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Thursday, October 16, 2008

Important new SNP's in the J2 tree

23 and Me has been offering testing using a new chip which scans the Y chromosome for over 2000 SNP's. 2 of these could be very significant to the structure of Haplogroup J2, M172. The first, rs34126399, seems to represent an SNP downstream of M410. This SNP was discussed in 23 and me's blog here. Testing done by Dr. Peter Underhill suggest that this SNP is equivalent to the deletion at DYS 413. And thus, it would appear that a major branch of the J2 structure will return at some point to the YCC haplogroup tree.

The second SNP being found in some J2 participants with 23 and me is rs35248080. Less is known about this marker except that it lies downstream of rs34126399 (ISOGG-J2a1). From the testing results received to date, we do know that one participant from the cluster pre-J2a1h (Haplogroup J project FTDNA) or J2a-Beta (J2 DNA project) is positive for this SNP. This group carries some distinctive repeats at DYS 445 and 450 and testing through Family Tree DNA has been ongoing for some time. We also know that 1 participant in Haplogroup J2a2 (ISOGG-J2a1b) which carry the M67 SNP and another in Haplogroup J2b (M205+) were negative for rs35248080. Thus it appears that this SNP could split J2a1's into 2 fairly large branches. Exactly which subclades and clusters are positive for this SNP will only be determined with more testing.

7 comments:

Anonymous said...

Both SNPs emerged one month ago from deCODEme results:
http://dna-forums.org/index.php?showtopic=2708&st=260&start=260
I put below the content of my post:
-----Post Start-------------------
Sep 19 2008, 06:03 PM Post #267

I have just added 2 new results here:
http://www.webalice.it/asquecco/deCODEMe_Y_DNA-Forums.xls

....SNIP......

Walter differs from the other available deCODEme J result for the following SNPs:
rs35248080
rs2032604 (J2/M172)
rs34126399

Is there any available information about rs35248080 and rs34126399 ?
Adriano Squecco
------------Post End--------------

m172 said...

rs34126399 seems to correspond with the deletion at DYS 413 while rs35248080 seems to include 1 candidate who falls into the cluster of J2a with distinctive repeats at DYS 445 and 450. It is referred to as J2a-Beta or pre-J2a1h. It may or may not carry other subclades downstream of DYS 413<=18?

BES said...

Very exciting news! These look like the SNPs we've all been waiting for. More results will surely clarify the exact correspondence of the positive/negative SNP results with our already identified clades and clusters.

Adriano, could you get in touch with me regarding Walter Krol? Knowing his haplotype would be very helpful, and if he is willing, it would also be great to get him into Ann Turner's spreadsheet of results which include both 23andMe and deCODEme, allowing us to compare all the results.

Best,
Bonnie Schrack
Y-haplogroup J project (Y-DNA_J)

Angela said...

I am hopeful that this new SNP ( rs35248080) will turn out to be a defining marker for J2a-Beta cluster!! ... a defining SNP for this group is item 1 on my wish list for new SNP discoveries.

Having said that its just as likely that this new SNP will not correlate exactly with the J2a-Beta cluster,.. it may be wider or narrower.... but in either case it still has the potential to be VERY useful indeed!!

I look forward to hearing more about this SNP marker in the future.

Angela
admin/researcher for J2 project

Pierre said...

Hello my haplogrupo is J2.likin to know because my DYS 393 is 14th most I know is 13.12.

m172 said...

Hi Pierre:

14 is rare but not unheard of for J2. I think I've even seen a 15 before. But, you are right, 99% are 12 or 13.

In the Italy DNA project at FTDNA, you will see a J2 with 15 at DYS393: http://www.familytreedna.com/public/Italy/default.aspx?section=yresults

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