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Author Topic: The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269 (B  (Read 9043 times)
Heber
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« on: August 24, 2011, 12:42:29 PM »

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates.As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.

http://rspb.royalsocietypublishing.org/content/early/2011/08/18/rspb.2011.1044.full.pdf+html

Dienekers posted the following on his blog:
"The paper could just as easily have been titled "An epitaph for Y-STRs". Of course, Y-STRs do carry information related to antiquity; and there are so many datasets collected from both academics and genealogist enthusiasts. Thus, they will continue to be used and analyzed for at least a few years more.
Nonetheless, the conclusion is inescepable that a very specific use of Y-STRs on modern populations, with the goal of discovering tight links with archaeological/historical events is all but dead.
The reason is simple: as clocks, they suck. A bad clock is not useless: it gives you some information about time. Moreover, you can often use several to iron out the inaccuracy of any single one of them".

The study make interesting reading and reviews the data from Myers, Balaresque and others.
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« Reply #1 on: August 24, 2011, 03:34:27 PM »

.
The reason is simple: as clocks, they suck. A bad clock is not useless: it gives you some information about time. Moreover, you can often use several to iron out the inaccuracy of any single one of them".


I haven't read the article myself but got the impression from other posts about this that problem was the data didn't support the authors hypothesis, namely that M269's spread appeared to resent, and hence there conclusion that STR data was unreliable.
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alan trowel hands.
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« Reply #2 on: August 24, 2011, 07:06:04 PM »

For those interested in L21 the supplimentary bit includes sample positions.  It shows how essentially useless Myres was in France and also even in this study they simply didnt sample between sites in the western half of France and Germany.  So basically the east of France is missing and the contouring simply assumes its the same as Germany.  The eastern limit of L21 shaded contours is simply a dot joining exercise between the easternmost French samples.  That is the real reason why it seems there is a stranded area of higher L21 in SE France.  Its because its the only part of eastern France sampled (its the Myres sample).  So, again, I think this gives a slightly misleading impression.  I think L21 probably decreases in a contoured kind of way from NW France towards south Germany. 
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Jdean
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« Reply #3 on: August 24, 2011, 07:21:12 PM »

For those interested in L21 the supplimentary bit includes sample positions.  It shows how essentially useless Myres was in France and also even in this study they simply didnt sample between sites in the western half of France and Germany.  So basically the east of France is missing and the contouring simply assumes its the same as Germany.  The eastern limit of L21 shaded contours is simply a dot joining exercise between the easternmost French samples.  That is the real reason why it seems there is a stranded area of higher L21 in SE France.  Its because its the only part of eastern France sampled (its the Myres sample).  So, again, I think this gives a slightly misleading impression.  I think L21 probably decreases in a contoured kind of way from NW France towards south Germany. 

Yes unfortunately Myres didn't exactly go to town on France, however there does seem to be quite a hot spot in the SE corner and I seem to remember the R-L21 project has had trouble picking up people in the middle of France as well.
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« Reply #4 on: August 24, 2011, 07:25:20 PM »

I haven't read the article myself but got the impression from other posts about this that problem was the data didn't support the authors hypothesis, namely that M269's spread appeared to resent, and hence there conclusion that STR data was unreliable.

That is a large part of what the paper is about. From the text:

"While recent evidence has increased support for the Neolithic spread of R-M269, [Balaresque, Myres] we conclude that at the present time it is not possible to make any credible estimate of divergence time based on the sets of Y-STRs used in recent studies."

Bushby concludes:

"For now, we can offer no date as to the age of R-M269 or R-S127, but believe that our STR analyses suggest the recent age estimates of R-M269 [Balaresque] and R-S116 [Myres] are likely to be younger than the true values"

However, he doesn't dismiss the use of STRs. He has used them himself to come to the conclusion that the age estimates by Balresque and Myres are too young. Rather he highlights the choice of STRs as being the critical factor.

"While researchers take into account STR mutation rates when estimating divergence time with ASD, commonly used STRs do not have the specific attributes that allow linearity to be assumed further into the past. The majority of haplogroup dates based on such sets of STRs may therefore have been systematically underestimated."

And he offers a mild rebuke about their practices,

"Furthermore, we show that it is the properties of Y-STRs, not the number used per se, that appear to control the accuracy of divergence time estimates, attributes which are rarely, if ever, considered in practise."

Other than the technical aspects of his research, there is discussion about what this means for the arrival and dispersal of M269 in europe. In addition to considering a paleolithic date for this, he does acknowledge that it may be even younger than either Balaresque or Myres suggest.

"If the R-M269 lineage is more recent in origin than the Neolithic expansion, then its current distribution would have to be the result of major population movements occurring since that origin."

Bushby however doesn't think this is likely for, in his own words:

"For this haplogroup to be so ubiquitous, the population carrying R-S127 would have displaced most of the populations present in western Europe after the Neolithic agricultural transition."

This last part however is nothing to do with genetics. The genetics allow for this possibility. He thinks it is unlikely because europe is already populated.

However, the arrival of the Indo European languages, which is beyond this study, is a possible scenario which may account for a later arrival of M269. In addition, the population studies by Shennan and Edinborough, 'Prehistoric population history: from the Late Glacial to the Late Neolithic in Central and Northern Europe' (2007) and Shennan, 'Evolutionary Demography and the Population History of the European Early Neolithic' (2009) suggest that after the initial steep rise in population levels at the beginning of the neolithic, the population crashed early in the 5th millenium BC, in some places to extremely low levels, and remained low for nearly a millenium, before a second steep rise in population occured. So we do have a possible gap between the early and later neolithic populations. The population increase may be a result of the arrival of M269.

In addition, correct me if I am wrong, from the few samples of ancient yDNA that we have, none from the LBK have been found to be R1b or R1a. Those that are found appear to be later.

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« Last Edit: August 24, 2011, 07:27:48 PM by authun » Logged
alan trowel hands.
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« Reply #5 on: August 24, 2011, 07:28:34 PM »

For those interested in L21 the supplimentary bit includes sample positions.  It shows how essentially useless Myres was in France and also even in this study they simply didnt sample between sites in the western half of France and Germany.  So basically the east of France is missing and the contouring simply assumes its the same as Germany.  The eastern limit of L21 shaded contours is simply a dot joining exercise between the easternmost French samples.  That is the real reason why it seems there is a stranded area of higher L21 in SE France.  Its because its the only part of eastern France sampled (its the Myres sample).  So, again, I think this gives a slightly misleading impression.  I think L21 probably decreases in a contoured kind of way from NW France towards south Germany. 

Yes unfortunately Myres didn't exactly go to town on France, however there does seem to be quite a hot spot in the SE corner and I seem to remember the R-L21 project has had trouble picking up people in the middle of France as well.

The real problem if I recall correctly was getting anyone to test in the middle of France.  I recall any sample was hard in large chunks of France and strangely the area where it was less difficult also happened to be the high L21 area.  However, I would consider that both Myres, the new study and the project have all not really sampled the landlocked part of France.  
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« Reply #6 on: August 24, 2011, 07:39:15 PM »

I only just glanced at that paper, so forgive me if I am mistaken, but didn't they exclude the Anatolian haplotypes because most of them were L11-? That seems to me a mistake if that is in fact what they did.

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« Reply #7 on: August 24, 2011, 08:11:37 PM »

The real problem if I recall correctly was getting anyone to test in the middle of France.  I recall any sample was hard in large chunks of France and strangely the area where it was less difficult also happened to be the high L21 area.  However, I would consider that both Myres, the new study and the project have all not really sampled the landlocked part of France.  

Depopulation of rural France is a bit of a headache in that country, could this also be our problem?
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« Reply #8 on: August 25, 2011, 04:47:58 PM »

Quote from: authun link=topic=10031.msg124118#msg124118 [i
"While recent
In addition, correct me if I am wrong, from the few samples of ancient yDNA that we have, none from the LBK have been found to be R1b or R1a. Those that are found appear to be later.

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authun


That is correct.
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authun
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« Reply #9 on: August 25, 2011, 06:14:36 PM »

I only just glanced at that paper, so forgive me if I am mistaken, but didn't they exclude the Anatolian haplotypes because most of them were L11-? That seems to me a mistake if that is in fact what they did.

They explain the rationale behind excluding Balaresque's Anatolian samples in the supplementary information.

http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp1.pdf

A
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« Reply #10 on: August 25, 2011, 06:40:26 PM »

I only just glanced at that paper, so forgive me if I am mistaken, but didn't they exclude the Anatolian haplotypes because most of them were L11-? That seems to me a mistake if that is in fact what they did.

They explain the rationale behind excluding Balaresque's Anatolian samples in the supplementary information.

http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp1.pdf

A

That seems like a mistake to me. The title of the paper indicates that the subject was R-M269. The Anatolian R-M269 samples were all M269+. They excluded them because most of them were S127- (L11-), but if the paper were addressing just R-L11/S127, then it should have indicated that was the case.

Obviously R-M269xS127 would be ancestral to R-S127. By excluding the Anatolian samples, Busby, et al, were rigging the game, at least in part, since every study I have ever seen has found Anatolian R-M269 diversity to be greater than European R-M269 diversity.
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« Reply #11 on: August 25, 2011, 06:52:57 PM »

I would like to comment on the frequency maps that appear in supplementary information section of the Busby, et al, paper. Notice the different shading scale applied to L21 (S145)? Why is that? It creates confusion and the illusion that, compared with S21 (U106) and S28 (U152), L21 is isolated in extreme NW Europe.

I noticed that, according to Busby, the northern tip of Jutland has about 9-16% L21.

Or am I seeing things?

Time to resurrect Faux's Cimbri theory!
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« Reply #12 on: August 25, 2011, 07:13:28 PM »

Here's another comment on the frequency maps in the supplementary info section.

Notice that S145 (L21) and S28 (U152), both mere subclades of P312, are compared with ALL of S21 (U106)? Why aren't a couple of S21's subclades shown instead? Or why isn't ALL of P312 compared with S21?

Why do I get the feeling that L21 has gotten the shaft in these last couple of reports?
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« Reply #13 on: August 26, 2011, 12:13:16 AM »

Here's another comment on the frequency maps in the supplementary info section.

Notice that S145 (L21) and S28 (U152), both mere subclades of P312, are compared with ALL of S21 (U106)? Why aren't a couple of S21's subclades shown instead? Or why isn't ALL of P312 compared with S21?

Why do I get the feeling that L21 has gotten the shaft in these last couple of reports?
Hey, I'm just happy that L21 specific data is provided... no longer just R-P312(S116*). This is a couple of papers in a row now.
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Maliclavelli
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« Reply #14 on: August 26, 2011, 03:19:58 AM »

(Sent to Dienekes, but I don’t know if he will publish it)

The great mathematician and a chemist as well Anatole Klyosov insists, but his calculations are completely wrong because he doesn’t take in consideration that there are mutations around the modal and a convergence to the modal as time passes, except for those clades that fix mutations far from the modal itself.
His theory doesn’t explain that R-L51 arose in Italy (a few minutes ago Janzen on Rootsweb: “This distribution would favour an origin of R-L51 in Eastern or Southern Europe, possibly in Italy”, what I am saying from many years) and why the 3 most important subclades were born: R-U152 in Central-North Italy, R-L21 in the British Isles and R-U106 in North Europe.
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« Reply #15 on: August 26, 2011, 04:36:45 AM »

The real problem if I recall correctly was getting anyone to test in the middle of France.  I recall any sample was hard in large chunks of France and strangely the area where it was less difficult also happened to be the high L21 area.  However, I would consider that both Myres, the new study and the project have all not really sampled the landlocked part of France.  

Depopulation of rural France is a bit of a headache in that country, could this also be our problem?

I remember visiting beautiful deserted villages in the Massif Central in the 80s. I understand some are now populated by visitors from the Netherlands and UK. Many of the great cafes of Paris are owned and run by exiles from Auvergne.
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« Reply #16 on: August 26, 2011, 04:50:28 AM »

Maju has an interesting analysis of the paper.

http://forwhattheywereweare.blogspot.com/2011/08/r1b-m269-debate-new-paper-vindicates-my.html

"Another serious criticism they make about Balaresque is the use of an Y-search dataset representing Ireland (surprisingly amateurish!) When compared with actual samples (Y-search relies on the good will of online reporters) the low diversity that Balaresque found for Ireland vanished".

Fro Busby Notes:

"Testing the variance calculations from the Irish population Balaresque et al used haplotypes downloaded from the online Ysearch database (http://www.ysearch.org) which is a repository for genetic genealogists to upload and compare haplotypes (P. Balaresque pers. comm.). We note, however, that 17-STR haplotypes, including the 9 STRs used in Balaresque et al’s analysis, are available for 681 Irish R-M269 derived individuals in Moore et al (3), which is, in fact, the study which Balaresque et al use to estimate R-M269 frequency in Ireland. A subset of the Moore et al samples were re-analysed in the current study for SNPs downstream of R-M269, and the original haplotype data are used here to calculate variance. To test if the Ysearch haplotypes were representative of the Irish R-M269 in Moore et al, we independently re-sampled the Moore et al dataset 10,000 times, selecting sub-samples of 75 haplotypes from which we estimated the variance using the same 9 STRs used in the Balaresque et al paper. The median
variance of these 10,000 repetitions was 0.354 with a 95% CI of (0.285-0.432). The lowest variance value out of the 10,000 samples was 0.242, which is still higher than the figure observed in the Balaresque et al Ysearch sample (0.208). We therefore believe our estimate of Irish R-M269 variance to be a more robust representation of the true variance than that estimated by Balaresque et al."

The L21/S145 map is quite interesting and clearly shows an Atlantic Facade and Isles cluster for L21.

The BBC has weighed in on the debate with a very clear analysis of the paper.

http://www.bbc.co.uk/news/mobile/science-environment-14630012

"A new study deals a blow to the idea that most European men are descended from farmers who migrated from the Near East 5,000-10,000 years ago.
The findings challenge previous research showing that the genetic signature of the farmers displaced that of Europe's indigenous hunters.
The latest research leans towards the idea that most of Europe's males trace a line of descent to stone-age hunters.
But the authors say more work is needed to answer this question."
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« Reply #17 on: August 26, 2011, 08:15:03 AM »

Here's another comment on the frequency maps in the supplementary info section.

Notice that S145 (L21) and S28 (U152), both mere subclades of P312, are compared with ALL of S21 (U106)? Why aren't a couple of S21's subclades shown instead? Or why isn't ALL of P312 compared with S21?

Why do I get the feeling that L21 has gotten the shaft in these last couple of reports?
Hey, I'm just happy that L21 specific data is provided... no longer just R-P312(S116*). This is a couple of papers in a row now.

Not me. Sloppy, badly done, inaccurate attention is worse than being ignored, in my opinion.

Myres did a crappy job (on L21, anyway), and this paper simply extends and perpetuates that legacy.
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« Reply #18 on: August 26, 2011, 09:00:20 AM »

. . .

The BBC has weighed in on the debate with a very clear analysis of the paper.

http://www.bbc.co.uk/news/mobile/science-environment-14630012

"A new study deals a blow to the idea that most European men are descended from farmers who migrated from the Near East 5,000-10,000 years ago.
The findings challenge previous research showing that the genetic signature of the farmers displaced that of Europe's indigenous hunters.
The latest research leans towards the idea that most of Europe's males trace a line of descent to stone-age hunters.
But the authors say more work is needed to answer this question."


Oh, brother! Not the "stone age hunters" bit again.

Busby, et al, conveniently discard the Anatolian M269 haplotypes, and nobody notices?

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« Reply #19 on: August 26, 2011, 09:06:28 AM »

Here's another comment on the frequency maps in the supplementary info section.

Notice that S145 (L21) and S28 (U152), both mere subclades of P312, are compared with ALL of S21 (U106)? Why aren't a couple of S21's subclades shown instead? Or why isn't ALL of P312 compared with S21?

Why do I get the feeling that L21 has gotten the shaft in these last couple of reports?
Hey, I'm just happy that L21 specific data is provided... no longer just R-P312(S116*). This is a couple of papers in a row now.

Not me. Sloppy, badly done, inaccurate attention is worse than being ignored, in my opinion.

Myres did a crappy job (on L21, anyway), and this paper simply extends and perpetuates that legacy.

One thing I will say about the "S145" map, if it is based on accurate information, I think it tends to show that L21 is by far the single most frequent y haplogroup in the British Isles, including England. Just compare it to the maps of "S21" and "S28".

Just the same, I am aggravated at the shading scale used for the L21 map. It helps us to see the L21 clines in the British Isles but practically obliterates the continental ones. I think all three maps should have had the same shading scales for ease of comparison.
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« Reply #20 on: August 26, 2011, 09:57:26 AM »

Sorry to post so many unanswered messages in a row, but, unless I missed something in reading back through Busby, it looks like they really just worked on R-S127 and not on R-M269. Am I wrong?

That seems a major shortcoming of the paper to me. S127 is pretty plainly descended from R-M269xS127. The maps in Busby of the distributions of R-M269 as a whole, then of R-M269xS127 and R-S127 show the progression from east to west. Leaving out R-M269xS127 from the calculations merely shows that S127 expanded rapidly once it hit central and western Europe. Had R-M269xS127 haplotypes been included, the increased STR diversity everybody sees in the East, declining as one moves west and north, would have been evident once again.

Everyone is missing this point and acting as if Busby is a major blow to the idea that M269 is fairly recent and arrived in Europe from the East.
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« Reply #21 on: August 26, 2011, 10:05:21 AM »

Just the same, I am aggravated at the shading scale used for the L21 map. It helps us to see the L21 clines in the British Isles but practically obliterates the continental ones. I think all three maps should have had the same shading scales for ease of comparison.

The maps cannot have the same shade, because the highest percentage of L21 is 79% and U152 has 43% and U106 a little lower. Anyway these maps show clearly where we have now the highest diffusion, which doesn't mean automatically the origin, but probably it isn't so far. Like I have said here and in other forums:
Central-North Italy for R-U152
The British Isles for R-L21
Central-North Europe for R-U106.

If we add that it is clear for everybody now that R-L51 was born in Italy (like many upstream haplogroups), probably it shouldn't be difficult to reconstruct the whole history.
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« Reply #22 on: August 26, 2011, 10:14:57 AM »

Sorry to post so many unanswered messages in a row, but, unless I missed something in reading back through Busby, it looks like they really just worked on R-S127 and not on R-M269. Am I wrong?

That seems a major shortcoming of the paper to me. S127 is pretty plainly descended from R-M269xS127. The maps in Busby of the distributions of R-M269 as a whole, then of R-M269xS127 and R-S127 show the progression from east to west. Leaving out R-M269xS127 from the calculations merely shows that S127 expanded rapidly once it hit central and western Europe. Had R-M269xS127 haplotypes been included, the increased STR diversity everybody sees in the East, declining as one moves west and north, would have been evident once again.

Everyone is missing this point and acting as if Busby is a major blow to the idea that M269 is fairly recent and arrived in Europe from the East.


Here's another thing . . . ahem . . .

If Busby resurrects the old "stone age hunter M269" malarkey, as some seem to think, why didn't they find evidence of STR differentiation out of the old Cantabrian Ice Age Refuge?

I mean, wow, if M269 was in the Cantabrian Refuge (or in Italy . . . cough) back during the last Ice Age, one would think that was plenty of time for STR mutations to tell the story.

But the Busby paper doesn't announce any such startling revelation. Instead, it leaves out the R-M269xS127 haplotypes, effectively rigging the game, and works on just the central and western European S127 (L11) stuff. Not only that, they failed to look at the widespread distribution of P312 (S116), instead choosing two of its subclades (L21 and U152) and concluding that their distributions are "markedly localized".
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« Reply #23 on: August 26, 2011, 10:20:30 AM »

. . .

The BBC has weighed in on the debate with a very clear analysis of the paper.

http://www.bbc.co.uk/news/mobile/science-environment-14630012

"A new study deals a blow to the idea that most European men are descended from farmers who migrated from the Near East 5,000-10,000 years ago.
The findings challenge previous research showing that the genetic signature of the farmers displaced that of Europe's indigenous hunters.
The latest research leans towards the idea that most of Europe's males trace a line of descent to stone-age hunters.
But the authors say more work is needed to answer this question."


Oh, brother! Not the "stone age hunters" bit again.

Busby, et al, conveniently discard the Anatolian M269 haplotypes, and nobody notices?

I don't see where Busby indicates an Europen Paleothic or Mesolithic origin for R-M269. I think this is just the BBC media spinning things a bit to liven up an old debate.

I noticed both the adjustments that Busby did to the Irish data, the removal of Anatolian data, and the lack of Near East data.

Even though they broke out subclades in some of their reporting, in the real analysis of diversity they lumped some things together.

If you read Supplement 2 you can see they go through various "re-analysis" stages. They start out showing and east to west client where diversity is highest in the east but after a couple of turns to the crank that got it slightly tilted the other way.
« Last Edit: August 26, 2011, 10:21:23 AM by Mikewww » Logged

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« Reply #24 on: August 26, 2011, 10:21:59 AM »

Just the same, I am aggravated at the shading scale used for the L21 map. It helps us to see the L21 clines in the British Isles but practically obliterates the continental ones. I think all three maps should have had the same shading scales for ease of comparison.

The maps cannot have the same shade, because the highest percentage of L21 is 79% and U152 has 43% and U106 a little lower. Anyway these maps show clearly where we have now the highest diffusion, which doesn't mean automatically the origin, but probably it isn't so far. Like I have said here and in other forums:
Central-North Italy for R-U152
The British Isles for R-L21
Central-North Europe for R-U106.

If we add that it is clear for everybody now that R-L51 was born in Italy (like many upstream haplogroups), probably it shouldn't be difficult to reconstruct the whole history.

They could have the same shading scale, but they didn't.

L21 did not originate in the British Isles, just as R-M269 did not originate in Spain, even though Spain has a much higher frequency of M269 than western Asia.

I am surprised at you. It is very much a beginner's error to think that a y haplogroup must have originated in the place where it is most frequent today.

I know of no one but you, Gioiello, who thinks M269 spent the Last Ice Age in Italy. You keep on insisting on it and producing what amounts to individual anecdotes to support it, but I haven't seen any real evidence for it.
« Last Edit: August 26, 2011, 12:06:05 PM by rms2 » Logged

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