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Author Topic: off the wall thought - both R1a and R1b spread through Corded Ware??  (Read 1467 times)
Mike Walsh
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« Reply #25 on: April 23, 2012, 08:38:05 AM »

By more to the story I mean this -  None of these paper was comprehensive, but if you look at long haplotypes and deep SNP testing you can see that R-L23* in SW Asia/Caucasus does have a significant step up in STR diversity over R-L11(S127).  There is the "paragroup" issue so nothing is conclusive... but keep in mind where home for R1 probably is, and brother R1a.  Even though it is outdated and the timeframes may be wrong, it is important to read Spencer Wells' paper -  "The Eurasian Heartland: A continental perspective on Y-chromosome diversity."
www.pnas.org/content/98/18/10244.long

Wikipedia, yes not the best, has R1* listed from a study including Iran.  I don't think any has been found in Europe?  

The SNP M173 marks R1. From the Wells study...
Quote from: Spencer Wells
Y chromosome microsatellites indicate that Central Asian (Pakistani) populations are the most diverse in Eurasia. The consistency of the biallelic and microsatellite results suggests that Central Asian populations are among the oldest on the continent. This pattern of high diversity is consistent with an early settlement of Central Asia by anatomically modern humans, perhaps 40,000–50,000 years ago (see below), followed by subsequent migrations into Europe, America, and India, dispersing M45-, M173-, and M17-derived lineages.

If we put pins on the map we get one for R1 over in Central Asia and then one for downstream R-L11 subclades over in Western Europe.   Some where and some time along the way there had to be a move from point A (R1) to point B (R-L11 downstream.)    My opinion is that R-L23 definitely was somewhere in the east but after that I don't where the geographic breaks in the phylogenetic trail via L51, L11 through P312&U106 are.  I just think there is a clue that P312 and U106 are about the same age and their interclade ancestor is also about the same age.
« Last Edit: April 23, 2012, 09:04:14 AM by Mikewww » Logged

R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
Mike Walsh
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« Reply #26 on: April 23, 2012, 08:47:02 AM »

The only thing I don't like about Busby is their logic flaws that, to me, are so obvious it brings up questions of the intent.

How obvious are the logic flaws of the Busby et al(2011) paper? I ask this because they aren't that obvious to me, perhaps you could expand on that?

There is a bit more to the story. One of the logic flaws that Busby had was the relegation in STR diversity calculations to R-L11(S127).

Not quite, refer to figure-2b and you will clearly see that they calculated the bootstrap variance for RxS127 or R1bx(L11), and it clearly shows that the highest variance occurs in Central Europe.  

Are you talking about the Supplementary Information where they refer to Figure S2 panel B?

Look at a little closer and read the notes.
Quote from: Busby
Figure S2: Reanalysis of Balaresque et al R-M269 Samples. The first panel, A, shows the significant correlation between longitude and mean (observed) variance found in their
original dataset.The second panel, B, shows the same data, including the Irish group but without the three Turkish (TK) populations. Removing the Turkish samples can be justified on the grounds that, in our dataset c.90% of Anatolian samples were un-derived at SNP S127,
whereas the majority of individuals in European populations were derived at this SNP
I don't like how Busby jacked around with removing data from the samples.  They didn't like Barlaresque's conclusions based on R-M269 (panel A) which shows Anatole (Turkey) with significantly higher variance.  They re-sample and deselect from Irish and then just plain throw away Turkey to get the outcomes they are looking for.

Busby calls it a "Reanalysis of Balaresque" but my gosh, reanalysis is poor term to use for this travesty. Let's go over to the Busby thread that Razyn pointed out if you want to debate Busby.

...  now you've got me going (EDIT: deleted)
« Last Edit: April 23, 2012, 09:16:31 AM by Mikewww » Logged

R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
JeanL
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« Reply #27 on: April 23, 2012, 09:13:58 AM »

Are you talking about the Supplementary Information where they refer to Figure S2 panel B?

No, I’m referring to figure-2b in the main study, the one that shows a map with the frequency of RxS127 on the left and a graph of bootstrap variance relative to a normalized longitude on the right.

I don't like how Busby jacked around with removing data from the samples.  They didn't like Barlaresque's conclusions based on R-M269 which shows Anatole (Turkey) with significantly higher variance.  They re-sample and deselect from Irish and then just plain throw away Turkey to get the outcomes they are looking for.

Let's go over to the Busby thread that Razyn pointed out if you want to debate Busby.

Well it wasn’t quite like that with the Irish, here is their explanation as to what they did:
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).
« Last Edit: April 23, 2012, 09:14:54 AM by JeanL » Logged
Maliclavelli
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« Reply #28 on: April 23, 2012, 11:07:43 AM »

I looked at your age estimate for Z253 Mike, and I know it is consistent with your other work, but as I've noted before, I have a great deal of difficulty reconciling the haplotype I have z5hg3 (Ysearch) with your age estimates of this subclade.  I know I don't fit the mold, but I have been tested positive for this SNP.
Of course if you are R-Z253 and your values don’t fit with the clade Mikewww has individuated for this subclade, it does mean that that clade was one of the clades of R-Z253 and yours is the witness of the fact that Z253 is more ancient than Mikewww thinks. The subclades of R-L21 have a casual order in the haplotree and we don’t know which is more ancient. Your values are the classical “outlier”, and the outliers are the witness of the mutations that a haplogroup has had beyond the lines extinct and the clades mutated around the modal. Every subclade like every haplogroup has a modal which is a fiction, till the outliers like yours demolish it.
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Maliclavelli


YDNA: R-S12460


MtDNA: K1a1b1e

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