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Author Topic: New paper: R1b1b2 (R-M269) spread from Near East in Neolithic  (Read 18947 times)
Jean M
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« on: January 19, 2010, 04:54:11 PM »

New paper from  (mainly) Leicester University's genetics team.

A Predominantly Neolithic Origin for European Paternal Lineages PLos Biology.
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« Reply #1 on: January 19, 2010, 06:02:38 PM »

New paper from  (mainly) Leicester University's genetics team.

A Predominantly Neolithic Origin for European Paternal Lineages PLos Biology.

Anybody know what you have to do with there DYS439 values to make them compatible with FTDNA?
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« Reply #2 on: January 19, 2010, 06:08:05 PM »

Vizachero is rejoicing in posting the paper of Barbujani (hereon Farfugliani) on “Genealogy-dna”. Farfugliani, the preferred pupil of Cavalli Sforza. Ydna R1b1b2 would come from Middle East , the old theory of farming expansion, demic diffusion and, why not, the Renfrew’s  oddity of the Indo-European from Asia Minor.
1)   Asia Minor isn’t Middle East. There is a fault between Indo-European Asia Minor and Semite Middle East: linguistically, cultural, chromosomal.
2)   From there would come Y but not mt. Do you imagine an horde of Asian Don Juans to  break a lot of European hearts?  And under the eyes of Mesolithic hunter gatherers with their murderous bows?
3)   Anyway a few joy for Vizachero: this would have happened not 4000ya as he is thinking but at least the double before: 8000ya. Something doesn’t  square.
4)   The science of Farfugliani is all pro domo sua: Italy, which has at least a 30% of its R1b1b2 as R1b1b2a (DYS393=12), has in his data pretty only  the more recent subclades: and Italy has R1b1*, R1b1a, R1b1b2/L23-, R1b1b2/L23*/150- (the unique over the world) etc.
5)   We are yet waiting  for the Rozen’s SNPs, con buona pace di Farfugliani. Farfugliani sleeps in peace.
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Jean M
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« Reply #3 on: January 19, 2010, 06:38:37 PM »

I can't speak for anyone else, but I am rejoicing simply at a paper in support of post-Mesolithic migration as the dominant force in creating Europe's present pattern of paternal lineages. At last!

But this is not the final word. Science proceeds in steps.

This paper was submitted back in May 2009. That was before the two aDNA studies that showed
1) how different the mtDNA of northern Europe was before and after the Neolithic.
2) that if you add Mesolithic and Neolithic mtDNA, you still don't get the present pattern. Something important happened later. I argue that it was the spread of Indo-European languages with technological changes of the Copper Age.
« Last Edit: January 19, 2010, 06:39:07 PM by Jean M » Logged
OConnor
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« Reply #4 on: January 19, 2010, 07:36:12 PM »

Vizachero is rejoicing in posting the paper of Barbujani (hereon Farfugliani) on “Genealogy-dna”. Farfugliani, the preferred pupil of Cavalli Sforza. Ydna R1b1b2 would come from Middle East , the old theory of farming expansion, demic diffusion and, why not, the Renfrew’s  oddity of the Indo-European from Asia Minor.
1)   Asia Minor isn’t Middle East. There is a fault between Indo-European Asia Minor and Semite Middle East: linguistically, cultural, chromosomal.
2)   From there would come Y but not mt. Do you imagine an horde of Asian Don Juans to  break a lot of European hearts?  And under the eyes of Mesolithic hunter gatherers with their murderous bows?
3)   Anyway a few joy for Vizachero: this would have happened not 4000ya as he is thinking but at least the double before: 8000ya. Something doesn’t  square.
4)   The science of Farfugliani is all pro domo sua: Italy, which has at least a 30% of its R1b1b2 as R1b1b2a (DYS393=12), has in his data pretty only  the more recent subclades: and Italy has R1b1*, R1b1a, R1b1b2/L23-, R1b1b2/L23*/150- (the unique over the world) etc.
5)   We are yet waiting  for the Rozen’s SNPs, con buona pace di Farfugliani. Farfugliani sleeps in peace.


393=12 shows up in Ireland as well. Could there be any L159.2 over the Alps?
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rms2
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« Reply #5 on: January 19, 2010, 08:20:59 PM »

I printed that paper out and read it on the train today on the way home from work.

I think it makes eminent good sense.

At last we're starting to move away from all that sappy "Paleolithic R1b" stuff. I never did think that made much sense.

One of the most important aspects of the paper is the variance map showing how R1b1b2 variance increases as one moves SE through Europe toward Anatolia.
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« Reply #6 on: January 19, 2010, 10:52:01 PM »

New paper from  (mainly) Leicester University's genetics team.

A Predominantly Neolithic Origin for European Paternal Lineages PLos Biology.

Its not opening
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Jean M
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« Reply #7 on: January 20, 2010, 04:26:17 PM »

New paper from  (mainly) Leicester University's genetics team.

A Predominantly Neolithic Origin for European Paternal Lineages PLos Biology.

Its not opening

PLoS was down for maintenance for a while. It's working now.
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secherbernard
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« Reply #8 on: January 21, 2010, 03:51:51 PM »

I can't speak for anyone else, but I am rejoicing simply at a paper in support of post-Mesolithic migration as the dominant force in creating Europe's present pattern of paternal lineages. At last!

But this is not the final word. Science proceeds in steps.

This paper was submitted back in May 2009. That was before the two aDNA studies that showed
1) how different the mtDNA of northern Europe was before and after the Neolithic.
2) that if you add Mesolithic and Neolithic mtDNA, you still don't get the present pattern. Something important happened later. I argue that it was the spread of Indo-European languages with technological changes of the Copper Age.
I am rejoicing also for this paper. I have just a remark about the dates given for TMRCA: Turkey between 4.400 and 11.000 years, Ireland between 4.000 and 7.400 years. With this incertitude, it is difficult to make a difference between the migration of the first european farmers and an indo-european migration during copper age.
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« Reply #9 on: January 21, 2010, 06:14:07 PM »

[quote author=secherbernard link=topic=9208.msg115469#msg115469
I am rejoicing also for this paper. I have just a remark about the dates given for TMRCA: Turkey between 4.400 and 11.000 years, Ireland between 4.000 and 7.400 years. With this incertitude, it is difficult to make a difference between the migration of the first european farmers and an indo-european migration during copper age.
[/quote]

Of course they can't make that distinction. The real problem is that it didn't occur to them that there was a choice. For decades now the debate has been solidly focussed on Mesolithc versus Neolithic. That will change I think, once demic diffusion is fully accepted as playing a major role in spreading farming. People will then be able to move on to thinking about later migrations. It won't be such a shock. :)
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« Reply #10 on: January 21, 2010, 09:30:35 PM »



Of course they can't make that distinction. The real problem is that it didn't occur to them that there was a choice. For decades now the debate has been solidly focussed on Mesolithc versus Neolithic. That will change I think, once demic diffusion is fully accepted as playing a major role in spreading farming. People will then be able to move on to thinking about later migrations. It won't be such a shock. :)

Exactly. That is why this paper is important. It finally drives a stake through the heart of that old undead Iberian, "Paleolithic European R1b".

Now that he has been dispatched, we can move on to refining the real history of R1b1b2 in Europe.
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« Reply #11 on: January 22, 2010, 12:38:45 AM »

Of course they can't make that distinction. The real problem is that it didn't occur to them that there was a choice. For decades now the debate has been solidly focussed on Mesolithc versus Neolithic. That will change I think, once demic diffusion is fully accepted as playing a major role in spreading farming. People will then be able to move on to thinking about later migrations. It won't be such a shock. :)
Exactly. That is why this paper is important. It finally drives a stake through the heart of that old undead Iberian, "Paleolithic European R1b".
Now that he has been dispatched, we can move on to refining the real history of R1b1b2 in Europe.
Agreed. 

I'm amazed at the discussion generated about farmers... everything from they must be sexy and more.  I'm a little frustrated that (mostly on other forums) the discussion and articles seem to have forgotten about the Copper/Bronze/Iron Ages, but I think  this all can be viewed that as incremental progress.  The Paleothic and Mesolithic alternatives are finally getting knocked down for the count.
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« Reply #12 on: January 22, 2010, 01:34:29 AM »

“The real problem is that it didn't occur to them that there was a choice.”


Isn’t it all about publication for that community? Stray outside the box and chances of publication are diminished. We do not have that constraint in the amateur on-line genetic community.
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« Reply #13 on: January 22, 2010, 06:12:51 PM »



http://i88.photobucket.com/albums/k178/argiedude/R1b1b2variance-ht15ht35.gif

I've finished estimating ht15 and ht35 diversity, it's taken me 2 days to do this, and I think the results are amazing. The diversity clines of ht15 and ht35 are almost polar opposites. I think these results seriously call into question the conclusion of the Balaresque study, which is what prompted me to look into this. There's no surfing-on-an-expanding-wave phenomenon occuring with ht15. It has its lowest variance in the supposed origination point: Anatolia.

The diversity of ht35 doesn't form a gradually decreasing cline. It seems to be uniformly similar from Iran to west Iberia, or at least up to Italy, because there are issues with the validity of the North African and Iberian data (small sample size in one case and confusion with ht15 samples, in the other). Its cline seems to be more north-south than diagonally from southwest to northeast. East European countries have the same ht35 diversity as West Europe, with the special consideration of the west Iberian results.

Some technical details to keep in mind. Ht15 can be differentiated from ht35 by barely 2 markers: 393 and 461. Few studies test 461, so most of the samples I used were chosen on the basis of 393 alone. But about 3% of ht15 and 10% of ht35 have the "wrong" value, becoming confused with the other group. This usually doesn't matter, exceot in countries where there is an overwhelming ratio difference between the frequencies of both groups, such as in Iberia, France, Britain, Netherlands, Anatolia, and the Levant. In these extreme cases, I've included, where possible, 2 pair of results. The top pair uses samples predicted as narrowly as possible, by using both 393 and 461. The bottom pair is the standard prediction using just 393. The top pair should be more accurate, but they tend to lack in sample size, so then again, maybe not. Notice in the case of Iberia, that the less restrictive result changes drastically from the more restrictive result, and ends up with identical values to Iberia's ht15 diversity estimate, suggesting most of the samples are in fact ht15 samples that are being confused for ht35 because they had a mutation in 393 to the modal value of ht35 on that marker. Curiously, this didn't happen in France, where I was only able to use the less accurate method (393 alone), and yet the result is notably low and different from France's ht15 diversity. I'd seriously take North Africa's high ht35 result (0,30) with a military-issue teaspoon of salt, it's just 5 samples. On the other hand, it's notoriously high ht15 diversity (0,28) is pretty solid.

To recap, Baralesque and all geneticists are stuck in a time warp, they're back in 2003, thinking R1b is just R1b. What a waste, after going through all the effort of collecting and processing the samples, to not have had the sense to test for a few extra key mutations that define some major subdivisions of R1b1b2 and are well known for more than 5 years. The conclusions they reached would then have been very different.

PS: Did you all notice that the French samples are mainly from west France and have a whopping 75% R1b1b2! Imagine if they had been tested for L21.
« Last Edit: January 22, 2010, 06:13:09 PM by argiedude » Logged

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« Reply #14 on: January 22, 2010, 08:07:47 PM »

Got to say that new paper is pretty well an exact expression of my own views. 
One thing I find interesting is is that their maps demand  that R1b1b2 had  dual spread into Europe from Anatolia - following both the Danubian route north of the Alps and the Mediterranean route.  One or the other of these alone only explains half the distribution.  That again is paralleled by the dual routes of the spread of farming west.  Their proposal of course does not fit the Bronze Age MRCA dates some suggest but I like the way the paper states the band of possible date range for each area rather than giving a single date (which is clearly nonsense statistically). 
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« Reply #15 on: January 22, 2010, 08:24:21 PM »

Argiedude-so, in simple terms, what are you suggesting that indicates in terms of the origin and movement of R1b into Europe? 
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« Reply #16 on: January 22, 2010, 08:31:57 PM »

I can't speak for anyone else, but I am rejoicing simply at a paper in support of post-Mesolithic migration as the dominant force in creating Europe's present pattern of paternal lineages. At last!

But this is not the final word. Science proceeds in steps.

This paper was submitted back in May 2009. That was before the two aDNA studies that showed
1) how different the mtDNA of northern Europe was before and after the Neolithic.
2) that if you add Mesolithic and Neolithic mtDNA, you still don't get the present pattern. Something important happened later. I argue that it was the spread of Indo-European languages with technological changes of the Copper Age.
I am rejoicing also for this paper. I have just a remark about the dates given for TMRCA: Turkey between 4.400 and 11.000 years, Ireland between 4.000 and 7.400 years. With this incertitude, it is difficult to make a difference between the migration of the first european farmers and an indo-european migration during copper age.

However, these wide date ranges are the reality of confidence intervals.  When people quote adn actual single date it is very misleading,  I remember in Oppenheimer'book Origins of the British he quoted actual dates but if you looked into the noted it became clear that something like 3000BC would actually be +/- 1500 years e.g. 4500BC-1500BC.  You are right that such ranges can mean that its impossible to fit into one epoch but the that is the reality.
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« Reply #17 on: January 22, 2010, 08:49:28 PM »

argiedude -

If HT35 is the ancestral form of R1b1b2, then no one actually believes HT15 originated in Anatolia and (pardon me) your conclusion is mistaken.

The idea is that the oldest R1b1b2, i.e., HT35, is found much more frequently in Anatolia and SE Europe than it is farther west, just as one would expect if R1b1b2 emerged from Anatolia, crossed into SE Europe and headed northwest. HT15, i.e., P310+, would have arisen somewhere in Europe.

The progression of SNPs show the same basic trail that R1b1b2 variance does: SE to NW.

And R1b1b2 is R1b1b2. It's all M269+.
« Last Edit: January 22, 2010, 08:54:57 PM by rms2 » Logged

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« Reply #18 on: January 23, 2010, 09:30:27 AM »

I am delighted such a credible bunch of scientists have produced a big picture paper for R1b1b2.   I think looking at the origins of R1b1b2 clades and subclades in isolation is not a fruitful approach to real understanding.  The way I look at the fact that this study uses R1b1b2 as a whole is no big deal.  Most western European R1b1b2  are S116 subclades or S21 and all of these shared a common ancestor around the same time and the SNPs that define them came in very quick succession acccording to variance.  OK it doesnt sort the fine detail of clades but it shows the big picture and that big picture is quite independantly supported (not even discussed in this paper)by the SNP based phylogeny  which also moves from SE to west/north-west.  
 
What this study adds is some idea of the routes.  It has never (due to lack of a systematic sampling and deep clade testing of eastern and SE Europe) been clear  from SNP phylogeny which route R1b1b2 took west but this study suggests a dual route which makes complete sense.   L21 has a distinctive north of Alps/north of Pyrenees distribution and its pretty clear that L21 (or at least its explosion in numners) is simply the last leg of the R1b1b2 journey west.   I really do not understand the small rump of people who think out of the whole R1b1b2 story from the Agean to the Atlantic some at he end of the trail suddenly went into reverse gear after a brief touch down on the isles and a handy SNP mutiation and sprinted back to the continent.  It is linteresting that the maps of this study suggests a dual route and that it seems from present distribution that S116 clades seem to be included on both the Med. route and the central European one wesrtwards.  That can only have happened if S116 happened at a common origin point shared by both the groups of farmers who followed the two routes.  The routes parted company somewhere around the Balkans so you could argue that S116 happened there.  

Now L21 seems to have the same variance as S116. If f S116 happened in SE Europe and has the same variance as L21, then its hardly likely that L21 SNP happened in the isles at the opposite end of Europe.  Even what are considered lightening speed spreads like the sprad of the first farmers took about 1500-2000 years to reach from SE Europe to the isles.  Clearly variance does not support the idea of 1500-2000 years between S116 and L21.  If S116 did happen iin SE Europe and L21 happend within only a few 100 years of that then (assuming it is linked to the Neolithic spread north of the Alps) then you can actually look at the radiocarbon dates for where the Neolithic farmers had spread to within a few hundred years of leaving the Balkans area. That would seem to imply that L21 could not have happened much after 5500BC and not much further west than south Germany.   The isles did not recieve the first farmers for a further 1500 years.  So, if the spread of R1b1b2 is overwhelmingly  due to the Neolithic farmers then it is impossible that L21 could have happened in the isles.  Now there are a lot of ifs and buts in that and it does involve rejecting the forumulas used to turn variance into ages but it is of interest to try and think this through.  

There are possible alternative scenarios like that S116 happened somewhere like Italy as R1b1b2 spread west along the Med. route (c. 5500BC) and the L21 SNP happened as they spread into France from the Med. and on into the NW and west-central Europe in the 5th millenium (middel Neolithic) .  However, the archaeological evidence for this scenario is not strong.
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« Reply #19 on: January 23, 2010, 09:50:33 AM »

However, these wide date ranges are the reality of confidence intervals.  When people quote adn actual single date it is very misleading,  I remember in Oppenheimer'book Origins of the British he quoted actual dates but if you looked into the noted it became clear that something like 3000BC would actually be +/- 1500 years e.g. 4500BC-1500BC.  You are right that such ranges can mean that its impossible to fit into one epoch but the that is the reality.
I have a question about these dates given in the Balaresque paper. These dates are TMRCA. How can we link these TMRCA with migration dates ?
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« Reply #20 on: January 23, 2010, 11:59:45 AM »

..... Now L21 seems to have the same variance as S116. If f S116 happened in SE Europe and has the same variance as L21, then its hardly likely that L21 SNP happened in the isles at the opposite end of Europe.  Even what are considered lightening speed spreads like the sprad of the first farmers took about 1500-2000 years to reach from SE Europe to the isles.  Clearly variance does not support the idea of 1500-2000 years between S116 and L21.  If S116 did happen iin SE Europe and L21 happend within only a few 100 years of that then (assuming it is linked to the Neolithic spread north of the Alps) then you can actually look at the radiocarbon dates for where the Neolithic farmers had spread to within a few hundred years of leaving the Balkans area. That would seem to imply that L21 could not have happened much after 5500BC and not much further west than south Germany.   .....
This sounds like a very reasonable match of information between R1b1b2 distribution and archeology. However, I'm still have an uneasy feeling about it.

The queasiness comes from two other dimensions of the information. First the R1b1b2 TMRCA information.  A 5500 BC TMRCA for L21 is 7500 ybp and that is double the kind of target dates that we've seen out of some very good estimation methods.  I won't name names if the statisticians don't want to speak up on this but being off by 100% just seems too high.  Anecdotally speaking, if you pour through R-L21* haplotypes as I have, it is apparent (at least to me) that these "younger" estimations are very credible.

The second dimension of information is the spread of Indo-European Languages.  They also have a dating of couple of thousand years more recent than the Neolithic advances.  Someone had to bring IE to Western Europe.  I agree it could have been a hegemonic spread, but surely there would be a larger folk movement than just that has been left behind by R1a1.

I don't know the answer, but I do think we will get to a fairly good answer prior to the day that aDNA provides more resolution.  Ironically, it seems like we understand folk movement better in the Neolithic Age in Europe than the Metal Ages.  Perhaps the movement during the Metal Ages were just plain faster and more complex, creating the difficulty in understanding.
« Last Edit: January 23, 2010, 12:05:22 PM by Mikewww » Logged

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« Reply #21 on: January 23, 2010, 11:59:51 AM »

argiedude -

If HT35 is the ancestral form of R1b1b2, then no one actually believes HT15 originated in Anatolia and (pardon me) your conclusion is mistaken.

The idea is that the oldest R1b1b2, i.e., HT35, is found much more frequently in Anatolia and SE Europe than it is farther west, just as one would expect if R1b1b2 emerged from Anatolia, crossed into SE Europe and headed northwest. HT15, i.e., P310+, would have arisen somewhere in Europe.

The progression of SNPs show the same basic trail that R1b1b2 variance does: SE to NW.

And R1b1b2 is R1b1b2. It's all M269+.

P310 must have occurred at a point before those travelling along the Med. and those travelling up the Danube had parted e.g the Balkans.  I think the distribution could suggest the same for S116 too.  I think however that distribution strongly suggests that L21 happened after the parting of the ways among the group going up the Danube towards west-central and north-west Europe.  Other calculations suggest L21 may have happened pretty soon after S116 so I cant see L21 having happened much further west than south Germany. There are other possible scenarios but this is the most intuitive when you compare DNA and the spread of farming.  I have suggested before that L21 occurred among the S116 Linearbandkeramik people in south Germany and spead to the Rhine and into northern France via the Mosselle and into the  Loire and Seine systems and then beyond.  I based my predictions for L21 distribution that it would have a strong Rhine and northern French showing on a lmodel of an origin and spread via late Linearbandkeramik and LBK-descended middle Neolithic cultures like Rossen etc before many L21 results had come in and so far its matched to a surprising degree (allowing for some later expansion).  
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« Reply #22 on: January 23, 2010, 12:12:58 PM »

...  I have a question about these dates given in the Balaresque paper. These dates are TMRCA. How can we link these TMRCA with migration dates ?
Benard, is this your question - should the TMRCA for a population have occurred prior to that populations' period of growth, during it, or after it?

If so, I have the same question.   My thinking is that the MRCA had to be prior (at least slightly) to great population growth and spread because he had to have enough descendants to get out there and lead the expansion and migrations. That's what accounts for the breadth of the spread of the descendant popultion.

I've never really heard a good discussion on this though, that I understood.  I do realize there can be bottlenecks reducing the TMRCA but it seems logical that's the point of the TMRCA being before the growth, so the ancestor's descendants could sufficiently "diversify" into multiple geographies and cultural variants, insuring more surviving lineages.
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« Reply #23 on: January 23, 2010, 12:25:46 PM »

Mike
Another way of putting it is what are the chances of two identical looking demographically massive looking explosive SE to NW spreads from Anatolia as far Atlantic Europe being entirely seperately identified by both the DNA experts and Archaeologists and them not being one and the same movement.  No other archaeologically indicated movement comes near to correlating with the geography and direction of the R1b1b2 spread but the spread of the Neolithic farmers is a perfect match in terms of origin, direction of spread, explosive demographic effect etc.  

Remember too when considering alternatives that the copper age experts are basically seeing beaker culture's origin as  Iberian with a spread from south-west to east/NW (although some would still see a secondary jumping off point at the contact zone between beaker and corded ware around the Rhine).  However, the geography and dates for those cultures in no way matches the R1b1b2 variance/diversity map.

Archaeology simply provides no alternative match to the R1b1b2 map in this new paper.  As for the later MRCA dates being discussed, while the youth of R1b1b2 is manifest and seems to rule out really old Palaeolithic origins (20,000 years old etc) it is clear to me from Tim Jansen's posts in the summer that the choice of markers as well as other variables is debateable and he demonstrated than an early Neolithic dating was within the bounds of possibility.  Even VV posted a couple of times that an earlier Neolithic dating was within touching distance of the confidence intervals of the Bronze Age dates any way.  
« Last Edit: January 23, 2010, 12:27:09 PM by alan trowel hands. » Logged
Mike Walsh
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« Reply #24 on: January 23, 2010, 12:35:55 PM »

....  I based my predictions for L21 distribution that it would have a strong Rhine and northern French showing on a lmodel of an origin and spread via late Linearbandkeramik and LBK-descended middle Neolithic cultures like Rossen etc before many L21 results had come in and so far its matched to a surprising degree (allowing for some later expansion).  
Would you include the Michelsberg culture as one of your "LBK-descended middle Neolithic cultures"?

If so, there may be evidence for your position with Hg I-L38, who may have been "tribal brother" of R-L21*. Hans De Beule makes the case that I-L38 and R-L21* have coincident distribution patterns in his paper and that they may have come out of the Michelsberg culture as it blossomed from c. 6400 to 5500 ybp.

Origins of Hg I-L38 (I2b2) Subclades - Hans De Beule – 5th of april 2009

BTW, I-L38 is also found in the Lichenstein Cave.

http://sites.google.com/site/haplogroupil38/
« Last Edit: January 23, 2010, 12:36:34 PM by Mikewww » Logged

R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
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