J2a3/4* (J-L26*): new SNPs to test: L250.2, L251.2, L1064

Any discussions about this haplogroup

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PostPosted: Mon Jun 04, 2012 7:12 pm
Everyone not in one of the subclades of J2a3/4 (J-L26) can be excited: there are 3 new SNP's that should be tested mainly by "cluster H" and some nearby samples: L250.2, L251.2, L1064. Bonnie (or maybe me) will give shortly more indications. If you can't wait and know you will be a candidate for these SNP's do the following steps:
Fund research of oldest Y-Haplogroup A00 - DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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PostPosted: Mon Jun 04, 2012 8:41 pm
Yes indeed, Chris, this is an exciting new development, and your cluster is right at the center of it. Thomas told me that these SNPs were discovered in some of its members when his ytree or ymap system showed more positive results for L250 and L251 than they thought there should be. They searched and found that Chris and two others were positive for those two SNPs, and also for a new one, L1064. These SNPs were inadvertently covered by tests that had been done in those samples for the nearby L229.

Because these test results were just uncovered by that indirect route, they don't show up on the personal pages of those participants, and they'll have to order these SNPs to have the results "officially" reported on their personal Haplotree pages. Sorry about that, it's FTDNA policy, not mine!

J2a3* "Cluster H" that Chris belongs to includes a bunch of members from Saudi Arabia, especially from the Najd region. They can be seen as a cluster in the J2 Arab project, for example.

L250 and L251 were originally found in E-V13, together with L252. The J-L26+ samples don't have L252, but they have L1064 instead. All of these SNPs are located close together, and are probably derived from an ancient recombination event of some kind, which happened separately at different times in each haplogroup.

If you look at the draft Ytree, Thomas has now added a new branch: "Approx. hg: J-L26 L250.2, L251.2, L1064"! :)

Now, it turns out that L250 and L251 aren't limited to Cluster H. We had a most curious case of an 11/12 match between a member of J2a3i-L198+, N104541 from Iran, with kit M6882, from Iraq. Strangely enough, M6882 turned out to be L198-. But he's L250.2+ & L251.2+! Not only that, but L1064-(negative)! I would still like to re-check the STRs of N104541, and we urgently need to upgrade him to 67 markers, but we haven't been able to contact him yet. If anyone can get in touch with him, it would be a big help.

Because of that case, we know that L1064 is found in only a part of the L250+ lineages. So we need to have people tested for L250.2 in a broader range of J2a3*/ J2a4*, as well as their being tested for L1064 so we can find out what the limits of that subclade will be.

I'll post some specific recommendations, and will place some people in a separate category in the J project. This doesn't mean they're necessarily "predicted" to be L250+, but we do need to cast a wide net to find the full range of L250.. It would be wise to test L251 as well, if possible, just in case, but it's probably found together with L250.

I've been waiting -- it seems like -- forever, for more helpful structure to be found within J2a3*! Let's take full advantage of this opportunity.

Bonnie
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PostPosted: Mon Jun 04, 2012 9:57 pm
Forgot to mention -- we know L250 isn't just equivalent to L26, or anything like that. As I understand it, it has only been found in those four samples so far, out of all who've been tested for L229, as part of their Deep Clade test in J2. I've also been told that my father, in J2a3i, is negative for it.

Bonnie
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PostPosted: Tue Jun 05, 2012 9:58 am
Rootsy wrote:L250 and L251 were originally found in E-V13, together with L252. The J-L26+ samples don't have L252, but they have L1064 instead. All of these SNPs are located close together, and are probably derived from an ancient recombination event of some kind, which happened separately at different times in each haplogroup.

I was trying to find something more about L250, L251 and L1064. By ISOGG SNP List (L1064 not in list):
There is no rs# (RefSNP ID) so it is not possible to Match rs# to a SNP. 23andMe Y-tree stops at E1b1b1a2 (ISOGG E1b1b1a1b, i4000247 / V13, i4000252 / V36) so probably there is no possibility to get any information out of 23andMe raw data.

Rootsy wrote:If you look at the draft Ytree, Thomas has now added a new branch: "Approx. hg: J-L26 L250.2, L251.2, L1064"! :)

Yes. Here is the link: ytree.ftdna.com Draft J2a4 (ISOGG: J2a3) L26, L27 (look at the bottom). Current infos from there (to log the count of derived/tested):
Name: L250.2
Type: snp
Description:
Source: other
Position: ChrY:6813387..6813387 (+ strand)
Length: 1
ISOGG_haplogroup: not listed
Mutation: A to G
YCC_haplogroup: Approx. hg: J-L26
allele_anc: A
allele_der: G
comments: Found in a hg J-L26 person.
count_derived: 4
count_tested: 349
primer_f: L15-f
primer_r: L15-r
primary_id: 41866
gbrowse_dbid: ymap:database

Name: L251.2
Type: snp
Description:
Source: other
Position: ChrY:6813389..6813389 (+ strand)
Length: 1
ISOGG_haplogroup: not listed
Mutation: A to G
YCC_haplogroup: Approx. hg: J-L26
allele_anc: A
allele_der: G
comments: Found in a hg J-L26 person.
count_derived: 3
count_tested: 360
primer_f: L15-f
primer_r: L15-r
primary_id: 41869
gbrowse_dbid: ymap:database

Name: L1064
Type: snp
Description:
Source: other
Position: ChrY:6813384..6813384 (+ strand)
Length: 1
ISOGG_haplogroup: not listed
Mutation: T to C
YCC_haplogroup: Approx. hg: J-L26
allele_anc: T
allele_der: C
comments: Found in a J-L26 person
count_derived: 3
count_tested: 359
primer_f: L15L23L76L79L130L142L147L192_F
primer_r: L15L23L76L79L130L142L147L192_R
primary_id: 41865
gbrowse_dbid: ymap:database
Fund research of oldest Y-Haplogroup A00 - DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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PostPosted: Tue Jun 05, 2012 5:27 pm
Hi Chris,

I've written to Thomas asking for clarification about the 4 people who are derived for L250.2, vs. the 3 people who are derived for L251.2 and L1064. I'll let you know what he says about that and any other news.

These SNPs will only appear in the ISOGG SNP Index with the .2 addition when we have fully illuminated where they belong in the phylogeny, and added them to the tree as a new clade.

Bonnie

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PostPosted: Tue Jun 05, 2012 7:08 pm
So, sometimes Thomas reports unofficial SNP results ;)
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PostPosted: Wed Jun 06, 2012 8:33 pm
Hi JaG,

So, sometimes Thomas reports unofficial SNP results ;)


OK, maybe that sounds funny, but they can't have a rule or definite process set up to deal with every unexpected eventuality. As you know, SNPs discovered through WTY aren't shown on the person's Haplotree page. An order still would have to be placed to do that. In this case, the SNPs were discovered sometime after a Deep Clade test had been done in which, when they were originally scored, it hadn't been noticed that other, unexpected SNPs were present. Someone else noticed later that the "derived" count had increased for the rare L250 & L251 SNPs, and it was traced back to this Deep Clade test.

So Thomas let me know, as a J project admin, and ISOGG phylotree curator for hg. J, that these SNPs had now been found in J, together with a third SNP, named L1064. Not that he wrote to me just for that! We were corresponding on other matters, and he mentioned it in passing.

So when I talk about a SNP being "officially" reported, that means after an order for them has been placed, to make them appear on the Haplotree page of the person in question. Anything outside of that could be regarded as "unofficial," but I don't think in any way questionable.

Is this clearer?

Bonnie
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PostPosted: Thu Jun 07, 2012 3:58 pm
L250.2+ is confirmed ufficially by FTDNA! The test was Ordered 04.06.2012 and Completed 07.06.2012 :)
L251.2 & L1064 are in Progress since 06.06.2012
Fund research of oldest Y-Haplogroup A00 - DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki
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PostPosted: Fri Jun 08, 2012 1:34 am
Wow, congrats, Chris! That sometimes happens when the test has already been done, and when your order comes in, they can just post the results immediately.

Any of you who have had L229 tested, as part of a recent Deep Clade test, should already have chromats on file that can be translated into fast results.

Hope we'll see some other orders coming in. Both members of Cluster I look like they will test, but these orders haven't quite appeared yet.

Other than that one, I'd like to see some members of clusters A1, A2, A3, A4, B, F, and of course H, ordering these SNPs.

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PostPosted: Sat Jun 09, 2012 10:43 pm
Hi Bonnie
I just discovered this forum thanks to Roberto Raciti
If I understood well the Najd,Qassim and al MAJMAAA cluster under J2-Middle East project are most probbaly L250.2+ right ?
do you think they are aslo 251+,L064?
Which SNP do advice them to test ?
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