Adventures in Big Y and YSEQ

Today I sent my kit back to YSEQ.

I first dipped a toe in the water at YSEQ when I used their “Wish a SNP” feature for my Elmer friends. For one dollar, you can wish for a testable SNP and they will examine it and order the primers for it.

Very nice when you’re digging into “family” level SNPs that are of little interest to the larger companies.

Why YSEQ and Big Y

The simple economic truth is that not everyone can afford FTDNA big Y or FGC Y Elite test to be able to identify new SNPs. So, we’re attempting to get key players to run the bigger more expensive tests that “blaze the trail” and discover new SNPs that might be valid for the family, with follow up “budget friendly” tests for others through companies like YSEQ.

In the long run we hope to build a panel of SNPs for any Y tester that wanted to figure out which branch of the “Edward Elmer” family they fall on. Also we’ll end up with a basic list of SNPs that belong to Edward. They will be the SNPs shared by all the Y testers. Those could be added to a panel of SNPs to take back to England.

What We Expect

Here is a quick chart that shows the Y lines and what we expect to find based on current STR testing. This is where we think everyone will be positioned in the tree when all is said and done. Please forgive my ms word charts. Click them for the enlarged view.

Sons of Samuel

We’re currently waiting on the the big Y test from “R1” to add a “Known Tree” counterpart to “L2”. These two tests form known pillars. We’re missing the middle known tree pillar from “G1” at this point, but we intend to pursue it in the future.

Brick wall testers L1 and M1 are expected to be related to R1. Likely through Samuel Elmer’s son Deacon John Elmer.

Brick wall M1 was our first big Y tester and blazed the trail for most of the SNPs we have today. He currently has four testable SNPs all to himself. We call them singletons because only one person has them at this time.

We think we will find that R1 and M1 share some of M1’s “singleton” SNPs. Making them private to that branch of the Elmer family. Depending on how many they share, we may be able to guess at a most recent common ancestor. L1 then plans to follow up with YSEQ testing of R1 and M1’s shared private SNPs along with their singletons to discover which tester they are most closely related to.

Sons of Edward 2.

L2 was our second big Y tester. He matched M1 on four testable SNPs that for the time being only belong to the Elmer family.  He currently has one testable SNP to himself. I’m Mike Thompson in that chart. I expect to be related to L2 through Hezekiah Elmer.

I tested for one SNP that was shared by the Knowlton family (A2277), four SNPs shared by our two Elmer testers (M1 and L2) so far (A2278, A2280, A2283, A2284) and the one singleton SNP of L2 (A5920).

This can all get kind of confusing when we’ve got all these numbers and letters floating around.

How About Another Picture

Visualizing this tree another based on SNPs. I added some little circles of color to represent SNPs. We’re assuming that Sam, John and Ed2 are pretty much like their dad, and get a yellow ball. Because of that, everyone gets a yellow ball. We all get those from Ed1. What I’m hoping for is that somewhere in there either Ed2 or Hezekiah added another SNP..the red ball. Then L2 and I will carry the red ball. It will be private to us and mark our branch of the family.

Along the same lines we’re following the sons of Samuel. Our thought is that they may branch off at his son John, but we’re not sure. I’ve added a purple ball in common for them. Some descendants of Samuel also have an orange ball, but not all of them. In that way, we can differentiate the branches coming from Samuel.

Of course, I’ll be excited to learn anything I can, but my expectation is that I will share at a minimum the one SNP shared by the Knowltons and the four SNPs the other Elmer testers have. That is the yellow ball in the picture above. Everyone gets it.

My bet is that I will share that single singleton from tester L2, (the red ball) but the odds are not in my favor with only one singleton to test. To put it in context, M1 has four good chances to match R1 and define that they are on the same branch of the family tree. I have only one chance.

The Knowlton Family, Unknowns and the Importance of Pillars

You may have noticed that I tested an SNP shared by the Knowlton family.

The Knowltons have joined us in Big Y testing. They actually share two SNPs with the Elmers, but I could only make one testable at YSEQ. They are also included in the yellow ball in my previous chart in that their SNP was carried by Edward Elmer 1. That’s the idea anyway.

The Knowltons are the closest Y relatives of the Elmers at 67 markers. The big Y test one of them completed shows that they are close relatives to the Elmers but we’re not certain exactly how close. So our YSEQ and Big Y testing should help put their matches in context as well.

We’ve got two Elmers Big Y tested. How can one more test put the Knowltons in context and why would there be any question about it?

Well, Big Y tests the area of the Y chromosome that FTDNA thinks will have the most chance of success. So they will  get a lot of great SNPs, but not all of them that exist. The Knowltons may share many more than two SNPs with the Elmers, but we will not know it.

Because we don’t know the relationship of  Big Y M1 and future big Y R1 based on a family tree, we can’t be completely sure that they are the most closely related. Even though they have all the same STRs in common. STRs suggest a relationship, but SNPs are the mark of it.

M1 and L2 share the most SNPs in common at this point in time. The others (including me) just aren’t tested yet and with unknowns there can be lots of surprises.

So our Big Y and YSEQ SNPs may show us a completely different path than we expect.

Expecting the Unexpected

Here is an “unexpected” SNP based tree that could include the Knowlton family. If it were to turn out that M1 and L2 were more closely related than expected then the tree could play out more like this, with the Knowltons included because the new base “yellow” ball is really the two SNPs they share.


The reference docs are pretty blurry in the 1600s and NPEs happen. It’s possible that John Knowlton (who all the Y STR matched Knowltons go back to) was really an Elmer adopted by the Knowlton family. The two SNPs shared with the Knowltons may just be the Edward Elmer SNPs we’re looking for.

The key thing is that without testing R1 or G1 and comparing them to L2, we don’t know what the structure of the tree is.  R1 and L2 as “pillars” of our structure will help define what those early 1600s SNPs were and in doing so, help place everyone involved.

Notes About the The Testing Process

So far, FTDNA’s Big Y has been pretty darn easy. Most of these men already had kits from Y STR and earlier SNP testing, so ordering an upgrade was really a matter of saving the money and waiting for a sale. Like falling off a log really. They identified an issue with M1’s stored sample early on and sent him a new kit in no time. The results also came back quicker than expected.

We have relied heavily on the volunteer admins at the U106 group and the Z18 group to analyze the results and give us some direction because FTDNA’s Big Y results matching has some issues.

I took those SNPs that FTDNA provided and our Y groups analyzed from M1 and L2 kits and added them to YSEQ through the Wish a SNP process. YSEQ has been fast and responsive. They assigned me a user account much like FTDNA did. Their website is not as polished but..really it’s the results and flexibility I’m after.

Their swab kit for my SNP test order came in the mail within a week of the purchase. Mailing it back was a minor adventure because I’ve never mailed a package to Germany. Less than the cost of a lunch at McDonald’s later, my kit is on it’s way. I have read on forums that they are lightening quick on turn around for these kits, so I’m very hopeful I’ll have my results fairly soon.


Partial Return from YSEQ



Fathers Day Y mile markers




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