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Author Topic: New paper: R1b1b2 (R-M269) spread from Near East in Neolithic  (Read 18705 times)
argiedude
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« Reply #150 on: March 28, 2010, 02:18:09 PM »

Italy's ht35 variance should be slightly higher than what the maps show, because a significant percentage of the Italian samples that I predicted as ht35 are in fact ht15 with 393=12. This only applies to Italy, there's no such issue in southeast Europe or Turkey.

About 20% of North Italian R1b1b2 with 393=12 are probably ht15. I made a quick test of how this would affect North Italy's ht35 variance by calculating the variance of North Italian R1b1b2 with 393=12, and then adding a number of R1b1b2 samples with 393=13, to simulate ht15 samples, so that the new set of samples would presumably have 40% ht15. I did this several times with random sets of R1b1b2 samples with 393=13 and observed that this caused the variance of North Italy to drop between 0,01 and 0,03, from an initial value of 0,30. This is reasonable, since North Italy's ht15 samples have a low variance of 0,22; they're hidden presence amongst the 393=12 samples is dragging down the variance calculations for ht35. I'd presume if we could calculate North Italy's ht35 variance using SNP-tested ht35 samples only, the estimate would be higher by 0,01 to 0,03, or about 0,32. I did the same test after removing the 392=14/389B=15 samples, and the increase was the same, though this time it started off from an initial estimate of 0,28. Thus, all things considered, between the elimination of the 392=14/389B=15 cluster that was increasing the results and the elimination of the hidden ht15 samples in North Italy that are dragging down its results, North Italy will possibly have a notably higher variance than Turkey, by a margin of 0,05 (0,30 versus 0,25).

In Sicily and south Italy, as much as 10% of the R1b1b2 samples with 393=12 are ht15. So their estimates could also be slightly higher, by just 0,01.
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Maliclavelli
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« Reply #151 on: March 29, 2010, 05:22:52 AM »

Dear Argiedude,
I have criticized many times this way to make clusters. What does it mean a “Jewish cluster” M269+L23- with DYS391=10, DYS426=11, DYS392=14 opposing to a cluster from Italy to Caucasus? And less a “Jewish cluster” M269+ L23+ which is the same with a cluster from Iberia to India except for DYS385b=15? I think having demonstrated many times that the “Jewish clusters” are due to a founder effect and that are very recent, then they have no autonomy.
The same for the Albanian cluster with DYS393=13 and DYS385b=11: you too have said that it is very recent. These clusters say only something about the origin of the cluster itself and nothing about the origin of the haplogroup. We can think that R-L23- with DYS 426=11 doesn’t go back to the origin of the haplogroup, but to an individual who had the rare mutation from 12 to 11, which may have been happened in any time between the origin of this particular cluster, also in recent times. Anyway only one individual survived with DYS426=11 and everybody is a descendant of him. Then this cluster was born in a precise place and not everywhere from Italy to Caucasus. And as you perhaps know I think in Italy.
The same is for R-L51+ with  DYS426=13. Everybody in this cluster descends from an individual who had the mutation of DYS426 from 12 to 13, and also this happened probably in the Alpine Region, when R was coming out from Italy to Central Europe, passing to East, as your map of R-L51- is demonstrating: the exit from Italy happened first from the Rhaetian Region to Austria and South Germany. In fact I have found (and signaled) some probable Italian R-L51+s in the Rhaetian Region. It is meaningful what you have said: “And since Italy and southeast Europe will have slightly higher ht35 variance than Turkey or the Levant”.

« Last Edit: March 29, 2010, 05:24:55 AM by Maliclavelli » Logged

Maliclavelli


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vineviz
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« Reply #152 on: March 29, 2010, 05:08:58 PM »

Italy's ht35 variance should be slightly higher than what the maps show, because a significant percentage of the Italian samples that I predicted as ht35 are in fact ht15 with 393=12. This only applies to Italy, there's no such issue in southeast Europe or Turkey.
Good lord, how much torture can this data withstand?  Hasn't it "confessed" enough?

Throw out this data, double-count out that data, redefine categories for this region but not that region, sample for one thing and call it another?  That's a recipe for doctoring the experiment to suit your preferred conclusion.
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argiedude
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« Reply #153 on: March 29, 2010, 08:21:45 PM »

Maliclavelli, I also think that the Jewish clusters are recent, but it's good to have them in the table because there are many Jewish samples of ht35 in public databases, and this can cause confusion. If there were thousands of Gypsy samples in public databases and they also had their own R1b clusters I would've included them, too, despite being obvious that the clusters must have been acquired only a few centuries ago.

Vineviz, I did only 2 things with the data. I chose the R1b1b2 samples that had 393=12, which mostly indicates an ht35 sample, and then I eliminated the samples that belonged to 2 obvious clusters, the Albanian 385=11/11 and the 392=14/389B=15 cluster. These 2 clades are clearly haplogroups who will eventually be properly identified with their own SNP mutation. By removing them, we can get a better estimate of the variance of the basal lineage, ht35* so to speak. As an example, the Arabian region seems to be split evenly between "normal" ht35 and the 392=14 cluster. Calculating the variance of all these samples together gives a result of 0,30. Calculating each cluster separately gives 0,20 for either. Same with the Irish M222+ cluster. By including this cluster in the estimate of ht15 variance, Ireland gets a high value, very different from its island neighbors, which makes it seem almost like the origin of ht15. But removing this cluster causes Ireland's variance to drop to 0,22 like its neighbors in Britain.
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OConnor
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« Reply #154 on: March 30, 2010, 11:35:08 PM »

I have 393=12 and I am L21+ and R-L159.2+

The model for L21 is 393=13

Is there a model value for all R's at 393 ?

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Maliclavelli
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« Reply #155 on: March 31, 2010, 12:54:42 AM »

My theory is that a marker mutates around a value with someone going to the tangent (plus and minus).
Then there isn't a modal, but a beginning's value for each cluster and haplogroup. You, as R-L21, derive from DYS393=13 and when a ancestor of yours had the mutation to 12, he began a new clade (yours), then probably 12 will be your modal and of your descendants for many time, being a slow mutating marker.
I am R1b1b2a-L23+/L150+ and I am DYS393=12 too, but probably my 12, derived from a previous 13, is the same from many thousands of years before your 12.
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Maliclavelli


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rms2
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« Reply #156 on: March 31, 2010, 09:24:33 AM »

I have 393=12 and I am L21+ and R-L159.2+

The model for L21 is 393=13

Is there a model value for all R's at 393 ?



Probably 393=13, because that is the most common value in R1b and R1a, but for R2 it looks like it's 393=14, and there are even many who are 393=15.

Of course, for P310- (what we used to call HT35) guys it appears to be 393=12.
« Last Edit: March 31, 2010, 09:32:41 AM by rms2 » Logged

vtilroe
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« Reply #157 on: March 31, 2010, 10:14:48 PM »

Italy's ht35 variance should be slightly higher than what the maps show, because a significant percentage of the Italian samples that I predicted as ht35 are in fact ht15 with 393=12. This only applies to Italy, there's no such issue in southeast Europe or Turkey.

About 20% of North Italian R1b1b2 with 393=12 are probably ht15. I made a quick test of how this would affect North Italy's ht35 variance by calculating the variance of North Italian R1b1b2 with 393=12, and then adding a number of R1b1b2 samples with 393=13, to simulate ht15 samples, so that the new set of samples would presumably have 40% ht15. I did this several times with random sets of R1b1b2 samples with 393=13 and observed that this caused the variance of North Italy to drop between 0,01 and 0,03, from an initial value of 0,30. This is reasonable, since North Italy's ht15 samples have a low variance of 0,22; they're hidden presence amongst the 393=12 samples is dragging down the variance calculations for ht35. I'd presume if we could calculate North Italy's ht35 variance using SNP-tested ht35 samples only, the estimate would be higher by 0,01 to 0,03, or about 0,32. I did the same test after removing the 392=14/389B=15 samples, and the increase was the same, though this time it started off from an initial estimate of 0,28. Thus, all things considered, between the elimination of the 392=14/389B=15 cluster that was increasing the results and the elimination of the hidden ht15 samples in North Italy that are dragging down its results, North Italy will possibly have a notably higher variance than Turkey, by a margin of 0,05 (0,30 versus 0,25).

In Sicily and south Italy, as much as 10% of the R1b1b2 samples with 393=12 are ht15. So their estimates could also be slightly higher, by just 0,01.
For the love of mike... and this is exactly why I can't take your charts at face value.  Why even mention ht15 and ht35?
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argiedude
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« Reply #158 on: March 31, 2010, 10:45:21 PM »

Italy's ht35 variance should be slightly higher than what the maps show, because a significant percentage of the Italian samples that I predicted as ht35 are in fact ht15 with 393=12. This only applies to Italy, there's no such issue in southeast Europe or Turkey.

About 20% of North Italian R1b1b2 with 393=12 are probably ht15. I made a quick test of how this would affect North Italy's ht35 variance by calculating the variance of North Italian R1b1b2 with 393=12, and then adding a number of R1b1b2 samples with 393=13, to simulate ht15 samples, so that the new set of samples would presumably have 40% ht15. I did this several times with random sets of R1b1b2 samples with 393=13 and observed that this caused the variance of North Italy to drop between 0,01 and 0,03, from an initial value of 0,30. This is reasonable, since North Italy's ht15 samples have a low variance of 0,22; they're hidden presence amongst the 393=12 samples is dragging down the variance calculations for ht35. I'd presume if we could calculate North Italy's ht35 variance using SNP-tested ht35 samples only, the estimate would be higher by 0,01 to 0,03, or about 0,32. I did the same test after removing the 392=14/389B=15 samples, and the increase was the same, though this time it started off from an initial estimate of 0,28. Thus, all things considered, between the elimination of the 392=14/389B=15 cluster that was increasing the results and the elimination of the hidden ht15 samples in North Italy that are dragging down its results, North Italy will possibly have a notably higher variance than Turkey, by a margin of 0,05 (0,30 versus 0,25).

In Sicily and south Italy, as much as 10% of the R1b1b2 samples with 393=12 are ht15. So their estimates could also be slightly higher, by just 0,01.
For the love of mike... and this is exactly why I can't take your charts at face value.  Why even mention ht15 and ht35?

What I said about Italy was a sidenote which I didn't include in the map because it's speculation. It's very reasonable, since Italy has a lot of ht15 samples, while southeast Europe and Anatolia don't, so I mentioned the possibility that its variance might be slightly higher than what appears in the map.

-------------------------------

I've made the final update to the ht35 variance map. After discovering that there's a major clade of ht35 defined by 392=14 & 389B=15, I recalculated all the figures excluding this cluster. This still isn't good enough, because there are still 2 clades with different modal haplotypes: M269* and L23*. To tell them apart one needs samples that have tested DYS426 (the former has 426=11), but that would reduce my eligible samples to almost nothing, so that problem remains.

http://i88.photobucket.com/albums/k178/argiedude/R1b1b2variance-ht35excludeallcluste.gif



This map is very different from the ht15 map which had an easily discernable, obvious pattern. I haven't drawn any contour lines as in previous maps because of this. I'd say the map could justify just as much the point of view of those who think ht35 came out of Anatolia as those who don't.

The main haplogroups of ht15 have nearly identical modal haplotypes, so an estimate of each haplogroup individually is very close to an estimate of all of them together. But ht35's 2 major clades have notable differences in their modal haplotypes, to the point that the result depended on the proportions of each clade in the tested population. For example, in southern Arabia I found 12 samples of ht35. Their variance was 0,30, a high value. But 6 samples belonged to the "normal" ht35 haplotype, and 6 to the 392=14 & 389B=15 haplotype. Calculating each set separately, they both had a variance of just 0,17, a very low value.
« Last Edit: March 31, 2010, 10:56:30 PM by argiedude » Logged

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Maliclavelli
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« Reply #159 on: April 02, 2010, 01:49:15 AM »

Argiedude writes on Rootsweb:

"L23+ L150- is apparently the result of cross-amplification of a distinct (previously unmapped) piece of DNA from someplace other than the Y"

Any truth to this?


Where are you quoting from?
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Maliclavelli


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argiedude
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« Reply #160 on: April 02, 2010, 02:10:08 PM »

Posting removed in it's entirety.

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« Last Edit: April 02, 2010, 04:42:45 PM by Terry Barton » Logged

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« Reply #161 on: April 02, 2010, 03:07:19 PM »

DNAForums was nothing but one argument after another for me. Glad I don’t even read the thing anymore.
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« Reply #162 on: April 02, 2010, 03:39:45 PM »

By the way, you might want to edit your previous post throwing out the offensive language. Otherwise, you will probably be banished from WFN. I was threatened with banishment for a lot less.    
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vineviz
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« Reply #163 on: April 02, 2010, 03:42:35 PM »

By the way, I said something funny to him, after he insulted me for the 8th or 10th time in the last 2 weeks:

Yeah, that's hilarious.  The sophisticated wit just slays me.

First, I didn't insult anyone.  I just pointed out a flawed analysis.

Second, that diatribe has so many factual errors I wouldn't know where to start correcting them.  Fortunately, the abusive language will probably get the post deleted so there is no need.
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Maliclavelli
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« Reply #164 on: April 02, 2010, 04:18:28 PM »

Not only posts are deleted. In my case also the persons, but certainly Ideas will survive. Some years ago I was alone, now we are many and you are always the same.
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« Reply #165 on: April 02, 2010, 10:00:05 PM »

Very few postings have ever been deleted from this forum - other than spam.   I would prefer that it was none - but a little decorum is necessary.

We've banned even fewer members for inappropriate postings.

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« Reply #166 on: April 26, 2011, 03:46:43 AM »

Wow, hopefully everybody's temperament has calmed down since the last posting of this thread. Starting from the beginning of the thread I really thought it was going to be interesting and then it just slowly eroded into a bloodbath of quips and attacks.
Ouch!

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