In late 2012, the way haplogroups were being named and referenced began changing. Before the introduction of the Geno 2.0 test in July 2012, there were approximately 850 SNPs identified on the haplotree, meaning 850 haplogroup names that all began with the letter of the haplogroup, but then had alternating numbers and letters that were added as new haplogroup branches were discovered.
The most common one in Europe is R1b1a2. This means that after haplogroup R itself was discovered, then another haplogroup, R1 was discovered, then R1b, and so forth. But now, for the fly in the ointment. Let’s say that a new haplogroup has been discovered and it needs to be inserted between haplogroup R1 and haplogroup R1b. What happens? This naming methodology is not conducive to insertions. It’s only been a couple of years that the tree was entirely rewritten, redrawn. Haplogroups that were previously called E3a became E1b1a. To say it was a large and very disconcerting shift is an understatement. Add to this that all of the academic papers on which we depend are written in the lingo of the time. So something that references haplogroup J1a in 2002 may not be talking about the same J1a, as defined by a SNP, in 2013 or some time in the future.
Now for the jolt. The Genographic project utilized over 10,000 new SNPs not before known or utilized for a total of over 12,000 Y DNA SNPs in their Geno 2.0 test introduced in July of 2012 . Therefore, the tree was going to have to be entirely drawn with the haplogroup branches renamed, once again. This was going to be a much bigger shift than before, simply due to the sheer magnitude, and more SNPs are being discovered almost daily. Therefore, a new methodology was needed.
Every haplogroup, such as R1b1a2, is defined by a specific SNP, in this case, M269. This SNP and haplogroup name have a specific location on the haplotree. The SNP locations can change without a problem, but the names of the haplogroups that need to change are the problem. This has already led to different trees maintained by different organizatiosn being out of sync with each other.
Today, at Family Tree DNA, this is what the top part of the haplogroup R tree looks like.
As new SNPs are discovered and inserted into the tree, there will no longer be a name assigned, shown in the right hand column. As the names are obsoleted because of shuffling of branches on the tree, they will not be renamed. Already, at Family Tree DNA, they are using just the SNP name as the haplogroup indicator, as you can see in the top bar where is says “Your confirmed haplogroup R-L21. This means haplogroup R, SNP L21, which occurs further down on the tree.
Today, R-L21 is still shown on the tree with its name, R1b1a2a1a1b4, but as the tree branches shuffle and this name no longer applies to R-L21, the name will be obsoleted and the haplogroup will only referenced as R-L21.
Max Blankfeld and Bennett Greenspan of Family Tree DNA recently wrote this explanation which is found on the haplogroup pages at Family Tree DNA.
Long time customers of Family Tree DNA have seen the YCC-tree of Homo Sapiens evolve over the past several years as new SNPs have been discovered. Sometimes these new SNPs cause a substantial change in the “longhand” explanation of your terminal Haplogroup. Because of this confusion, we introduced a shorthand version a few years ago that lists the branch of the tree and your terminal SNP, i.e. J-L147, in lieu of J1c3d. Therefore, in the very near term, Family Tree DNA will discontinue showing the current “longhand” on the tree and we will focus all of our discussions around your terminal defining SNP.
This changes no science – it just provides an easier and less confusing way for us all to communicate.
Obviously, more than a decade’s worth of information exists that references the haplogroups in both formats. Other companies in this space are not doing this level of testing and do not yet need to address this type of issue, so their data bases and references will likely stay the same, at least for the time being. For some time to come, we will be dealing in a dual world where both methodologies are utilized and yes, some amount of confusion will certainly result. In preparation, I wanted you to understand what has happened in the past, the recent changes, what the future holds, and why.
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Dear Roberta,
Thanks for such a timely article.
A new member in the FTDNA McDuffie Group has been the recipient of a forward of your article immediately. An attempt to explain this subject to the kit owner—the daughter of the person being tested—was being plotted by me when lo and behold your always welcome blog appeared in my inbox.
The new member’s yDNA results had to have a backbone test and thus the results were awhile showing up. The first marker result of this new member’s results being DYS 393 equals 16 was an unfamiliar result for me also and the haplogroup given as M269 following what looked to me like a battery of SNP tests by the lab sent me scrambling to try and figure out the ramifications of same to grouping the member’s results. The only match with the new kit results is an L21 and I am like well does that work with M269? So, I forwarded the whole shebang over to Mike at R1b L21 for help also.
I believe your article will explain to the new FTDNA kit owner the SNP–STR–etc situation far better than my fledgling efforts. And, certainly helps me out also. Thanks, as ever, for your work here.
Linda
Haplogroup administrators are generally the most knowledgable people about their particular haplogroup because they work actively with it every day. When it doubt about something haplogroup related, it’s always a good idea to touch base with the admin.
Roberta
Thanks for using me as an example.
Both my father and I are R-L21+. But now we have a problem. We have tested all of the available FTDNA R-L21+ subclades and found them to be negative.
I presume this means that we are a subclade which is not yet available at FTDNA. I have tested at Gen 2.0 and attempted to upload those results to FTDNA.
I recently read the article about 10% of Scots men being S530/L1335 indicating they are related to the Picts. It appears that this SNP is not available at FTDNA.
Where do we go from here?
Thomas R McKee
Hi Thomas,
The L SNPs were discovered at the Family Tree DNA lab, so L135 has to be avaialble there. I don’t know when it was discovered so I don’t know if it’s on the Nat Geo chip or not. That article about that SNP being equivalant to Pict has come under heavy criticism. So don’t take it to heart quite yet.
Roberta
I’m confused– where does this leave m269?
Today M269 is still R1b1a2, but one day in the future, if the tree shifts upstream of M269, it may not be called by that name anymore. Rather than rename it, it will just be shifted on the tree and called by M269. The examples in this article were only examples.
Thank you for the article. All of the new SNPs will cause a greater challenge in our communications. However, I’m glad we have the new SNPs. I do wish there were better standards in naming identical physical SNPs. For example, U152 and S28 are the same thing. In this new SNP based naming system, if one person is R-U152 and another R-S28 they may not realize they are the same thing. It gets much more complex. For instance L21 is also named S145, but that is not the end of it. Z245, L459 and Z290 all are phylogenetically equivalent to L21. In our old system, we had one thing we could call them to represent that branch on the Y DNA tree. That one thing was R1b1a2a1a1b4. Any of the multiple equivalents for L21 could point to this. However, since that is gone or soon will be, we need some kind of standardization on which SNP name is the “lead” name for that particular branch on the Y DNA tree.
Roberta, Many of the participants in Moore Worldwide “Group 2” have not SNP tested and their haplogroup is predicted R1b1a2. We who have SNP tested are R1b1a2a1a1b4* or R-L21.
Will those who have not SNP tested be shown as M269 and us who have as R-L21? If so, since FTDNA was able to predict the R1b1a2 isn’t there a way to predict that if SNP tested their results would be R-L21?
Thanks for this article. Your articles and examples are so good! Janice Moore Cronan
Roberta, Will this shorthand be used on the surname group pages?
Moore Worldwide Group 2 has many participants who have not SNP tested and are listed as predicted R1b1a2. Some of us have and we are listed as R1b1a2a1a1b4. When FTDNA changes to the shorthand method will the predicted haplogroup be shown as M-269 and those of us in group 2 who have SNP tested be R-L21? Thanks so much for this info, Janice
Family Tree DNA predicts haplogroups based on an exact match to someone who has SNP tested on the first 12 markers. You can’t reach the L21 kind of definition with that criteria. Sometimes you can predict who will be L21 based on other criteria. The best way would be to look at their highest level matches and see if thier haplogroups are L21. If you see a mixture, it means they haven’t tested at a high enough level.
I believe they will transition to the SNP methodology for groups as well, but I have not confirmed this with them nor do I know a timeline.
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We have questions about assigning and maintaining Y subclade names.
My understanding is that when a new Big-Y test comes in with one or more non-SNP variants matching private variants of another tester in the same subclade, the common private variants are assigned SNP names and a new subclade is born. (Call this new one subclad #1 and assume there are several previously unnamed variants in common with an existing tester.) The new subclade is then labeled with reference to the name of one of the new SNPs. Since it is apparently not possible to tell which of the new SNPs is the oldest, I assume the SNP used for the subclade label is effectively arbitrary (?).
If another tester is then discovered with one or more of these new SNPs, but not the labeling SNP, can I assume he is in a new subclade senior to (older than) the one established above? I have not seen this in practice and it seems somewhat problematic but I have not seen a lot of examples and cannot see how else it might be handled.
Even more of a conflict seems to arise if there are multiple new SNPs as described in the first paragraph above and the labeling (defining) SNP is then found in a new tester who is missing one or more of the others. How are names adjusted? Clearly the paragraph 1 subclade would not include all men with that defining SNP name so the newest combination (with the SNP used to name subclade #1 above but missing at least one other) must be higher in the hierarchy (older). Does the new one now take the SNP name but with all prior members of the subclade going to a new subclade? That does not seem ideal but I’m not finding a better solution.
If everyone has all the SNPs, they are considered equivalent until someone comes along that does NOT have one of those, then they form a new branch. Sometimes branches are divided. It doesn’t change the SNP name, just changes the branching tree structure and sometimes the age estimate for all the SNPs. This process has been going on since the tree was begun, which is how the tree grows.