10 AM by Jean M » Logged
Richard Rocca
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« Reply #16 on: June 11, 2012, 09:58:25 AM »

We may never get a good Y-DNA sample from the Mesolithic, but with every non-R1b Neolithic sample that turns up, the chances that R1b was in Western Europe during the Mesolithic gets reduced. I mean, what are the odds that R1b was hiding out in some corner of Western Europe and did not mix with a single Neolithic group during a span of thousands of years?

Under the model I'm proposing, very high, just as the odds that I1 was hiding out in some corner in NW Europe and did not mix with a single Neolithic group during a span of thousands of years.

If Neolithic samples from Ireland turn out to be non-R1b, then you probably need to re-think your model substantially.
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JeanL
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« Reply #17 on: June 11, 2012, 10:17:03 AM »

If Neolithic samples from Ireland turn out to be non-R1b, then you probably need to re-think your model substantially.

Ok, it would be good to get some aDNA from Ireland and the UK.
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Jdean
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« Reply #18 on: June 11, 2012, 10:27:49 AM »

If Neolithic samples from Ireland turn out to be non-R1b, then you probably need to re-think your model substantially.

Ok, it would be good to get some aDNA from Ireland and the UK.

I don't think many here would disagree with that but I apparently there are a few problems getting aDNA from Irish samples, lots of bonfires and peat bogs seem to preserver everything bar DNA.
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Jean M
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« Reply #19 on: June 11, 2012, 10:28:18 AM »

Ok, it would be good to get some aDNA from Ireland and the UK.

There is some, but all mtDNA so far.
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Jean M
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« Reply #20 on: June 11, 2012, 10:30:54 AM »

apparently there are a few problems getting aDNA from Irish samples, lots of bonfires and peat bogs seem to preserve everything bar DNA.

I didn't know that there had been any attempt to get DNA from Irish bog bodies. The only aDNA I know about from Ireland was from Glencurran Cave (1500 BC). Not all human remains from Ireland ended up cremated or tossed into bogs.  
« Last Edit: June 11, 2012, 10:33:38 AM by Jean M » Logged
Jdean
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« Reply #21 on: June 11, 2012, 10:36:59 AM »

I don't think many here would disagree with that but I apparently there are a few problems getting aDNA from Irish samples, lots of bonfires and peat bogs seem to preserve everything bar DNA.

I didn't know that there had been any attempt to get DNA from Irish bog bodies. The only aDNA I know about from Ireland was from Glencurran Cave (1500 BC). Not all human remains from Ireland ended up cremated or tossed into bogs.  

Usual thing with me, the information about peat bogs was posted by somebody on this site but I can't remember who, from what I remember peat bogs pretty much eat DNA.
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Jean M
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« Reply #22 on: June 11, 2012, 10:47:31 AM »

..  peat bogs pretty much eat DNA.

I read the same thing somewhere, but I don't think it came from Ireland. Frankly I don't think the British and Irish have wanted to spend the cash looking for it hitherto.  There is a mention of the lack of cellular and DNA preservation  in Jan M. Pestka et al., Skeletal analysis and comparison of bog bodies from Northern European peat bogs, Naturwissenschaften, Volume 97, Number 4 (2010), 393-402.

But as I say, bog bodies are not the whole story of Ireland's human remains. Actually you can even get DNA from cremated bone, I just found.
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Jdean
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« Reply #23 on: June 11, 2012, 11:14:37 AM »

..  peat bogs pretty much eat DNA.

I read the same thing somewhere, but I don't think it came from Ireland. Frankly I don't think the British and Irish have wanted to spend the cash looking for it hitherto.  There is a mention of the lack of cellular and DNA preservation  in Jan M. Pestka et al., Skeletal analysis and comparison of bog bodies from Northern European peat bogs, Naturwissenschaften, Volume 97, Number 4 (2010), 393-402.

But as I say, bog bodies are not the whole story of Ireland's human remains. Actually you can even get DNA from cremated bone, I just found.

Well at least my memory held up this time, actually it's not that bad but I think it could do with being defragmented :)

If they can get DNA out of ash Ireland shouldn't have any problem, but of course as you said before it’s the people with the purse strings that need convincing
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« Reply #24 on: June 11, 2012, 02:17:13 PM »

..  peat bogs pretty much eat DNA.

I read the same thing somewhere, but I don't think it came from Ireland. Frankly I don't think the British and Irish have wanted to spend the cash looking for it hitherto.  There is a mention of the lack of cellular and DNA preservation  in Jan M. Pestka et al., Skeletal analysis and comparison of bog bodies from Northern European peat bogs, Naturwissenschaften, Volume 97, Number 4 (2010), 393-402.

But as I say, bog bodies are not the whole story of Ireland's human remains. Actually you can even get DNA from cremated bone, I just found.

That is interesting.  I found this recent paper

http://www.ncbi.nlm.nih.gov/pubmed/20609539

Another aspect of cremation is the slow move from deposition of whole cremated bodies carefully gathered and deposited in the Early bronze Age to token pinches of cremated bones later on (well that is the general trend in ireland).
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