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ADW_1981
11-27-2013, 04:44 PM
I'd like to donate some money to discovering early branching of R1b1-L278*. In fact, this would apply to downstream M73 branches and confirming M73+ individuals. If I have some spare money over Christmas and the new year, this would be better spent than elsewhere since it is something that interests me, rather than determining yet another SNP below P312+.

I did have a question regarding the current draft R1b tree. I cannot find any individual who is V88+ but has tested L389, and shows as L389-. I may be missing a piece of logic but shouldn't we solidify this to confirm the placement of L389? In any event I suppose that's why it's a draft tree.

I do have a concern regarding the FTDNA interface. It appears like the prediction tool is erroneously showing green "confirmation" for some of these predictions. I am a little skeptical that some SNPs like M269 were even tested in some cases. Can anyone here refute or agree with my comment? If this is the case, I have lost faith in some of this a la carte testing.

In any case, feedback or PM would be appreciated.
Thanks

Rathna
11-27-2013, 04:57 PM
ADW_1981, there are three persons tested V88+ and L388/L389-: they are on the "R1b1 FTDNA Project", tested for Geno 2.0: Kasdin, Vass and Alvarez.

Joe B
11-27-2013, 05:23 PM
I'd like to donate some money to discovering early branching of R1b1-L278*. In fact, this would apply to downstream M73 branches and confirming M73+ individuals. If I have some spare money over Christmas and the new year, this would be better spent than elsewhere since it is something that interests me, rather than determining yet another SNP below P312+.

I did have a question regarding the current draft R1b tree. I cannot find any individual who is V88+ but has tested L389, and shows as L389-. I may be missing a piece of logic but shouldn't we solidify this to confirm the placement of L389? In any event I suppose that's why it's a draft tree.


I do have a concern regarding the FTDNA interface. It appears like the prediction tool is erroneously showing green "confirmation" for some of these predictions. I am a little skeptical that some SNPs like M269 were even tested in some cases. Can anyone here refute or agree with my comment? If this is the case, I have lost faith in some of this a la carte testing.

In any case, feedback or PM would be appreciated.
Thanks

ADW_1981,
That is a nice offer.
Looking at the R1b1(xP297) DNA Project SNP (http://www.familytreedna.com/public/r1b1asterisk/default.aspx?section=ysnp) page, it seems like the L389+/- split is occurring at the L25 level. I think FTDNA does not show the negative SNP results for Geno 2.0 so those L389- results are not shown for the R-V88 folks.

N26020 R1b1 R-P25 L389+ Geno 2.0
267597 R1b1 R-P25 L389-? Geno 2.0
N93357 R1b1 R-P25 L389- Sanger sequencing

Page 37 of Chris Morley's Experimental Y-SNP Phylogenies (http://ytree.morleydna.com/experimental-phylogeny) shows a predicted placement on the tree.
Mike's Early R1b Phylogenetic Tree (https://dl.dropboxusercontent.com/u/17907527/R1b_Descendency_Tree.jpg) has L389 in a cloud.
This is an interesting part of the tree.

Rathna
11-27-2013, 05:28 PM
ADW_1981,
That is a nice offer.
Looking at the R1b1(xP297) DNA Project SNP page, it seems like the L389+/- split is occurring at the L25 level. I think FTDNA does not show the negative SNP results for Geno 2.0 so those L389- results are not shown for the R-V88 folks.

N26020 R1b1 R-P25 L389+
267597 R1b1 R-P25 L389-?
N93357 R1b1 R-P25 L389-

Page 37 of Chris Morley's Experimental Y-SNP Phylogenies (http://ytree.morleydna.com/experimental-phylogeny) shows a predicted placement on the tree.
Mike's Early R1b Phylogenetic Tree (https://dl.dropboxusercontent.com/u/17907527/R1b_Descendency_Tree.jpg) has L389 in a cloud.
This is an interesting part of the tree.

Of course Geno 2.0 doesn't show the negative results, but Vass is on the "Itai Perez spreadsheet" and you can see there his L388/L389-.

GailT
11-27-2013, 05:30 PM
I do have a concern regarding the FTDNA interface. It appears like the prediction tool is erroneously showing green "confirmation" for some of these predictions. I am a little skeptical that some SNPs like M269 were even tested in some cases. Can anyone here refute or agree with my comment?

Here are the SNP results my paternal line, L2+, L1-, L135-, L196-, L20-, L209-, U106-

As far as I know, they did not test or cofirm any of the upstream SNPs. The only confirmed positive SNP was L2. So I think you will need Big Y or FGC to check for the possibility of back mutations on any upstream SNPs. But even with those test, there can be uncertainty in some of the SNP calls for next generation sequencing. So Thomas Krahn's new company is the best option for anyone who wants certain confirmation of a specific SNP.

ADW_1981
11-27-2013, 05:33 PM
ADW_1981, there are three persons tested V88+ and L388/L389-: they are on the "R1b1 FTDNA Project", tested for Geno 2.0: Kasdin, Vass and Alvarez.

Where in the Geno2.0 does it say this though? What is the SNP called? It can't be labeled as L388 or L389.

Rathna
11-27-2013, 05:37 PM
I have denounced from many years that many M269+ of FTDNA (signed in green) are actually from their markers values something else: see Marchesi, before Mangino, DeMao was accepted after many letters of mine and now has his Geno 2.0, not published by the "R1b1 FTDNA project" but whose I have the data and now is also on the "Itai Perez spreadsheet" and so on.

Rathna
11-27-2013, 05:40 PM
Where in the Geno2.0 does it say this though? What is the SNP called? It can't be labeled as L388 or L389.

Geno 2.0 tests L388 and L389 which are on the same plane and if you don't find them like + it means that they are -. If you suppose that there have been some no-calls, go to the "Itai Perez spreadsheet" and you can see.

ADW_1981
11-27-2013, 05:42 PM
Geno 2.0 tests L388 and L389 which are on the same plane and if you don't find them like + it means that they are -. If you suppose that there have been some no-calls, go to the "Itai Perez spreadsheet" and you can see.
Thanks, I did not test Geno 2.0 and wasn't aware of these additional repositories. Come to think of it, it makes sense that we would not display the negatives....

smal
11-27-2013, 05:50 PM
It is better to test for L389 the kits of Cluster A3 and A4, because they were not really tested for L389.

ADW_1981
11-27-2013, 05:59 PM
Geno 2.0 tests L388 and L389 which are on the same plane and if you don't find them like + it means that they are -. If you suppose that there have been some no-calls, go to the "Itai Perez spreadsheet" and you can see.

Looking at that spreadsheet now, it's amazing. So that puts the nail in the coffin for my previous question...

I guess from my perspective I would want to fund a solution which would test L389 and V88 at minimum on some of these guys who are already hooked up with FTDNA. Possibly throw in the M73 speculatives as well. I'd also consider looking at third party data, samples from the research projects that are in mostly untapped regions of the world. If anyone has connections to those people, I would looking at funding the transfer and liaison of that information too.

Joe B
11-27-2013, 06:40 PM
Looking at that spreadsheet now, it's amazing. So that puts the nail in the coffin for my previous question...

I guess from my perspective I would want to fund a solution which would test L389 and V88 at minimum on some of these guys who are already hooked up with FTDNA. Possibly throw in the M73 speculatives as well. I'd also consider looking at third party data, samples from the research projects that are in mostly untapped regions of the world. If anyone has connections to those people, I would looking at funding the transfer and liaison of that information too.
This study comes up all the time with V88 and may have some leads for researchers and projects.
Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages (http://www.nature.com/ejhg/journal/v18/n7/abs/ejhg2009231a.html) Fulvio Cruciani et al. with correspondence directed to Professor R Scozzari, Dipartimento di Genetica e Biologia Molecolare, Sapienza UniversitÓ di Roma. Address, email ect. is all there.

GTC
11-27-2013, 09:32 PM
Which particular interface do you mean?

[quote]It appears like the prediction tool is erroneously showing green "confirmation" for some of these predictions. I am a little skeptical that some SNPs like M269 were even tested in some cases. Can anyone here refute or agree with my comment? If this is the case, I have lost faith in some of this a la carte testing.


My understanding is that green denotes an actual SNP confirmation, as opposed to red for a prediction based on STRs.

ADW_1981
11-28-2013, 04:25 PM
Which particular interface do you mean?



My understanding is that green denotes an actual SNP confirmation, as opposed to red for a prediction based on STRs.

Yes that is how I understand it as well. However, some recent R1b samples which have entered some of the projects have been declared M269+ and highlighted as green and are questionable based on the haplotype IMHO. It's happened fairly regularly, rather than a one time thing..which is why I've brought it up. Haddad, Mansour, Blalb...all are Near Eastern or N.Africa and have been declared M269+ even though they have atypical haplotypes. It's just strange that's all

Rathna
11-28-2013, 04:38 PM
Yes that is how I understand it as well. However, some recent R1b samples which have entered some of the projects have been declared M269+ and highlighted as green and are questionable based on the haplotype IMHO. It's happened fairly regularly, rather than a one time thing..which is why I've brought it up. Haddad, Mansour, Blalb...all are Near Eastern or N.Africa and have been declared M269+ even though they have atypical haplotypes. It's just strange that's all

Blalb was put amongst the V88+ after a letter of mine, even though it is always signed M269 in green. Haddad is perhaps a R1a*, but we are waiting for a SNP test.
It went better for me for "Buono Di Bello" in the "Italy FTDNA Project" I predicted R1b1* after his 12 markers, practically sure for me after his 37 ones, and, tested M343+ and M269-, was put by Richard Rocca amongst the R1b1*. But I am always waiting a test on Mangino, Marchesi and others, but I am sure, so that I founded upon them my theories.

GTC
11-28-2013, 10:35 PM
Yes that is how I understand it as well. However, some recent R1b samples which have entered some of the projects have been declared M269+ and highlighted as green and are questionable based on the haplotype IMHO. It's happened fairly regularly, rather than a one time thing..which is why I've brought it up. Haddad, Mansour, Blalb...all are Near Eastern or N.Africa and have been declared M269+ even though they have atypical haplotypes. It's just strange that's all

Has anybody asked FTDNA exactly how they go about haplogroup confirmation? I have always thought that if they declared M269 in green it's because they had actually tested for it.

Joe B
11-29-2013, 04:33 AM
Has anybody asked FTDNA exactly how they go about haplogroup confirmation? I have always thought that if they declared M269 in green it's because they had actually tested for it.
A suspected R1b-V88+ was backboned about a month ago. They used two SNPs. M343+, M269-
This is what FTDNA has and the SNP list looks very dated.
What is a Y-chromosome (Y-DNA) Backbone SNP test? What is SNP Assurance? (http://www.familytreedna.com/faq/answers.aspx?id=8#515)

GTC
11-29-2013, 06:37 AM
A suspected R1b-V88+ was backboned about a month ago. They used two SNPs. M343+, M269-
This is what FTDNA has and the SNP list looks very dated.
What is a Y-chromosome (Y-DNA) Backbone SNP test? What is SNP Assurance? (http://www.familytreedna.com/faq/answers.aspx?id=8#515)

Yes, I'm familiar with backbone testing, which is in essence a free deep clade test. Deep Clade -- no longer on their customer purchase list since the introduction of Geno 2 -- is where they go searching down the paths of the haplotree for your haplogroup by testing for various SNPs until they find the "deepest" one in your clade, that is, deepest according to the outdated FTDNA version of the haplotree.

In cases where they have confirmed M269, my assumption has been that they have performed a targeted SNP test for M269 based on the haplotype.

So, is my assumption correct?

If I am correct in my assumption, then those who have a green M269 will have actually tested positive for that SNP and, unless (shock! horror!) M269 appears in another part of the tree, one can state categorically that those people are R-M269.

ADW_1981
11-29-2013, 06:25 PM
I have a hard time believing these haplotypes are M269+. I might be cherry picking the first 12 markers, but you rarely see M269+ which looks like this. All have been declared M269

13 22 15 11 14-15 12 12 12 14 13 30
13 25 15 10 13-15 12 12 12 14 13 32
13 23 14 11 12-12 12 12 12 13 13 29

It just seems very strange that's all...

GTC
11-29-2013, 10:54 PM
I have a hard time believing these haplotypes are M269+. I might be cherry picking the first 12 markers, but you rarely see M269+ which looks like this. All have been declared M269

13 22 15 11 14-15 12 12 12 14 13 30
13 25 15 10 13-15 12 12 12 14 13 32
13 23 14 11 12-12 12 12 12 13 13 29

It just seems very strange that's all...

Yes, but as we know only further SNP testing on those kits will reveal the truth.

GTC
11-29-2013, 10:57 PM
I have a hard time believing these haplotypes are M269+. I might be cherry picking the first 12 markers, but you rarely see M269+ which looks like this. All have been declared M269

13 22 15 11 14-15 12 12 12 14 13 30
13 25 15 10 13-15 12 12 12 14 13 32
13 23 14 11 12-12 12 12 12 13 13 29

It just seems very strange that's all...

Yes, but as we know only further SNP testing on those kits will reveal the truth.

According to reports from the FTDNA Annual Conference, there is a suggestion that some form of Deep Clade test may reappear.

And Thomas Krahn's new business venture may provide opportunities to do selective further testing on a budget.