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Author Topic: The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269 (B  (Read 9210 times)
rms2
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« Reply #25 on: August 26, 2011, 10:24:11 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 . . .


If you look at what I quoted, you will see I was responding to Heber's posting of an article from the BBC which mentioned the "stone-age hunters" thing.
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« Reply #26 on: August 26, 2011, 10:46:55 AM »

As I read it, the logic for Busby et alii to let out the Turkish M269 (xS127) is because M269 in Europe is overwhelmingly S-127, so it can´t be directly derived from the Turkish xS127 population. the logic is.
S-127 is dominant in Western Europe
S-127 alone (excluding xS127) shows no higher diversity in Turkey than in Western Europe
Then, S-127 did not originate in Turkey, so it wasn´t direclty related to a Neolithic expansion.
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« Reply #27 on: August 26, 2011, 10:47:12 AM »

.... 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.
This is kind of like the "Revenge of the Nerds" . (No offense, nerds are smart!) They've been building up frustration and now have a counter-argument to wield. I think I have this right, but one blogger said "STRs suck". LOL.  Oh, well.

I think this is an opportunity for growth. I have seen what Tim Janzen and Dienekes have seen and Busby tried to demonstrate. STR variance is not a pure straight line correlation with time/generations and some STR's may misbehave. This is no reason to throw the baby out with the bath water, though.  

On another forum, a sharp fellow who goes by Myth69 has tried to calculate the length of time that individual STR's show linear variance growth. This is a step in the right direction. Ironically, Myth69's analysis shows that three 3 of the 10 STRs that Busby used across the board in his diversity calculations are not useful for more than about 3000 years and a 4th about 5000 years. The Neolith advances were about 7000 years ago so 4 of Busby's 10 markers should have been thrown out for his diversity calculations, by his own argument. Apparently, Busby's analysis of these 4 STRs was different than Myth69's.

Here is where the growth comes in. Folks like Ken Nordtvedt have maintained that these STR non-linearity issues are insignificant and report that as a result of their simulations. I think this is true in some circumstances, probably most, but I have to agree with Janzen and Dienekes that sometimes the issues make a difference. It would take someone like Ken, but hopefully, we'll see a new round of TMRCA estimators that try to account for STR mutation / time linearity issues beyond just throwing the multi-copy markers out.
« Last Edit: August 26, 2011, 10:48:38 AM by Mikewww » Logged

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« Reply #28 on: August 26, 2011, 10:50:22 AM »

As I read it, the logic for Busby et alii to let out the Turkish M269 (xS127) is because M269 in Europe is overwhelmingly S-127, so it can´t be directly derived from the Turkish xS127 population. the logic is.
S-127 is dominant in Western Europe
S-127 alone (excluding xS127) shows no higher diversity in Turkey than in Western Europe
Then, S-127 did not originate in Turkey, so it wasn´t direclty related to a Neolithic expansion.
A bit of circular reasoning! eh?

This is what "re-analysis" can do for you.
« Last Edit: August 26, 2011, 10:50:52 AM by Mikewww » Logged

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« Reply #29 on: August 26, 2011, 10:56:04 AM »

...  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.
I have to say I have the same disappointment. This reminds me a bit of political argument. Throw around enough stats about this or that: 1) 15 STRs when you only use 10 across the board, or 2) or subclade maps but the key diversity cacluations lump and divides a bit haphazardly ... and through the convolution claim victory.

I also see the classic strawman logical fallacy of extension. Pick out an opponent's argument where there are issues that are not fully resolved and band on that argument (STR variance in this case) and ignore the other pro-arguments that may not fit your counter. Also don't provide an alternative (oops, I almost said "budget") at all. LOL.

I guess, I shouldn't be disappointed. Why would academics be immune from politics?
« Last Edit: August 26, 2011, 11:00:14 AM by Mikewww » Logged

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« Reply #30 on: August 26, 2011, 11:17:49 AM »

As I read it, the logic for Busby et alii to let out the Turkish M269 (xS127) is because M269 in Europe is overwhelmingly S-127, so it can´t be directly derived from the Turkish xS127 population. the logic is.
S-127 is dominant in Western Europe
S-127 alone (excluding xS127) shows no higher diversity in Turkey than in Western Europe
Then, S-127 did not originate in Turkey, so it wasn´t direclty related to a Neolithic expansion.
A bit of circular reasoning! eh?

This is what "re-analysis" can do for you.
Yes, however they go out of the circle in their conclusions by stating that
1) S-127 originated in Europe before the expansion of Neolithic
2) Then, their subhaplogroups are linked to the Neolithic expansion within Europe At the subhaplogroup
level, then, R-M269 is split into geographically
localized pockets with individual R-M269 subhaplogroups
dominating, suggesting that the frequency
of R-M269 across Europe could be related to the
growth of multiple, geographically specific sub-lineages
that differ in different parts of Europe.
A recent analysis of radiocarbon dates of Neolithic sites
across Europe [46] reveals that the spread of the Neolithic
was by no means constant, and that several ‘centres of
renewed expansion’ are visible across Europe, representing
areas of colonization

So, Busby et alii scenario would be
1) M-269 arrives into Europe before Neolithic
2) S_127 is born from this pre-Neolithic population in Europe
3) THe expansion of S-127 subhaplogroups is linked to the Neolithic second wave.
4) So, by default, the first wave of Neolithic population in Europe was no R-M269 related, and din´t make a significant contribution to the present population of Western Europe
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rms2
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« Reply #31 on: August 26, 2011, 11:58:48 AM »

If S127 (L11) was born in Europe, he was the offspring of an M269xS127 father, so leaving out M269xS127 haplotypes is clearly a mistake, since the point, it seems to me, is to track the origin of European S127 (although the paper's deceptive title mentions the "cautionary tale of . . . M269", not S127). It's a little like knowing who someone's father is and where he was born and then attempting to trace the family tree without including him.

Personally, I think it quite likely that the expansion of M269 and its descendant S127 (L11 - Man, I hate having to switch to these "S" equivalents!) is connected to the spread of the Indo-Europeans rather than to the Neolithic farmers, if the two are separate.

I suspect no modern scientist is going to grab the M269-is-Indo-European ball and run with it. That would be too big a political hot potato, given Europe's recent history and the current dominance of political correctness.
« Last Edit: August 26, 2011, 12:00:26 PM by rms2 » Logged

Maliclavelli
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« Reply #32 on: August 26, 2011, 12:07:44 PM »

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.
I thank IALEM for having said by words that everybody can understand what is the real meaning of this paper.
To Rich I would say that what the paper says now is what I have said in other words, simple like those of IALEM (if my bad English aids me), in these last 5 years. He knows that I don’t consider him like those who banned me from Rootsweb and “forums-dna” and if I am here that is due to him. But now I say to him that, if he hasn’t understood the paper, he can go an read my thousands of letters of these last years.
1)   I haven’t said that R1b1b2 is Palaeolithic. I have linked it to the Italian Younger Dryas, which is a little before the Mesolithic.
2)   R1b1b2 is predominant in West Asia but probably was also in Europe and in Italy in the same times.
3)   It isn’t said that they are the same. They could be different, and now we are finding some SNPs of the Eastern R1b1b2 and it isn’t said that Eastern R1b1b2 hasn’t come from Europe.
4)   What I have said is that the most ancient R1b1b2 was born in Italy and is the Italian YCAII=17-23, that R-L51 was born in Italy (now also Janzen thinks that) and that the SNP L150, present ancestral only in the Italian Romitti, was a sign of this. Then Italy has the pathway from R-M207 (2 Tuscans out 50 in 1000 Genomes Project, the other 3 Puertoricans but no one amongst Spaniards) to at least R-L51. After Italians went out but also 1 of the 3 most diffused subclades of R1b1b2, R-U152, was born here.
5)   The expansion happened with agriculture, demic to South Balkans and perhaps South Italy, but cultural from previous hunter-gatherers and foragers. The Grotta delle Arene Candide in Liguria was one of the point from where the seafarers diffused the agriculture to West, South France and Iberia.

I have said much more but for now it is enough. Lastly I would say that the only Italian scholars who replied to my letters are here: Cristian Capelli and Gianmarco Ferri. But it is from Fulvio Cruciani that I am waiting for the definite proofs of all that.
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Maliclavelli


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« Reply #33 on: August 26, 2011, 12:19:15 PM »

The point of the article is the "Peopling of Europe", so they are leaving out those M-269(xS127) haplotypes because they considere them irrelevant and misleading to that aim.
They consider the possibility of a post Neolithic arrival of M269 and the subsequent explosion of S-127 derived haplogroups in Europe, but they find it unlikely because they would have found the descendants of the Neolthic population expansion.
In that regard it is odd they cite Bocquet and de Miguel study on Neolithic demography. Mari Paz de Miguel (I know her personally) has stressed the 2 cicles in Neolithic population expansion, because it could fit equally a postNeolithic arrival with second wave of Neolithic population expansion
« Last Edit: August 26, 2011, 12:20:12 PM by IALEM » Logged

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« Reply #34 on: August 26, 2011, 12:19:52 PM »

I don't think this current paper says much of anything that is of much use. Its authors' decision to exclude the M269xS127 haplotypes renders it impotent, in my opinion. I realize I am no scientist, but it is not hard to see that M269xS127 is ancestral to S127.

L150 and L51 are so new that I don't think any major studies have included them yet. Gioiello's mention of them is precisely what I meant about individual anecdotes rather than real evidence. This individual Italian or that one who is R-L51* is not proof of anything, any more than finding a y-haplogroup A Englishman proves the Garden of Eden was somewhere near Manchester.
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« Reply #35 on: August 26, 2011, 12:35:17 PM »

You speak of descent, and I think having demonstrated that from an Italian R1b1b2 was born an R1b1b2a (like Romitti), an R-L150+ (like me), an R-L51, overwhelming in italy, and so on. This till R-S127 which generated R-U106 and R-P312. And this is an European history, above all Italian I think at least in its beginning but also in one the most diffused R-subclades like R-U152. What more?

I have written in this blog also about R-M335, R1b1b1 and others. Also on R1a (M420), overwhelming European and Italian, disappointing a Nationalist Indian who kept silent after.
« Last Edit: August 26, 2011, 12:36:50 PM by Maliclavelli » Logged

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« Reply #36 on: August 26, 2011, 01:52:52 PM »

Note how shy are these Italian scholars who speak to the Lords of the World: “R-S21 has a frequency of 44 per cent in Friesland, and R-S28 reaches 25 per cent in the Alps” (page 7).

Italy has the 5 highest lines of frequency (from 23 to 43 per cent) that no other country has and the top, from 40 to 43 per cent, is reached in Piedmont and Central Italy.
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« Reply #37 on: August 26, 2011, 03:03:28 PM »

I haven't read the whole study, but from what I can gather from the discussion is..

1) The subclade selection is spotty and not as inclusive as what is in the amateur projects.
2) STR variance does not accumulate in a linear fashion and is therefore unreliable.

Number 1 would seem to make number 2 a questionable conclusion, imo.  Also, does this change the fact that numerous observances have the
R1b snp phylogeny running east to west.  The str variance is more or less showing the same pattern by subclade as well.  Number 2 may very well be accurate, but I think the most recent observable pattern is east to west thus reflecting something like the Neolithic or Bronze age.
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« Reply #38 on: August 26, 2011, 03:36:56 PM »

So, Busby et alii scenario would be
1) M-269 arrives into Europe before Neolithic
2) S_127 is born from this pre-Neolithic population in Europe
3) THe expansion of S-127 subhaplogroups is linked to the Neolithic second wave.
4) So, by default, the first wave of Neolithic population in Europe was no R-M269 related, and din´t make a significant contribution to the present population of Western Europe

Not quite, Busby acknowledges that it may be more recent than the start of the neolithic:

"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."

He doesn't think it is likely as, if this was the case, its dominance in europe could only be explained by a replacement of the early neolithic farmers. However, he doesn't appear to be aware of the population crash at the end of the LBK reported by Shennan and Edinborough. The crash which affected several parts of northern europe reduced the populations to their low mesolithic levels and remained at these low levels for nearly 1000 years.

best
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« Last Edit: August 26, 2011, 03:38:09 PM by authun » Logged
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« Reply #39 on: August 26, 2011, 03:54:45 PM »


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!

I think one of the most interesting things in the Myres' data for Denmark is that all R1b subclades for which they tested: U106(XU198), U198, L21, U152 and P312* have their highest frequencies in northern Denmark- presumably northern Jutland. I can't believe this is coincidental, but I don't know what conclusion to draw from it. I doubt very much the resurrection of Faux's Cimbri theory is the solution. However there might be some connection with the map recently mentioned by Authun which shows the heaviest concentration of Bronze Age sword (Griffzungen) finds in northwest Jutland.
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« Reply #40 on: August 26, 2011, 04:01:26 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?

It is a constant irritation to me that every study of R1b in Europe compares all of U106 (occasionally with the exception of U198) with individual P312 subclades such as L21, U152, etc., which is obviously comparing apples with oranges. How informative would it be to compare all of P312 with U198, L48, L271 etc.?

Although I know I will never live long enough to see peace in the Middle East, I am now beginning to doubt that I will ever see in my lifetime a reliable academic study on R1b in Europe.
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« Reply #41 on: August 26, 2011, 04:56:26 PM »

rms2

"This individual Italian or that one who is R-L51* is not proof of anything, any more than finding a y-haplogroup A Englishman proves the Garden of Eden was somewhere near Manchester."


http://freepages.genealogy.rootsweb.ancestry.com/~nolenancestry/nolan_DNA_contact_info.html

* Garden of Eden setting equals (Central Asia) Almaty, Kazakhstan: The Fatherland of Apples

"An earlier traveler through the region, one Victor Vitkovich, proclaimed these naturally occurring groves to be “a marvelous garden where apples and pears look down on you from the trees and beg to be eaten.”


http://s1230.photobucket.com/albums/ee494/glennnolen/Tien%20Shan%20with%20Lake%20Issyk-kul/

Gates or Mountain Passes to the Garden of Eden: Tien Shan with Lake Issyk-Kul

Glenn Allen Nolen
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« Reply #42 on: August 26, 2011, 05:31:30 PM »

. . .

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?



Here's a quote from the BBC article:

Furthermore, they suggest that some of the markers on the Y chromosome are less reliable than others for estimating the ages of genetic lineages. On these grounds, they argue that current analytical tools are unsuitable for dating the expansion of R-M269.

If they're saying that the markers( or some) are unreliaable,how can they then decide that most European men have ancestry dating back to hunter gatherers? Another question, have  they found any  aR1b in European hunter gatherer populations?

Another quote from the BBC article:

Co-author Dr Jim Wilson from the University of Edinburgh explained: "Estimating a date at which an ancestral lineage originated is an interesting application of genetics, but unfortunately it is beset with difficulties."

The more I look at this, the more I'm convinced it's pseudo-science!
« Last Edit: August 26, 2011, 06:06:02 PM by Bren123 » Logged

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« Reply #43 on: August 26, 2011, 06:04:45 PM »

I think one of the most interesting things in the Myres' data for Denmark is that all R1b subclades for which they tested: U106(XU198), U198, L21, U152 and P312* have their highest frequencies in northern Denmark- presumably northern Jutland.

The sampling locations are given in the map Fig S1 in the supplementary information,
http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp1.pdf

The supplementary data is given in Excel format at:
http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp2.xls

The Hg frequency for northern Denmark is 9.5%, as opposed to 4.1% and 5.3% for Southeast Denmark and West Denmark resp. Also, the Norwegian sampling location is 8%, nearly twice that of southern Jutland.

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« Reply #44 on: August 26, 2011, 06:38:26 PM »


Here's a quote from the BBC article:

Furthermore, they suggest that some of the markers on the Y chromosome are less reliable than others for estimating the ages of genetic lineages. On these grounds, they argue that current analytical tools are unsuitable for dating the expansion of R-M269.
I've been saying let's not throw the baby out with the bath water. First, I'm not convinced that Busby et al's perspective on STR variance correlation with time is as dire as they say. Almost everybody from Myres, Balaresque, Wells/National Genographic to FTDNA uses STR variance. Second, I disagree with Busby's implication that "more" data is not better. That defies the law of large numbers in statistics.

I agree using junk data is not useful. I agree STR variance correlation with time is a legitimate issue and more work needs to be done. Busby seemed to be taking a step by evaluating the period of time individual STRs are correlated linearly with time. Supposedly, they used their approach to pick 10 STRs to evaluate. I think they, like most, are constrained by the available data.

Other people are also addressing this. There is a fellow who goes by Mth69 on another forum who seems to be pursuing this in a reasonable way. He posted his analysis on how long individual STRs are useful.

Quote from: Mth69
Based on the above mentioned, one can roughly estimate the timeframe for each locus where saturation effects are relatively insignificant. The idea is that up/down ratio will not change very much due to repeat number changes that can occur. Variance formulas do not care about specific ratio of up and down mutations, but require that the ratio is approximately constant.
Here is the link where he posted his results:  http://beforepresent.dyndns.info/misc/loci.xls

I added this comment
Quote from: Mikewww
As an aside, I find it a bit ironic that the recent Busby study on R-M269 cites the problems with STR variance and a linear association with time, but then they use the following on their STR list that they used across the board.

389i, 391, 439 which would be applicable no more than 3300 years. 389b which is applicable less than 5000 years. Four of Busby's ten may not be applicable for studying a period as long ago as the initial Neolithic advances.

Mth69's analysis is not published so not worth for formal argument purposes. Anectdotally, I definitely think 439 is a poor choice for Busby's inclusion.
« Last Edit: August 26, 2011, 06:46:24 PM by Mikewww » Logged

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« Reply #45 on: August 26, 2011, 06:49:52 PM »

Interesting that the sample from SE France was nearly 20% L21+ (S145+), while U152 (S28) was about 13%. P312xL21,U152 was 29% there, but that would be divided up among the subclades not tested for this paper and would probably not all be P312*.
« Last Edit: August 26, 2011, 06:50:52 PM by rms2 » Logged

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« Reply #46 on: August 26, 2011, 07:24:58 PM »

Interesting that the sample from SE France was nearly 20% L21+ (S145+), while U152 (S28) was about 13%. P312xL21,U152 was 29% there, but that would be divided up among the subclades not tested for this paper and would probably not all be P312*.

Here are some interesting facts from the Busby paper relative to L21, facts that are really hardly if at all discernible from the L21 (S145) map in the supplementary info section.

Rennes in Bretagne had a frequency of 40% L21xM222 (not surprising).

Poitiers had 14%.

Marseille was 11% L21xM222.

Lille, up in the northeast near the Belgian border, had 10% L21xM222 (that one did surprise me - it is higher than I thought it would be).

Paris had 10% L21xM222.

Chalon-sur-Saône, in the east, near Dijon, had 8% L21xM222.

These frequencies are percentages of the total y-dna. That means L21 is actually huge all over France. I mean, 8% of the total y-dna in an area is pretty significant, let alone 10% and up.

If the shading scale on Busby's L21 map had been like those of its U106 and U152 maps, the true L21 picture in France would have been more readily apparent.
« Last Edit: August 26, 2011, 07:25:20 PM by rms2 » Logged

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« Reply #47 on: August 26, 2011, 09:54:13 PM »

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?

I’m sorry to break it to you, but I think that you are in fact wrong. Busby et al(2011) did do an analysis of the STR variance of R1b-M269xS127, it is shown in Figure-2b)



http://rspb.royalsocietypublishing.org/content/early/2011/08/18/rspb.2011.1044/F2.large.jpg

They did not exclude the Anatolian R1b-M269 from that initial analysis (Figure-2 BTW doesn’t show the Anatolian samples taken by Balaresque et al(2009), but those collected by Myres et al(2010) and new ones from this study), in fact they did not exclude the Anatolian R1b-M269 at all*(I’ll explain what exactly happened). This is what Busby et al(2011) says about it exactly.
 
Quote from: Busby et al(2011)
We next calculated STR diversity for each population for the whole R-M269 lineage, and for the R-S127 and R-M269(xS127) sub-haplogroups, and investigated the relationship between average STR variance and longitude and latitude in exactly the same fashion as Balaresque. We provide estimates of uncertainty for these values by bootstrapping over individuals, and report the median of the observed variance values and its 95 per cent CI (figure 2). We normalized latitude and longitude, and performed a linear regression between these values and the median microsatellite variance for the three R-M269 sub-haplogroups. We found no correlation with latitude (data not shown) and, contrary to Balaresque, we did not find any significant correlation between longitude and variance for any haplogroup.

So in fact your confusion comes from an additional analysis done on Balaresque et al(2009) that was performed in the supplementary section, where they did test for variance excluding the Turkish haplogroups, and including them. Figure-2b shows that the highest variance for R1b-M269xS127 is not in Anatolia, and there is no East-West gradient, as the highest variance appears in Central Europe, rather than Anatolia. What differentiates Busby et al(2011) from Balaresque et al(2009) is that Busby et al(2011) tested for downstream SNPs(i.e. S127/L11, S-116, U-106, etc) and took the variance of R1b-M269xS127, and R1b-S127 separately; unlike Balaresque et al(2009) that did so without discriminating between the downstream clades and the basal clades. In any case, Figure-2a which is very similar to Balaresque et al(2009) where the total variance of R-M269 is taken regardless of subclades reveals that there is no such thing as an East-West pattern, and the Eastern-most variance appears in par with the Western-most, with the peak happening somewhere in the center(Coinciding with  the peak of variance in Figure-2b which also happens in Central Europe). 

Quote from: Busby et al(2011)
The Balaresque dataset presents genotype data only to the resolution of SNP R-M269. Our results show that the vast majority of R-M269 samples in Anatolia, approximately 90 per cent, belong to the R-M269(xS127) sub-haplogroup. Removing these Turkish populations from the Balaresque data and repeating the regression removes the significant correlation (R2 = 0.23, p = 0.09; details in the electronic supplementary material and figure S2). These populations are therefore intrinsic to the significant correlation.

So what they did was to test the Balaresque et al(2009) dataset by removing the Turkish populations, which is shown in Figure 2-B of the supplementary info pdf file. This removal showed that once the Anatolian samples are removed there is no longer an East-West gradient in terms of variance. Then recalculated they changed the Irish sample provided in Balaresque et al(2009) for one they gathered, and displayed both the Irish population and the Anatolian(Turkish) populations on the same figure-2D of the supplementary info pdf, and it turns out the Irish have a higher diversity than all of the Turkish population.  This is their procedure:

Quote from: Busby et al(2011)

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. However, we note that the positive correlation between longitude and variance is still present after removing only the Irish and retaining the Balaresque et al Turkish populations. If we replace the variance calculated by Balaresque et al with that calculated from our repetitions, then the correlation is no longer significant, independent of whether or not we remove the Turkish samples (Figure S2).

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.[/size]

There is no major shortcoming, as I already showed above they did include R1b-M269xS127 variance calculation, and there is no East-West gradient, instead the highest diversity appears to happen in Europe(Possibly Central Europe, or Western Balkans). Again your whole argument here is based on the fact that you misunderstood the paper, not that the paper has any shortcomings.

« Last Edit: August 28, 2011, 10:09:45 PM by JeanL » Logged
GoldenHind
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« Reply #48 on: August 27, 2011, 12:28:39 AM »

I think one of the most interesting things in the Myres' data for Denmark is that all R1b subclades for which they tested: U106(XU198), U198, L21, U152 and P312* have their highest frequencies in northern Denmark- presumably northern Jutland.

The sampling locations are given in the map Fig S1 in the supplementary information,
http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp1.pdf

The supplementary data is given in Excel format at:
http://rspb.royalsocietypublishing.org/content/suppl/2011/08/18/rspb.2011.1044.DC1/rspb20111044supp2.xls

The Hg frequency for northern Denmark is 9.5%, as opposed to 4.1% and 5.3% for Southeast Denmark and West Denmark resp. Also, the Norwegian sampling location is 8%, nearly twice that of southern Jutland.

cheers
authun

The data from Denmark is just a repeat of the Myres' data, but that from Norway is new to this paper. Thanks very much for pointing that out. I find it so interesting that I'll start a new thread on it. Is there anyway of determining the size of their Norway sample?
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Maliclavelli
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« Reply #49 on: August 27, 2011, 01:21:26 AM »

There is no major shortcoming, as I already showed above they did include R1b-M269xS127 variance calculation, and there is no East-West gradient, instead the highest diversity appears to happen in Europe(Possibly Central Europe, or Western Balkans). Again your whole argument here is based on the fact that you misunderstood the paper, not that the paper has any shortcomings.

I appreciated your posting, whoever you are, but I'd make you note that Central Europe and Western Balkans are nearby Italy. If there is smoke, there is fire, and they are simply the regions of superimposition of different migrations of R1b1b2 from elsewhere, but the fire, I think, is in Italy. My studies about R-L51, published on many forums, demonstrated that its frequency crashes down to East, out of the Italian border.
« Last Edit: August 27, 2011, 01:23:30 AM by Maliclavelli » Logged

Maliclavelli


YDNA: R-S12460


MtDNA: K1a1b1e

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