From STRs to SNPs – An update on my yDNA Testing

Back in 2014 one of my earliest blogs was about my yDNA testing (If you remember your school biology, yDNA is the sex-chromosome that sons get passed, virtually intact, from their father, daughter’s get a second x chromosome). Things have moved on since then, so I thought today would be a good chance to update this. I also want to use this blog to explain the processes I went through to get further information on my paternal line.

Background

My GGG-Grandfather was Henry Grass (1764-1845). He is recorded as “Base born” i.e. born outside marriage. His mother, Elizabeth Grass, was a widow and we have no record of who his father was. I’ve been hoping that by having my yDNA tested I will find a match descended from an earlier, common paternal-line, ancestor of both myself and my match.

In 2014 I had the results of a 37 marker yDNA test. They were rather disappointing. No matches at the 37 marker level, suggested that there was no-one on the FamilyTreeDNA  (hereafter ftDNA) database that shared a recent common, direct-paternal-line, ancestor.

More STR Testing

Last year I upgrade my yDNA STR test (Short Tandem Repeats – remember) to 67 markers. The rational being, that sometimes you have a close match at 67 markers who may just have enough mutations at the 37 marker level not to be matched at that level. Sadly no-one matched me.

As a result I thought it was time to switch track a little and look at my yDNA Haplogroup. As the ISOGG wiki nicely defines it:

A haplogroup is a genetic population group of people who share a common ancestor on the patrilineal or matrilineal line. Haplogroups are assigned letters of the alphabet, and refinements consist of additional number and letter combinations”

You may find some companies marketing haplogroups as “tribes”, such as Vikings or Picts. I hate this simplification. Personally I doubt that all members of any of the recent (i.e last 2000 years) historical peoples were descended from a single source. I find it far more likely that “tribes” were much more mixed, as people joined in/were invaded/were made slaves etc.

(Sorry if I was ranting there, back on-topic). Haplogroup information can be used to make a phylogenetic tree, identifying branches based on mutations of the yDNA from a common root (in this case the y-Chromosomal Adam). The International Society of Genetic Genealogists maintains such a yDNA tree.

My basic Haplogroup results were found from a DNA test I took as part of the National Geographic’s Genographic Project. There I was found to be I-Z138, as the graphic below shows:

This branch of Haplogroup I makes me among a mere 1% of the men who've taken this test.

This branch of Haplogroup I makes me among a mere 1% of the men who’ve taken this test.

At this point I should mention that that there is an old and a new format for yDNA Haplogroup names. Originally Haplogroups were named in an alternating Alphabet/Numeric pattern, based on the branching of the tree. For example I-Z138 is sometimes referred to as I1a2b. Over time this naming structure has proved unwieldy and is now being replaced by a basic Haplogroup (I in my case) followed by the final, defining SNP. A SNP being a Single nucleotide polymorphism – a mutation at a defined point in our DNA.

Let me try and put this in context. I-Z138 is a “sub-clade”, or branch, of I-M253 (or I1 in old terminology). I1 is most-often found in Fenno-Scandia, but also, with decreasing frequency, throughout the rest of Northern Europe. It is often “associated with the Norse ethnicity” and is normally assumed to come from early European hunter-gatherer populations. The “Time to Most Recent Common Ancestor” (commonly known as TMRCA) for I-M253 is estimated as 4,700 ybp (Years Before Present), however it’s estimated that the mutation occurred sometime between 45,700 and 40,300 ypb. The vast difference in time is due to the fact that a small population basically got stuck, or “bottlenecked” during the “Last Glacial Maximum”. This resulted in the same small pool of genes being continually recycled through the generations, with occasional mutations occurring in the yDNA. As a result Haplogroup I1 is “defined by at least 25 unique mutations“. By contrast, my haplogroup, I-Z138 has a TMRCA of 4,400 ybp, but was formed around 4,700 ybp. Remember these are all rather fuzzy estimates.

Back to me. Knowing that I was I-Z138 I joined the I-Z138 project at ftDNA and the I-Z138 Project’s Facebook group.  This is an incredibly useful and knowledgeable group of people who, as the name implies, are researching and refining the whole I-Z138 branch.

In addition, earlier this year I stumbled across a website, nevgen.org, which takes your STR data and predicts your Haplogroup from this data. I must admit I know very little about this site, but there is plenty of background reading for those interested.

Entering your yDNA data on nevgen.org is actually quite easy. So, if anyone with yDNA results, wants to try the site just do the following 4 steps:

  1. Sign in to familytreedna.com and go to your results page.
  2. Download your results as a .csv file by clicking on the CSV button at the bottom right hand side of the page.
  3. Find the .csv file you just created using “File Explorer” (Windows 10) or Windows Explorer (Windows 7). Right click and select the option to “Open with” Notepad.
  4. Copy and Paste the second line of your csv file into the box on nevgen.org marked “Enter your results as follows”, then click on calculate.

Following the above procedure I got the following result (along with some statistical analysis, which I won’t bore you with).

The result of my yDNA 67 marker data in nevgen.org

The result of my yDNA 67 marker data in nevgen.org

The result couldn’t have been clearer. I was predicted to be I-Z2541, which is a downstream (i.e. a more precise) sub-branch of Haplogroup I. It also implied that I was positive for the intermediate marker S2293.

Testing at yseq.org

To test for individual markers within the y chromosome you have two main choices, either through familytreedna.com or through Germany’s very-own testing lab yseq.net set up by geneticist Dr.Thomas Krahn. Since my needs were very specific I went for the German option (available at $17.50 or €13.92 per SNP). The results arrived approximately one week after testing. I was indeed positive for both S2293 and Z2541.

These successes inspired me to do further testing. The I-Z138 Project, that I mentioned earlier, has quite a detailed phylogenetic tree for their sub-branch. As a result I could see that downstream of Z2541 there were 2 main branches (S2268 and Y7043 if you’re interested). On a whim I tested both. The result is that I’m now I-S2268. Currently, this is the end-point on my personal yDNA journey.

Final Thoughts

I’m pleased to have got this far with my haplogroup testing. I hope that through testing, I’ve somehow contributed a little to the research in this area.

There is nothing I can really test that would further define me within the I-Z138 phylogenetic tree. The only other options would be to do go for one of the major yDNA tests, such as the Big Y test. This would normally identify virtually all relevent yDNA SNPs, including, potentially, private SNPs unique to my family line. At around $500 this is not a cheap product and not one I’m currently ready to invest in.

I’m now in a group of one within the I-Z138 project, based on the combination my SNP and STR results. Basically I’m an outlyer. I’m hoping that, eventually, others will join me in this group.

Among the few, distant, relatives I have from my STR results, 2 have Danish ancestry.  Based on this, and my own Suffolk patrilineal line, I wonder if my ancestors may be associated with either the Anglian or Danish Viking invasions of Britain, although I doubt the real story is so simple.

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8 Responses to From STRs to SNPs – An update on my yDNA Testing

  1. Pingback: My LivingDNA Test Results | learnalittleeveryday

  2. Pat Davis says:

    I’m also folo’g I-Z138, for my DAVIS cuz… yDNA matches with SCHWEITZER (SWITZ, GER) … CORBIN (ENG)… BOGAERT (NETH)… DAVIS migrated thru early WinchesterVA area, Old Frederick Co., from near early NYC… to seOH, 1810 census.

  3. James Woodard Bray says:

    Hi Phil
    I did my ydna test through Living DNA – I’m l1-Z138. I was born in Michigan and descend from Henry Bray, d. 1794 in Chatham Co., NC. He was born ca. 1705+/- in Prince George Co., MD. I have been unable to identify either his father or grandfather Bray. There is some evidence that my line of Brays may have lived in Norfolk or Suffolk counties, England in the 17th century.

    I looked at ftdna’s British Isles ydna project – at least 5000 members? No Brays. Same for the East Anglia project. I belong to both the Norfolk and Suffolk Famiily History Societies. Can suggest other areas or organizations for leads on Bray family researchers in the UK?
    Thanks,
    Jim Bray
    San Manuel, Arizona

    • Phil Grass says:

      Hi Jim,

      apologies for the late reply. Can I suggest you have a look at the I1-Z138 Project at ftDNA (see https://www.familytreedna.com/public/I1-Z138Y-DNA?iframe=ycolorized) There is one Bray there, with an earliest known ancestor of Henry Bray b.1755. If you are on Facebook there is also the “I1-Z138 YDNA Project” where you can ask – it’s the main communication tool of the group (I’m a member of this group).

      One general comment on researching British ancestors. My experience is that there are very few useful English Parish records existing from the 17th century. What there are tend to be very uninformative e.g. Thomas the son of Thomas Smith baptized …” Given this situation, yDNA testing is the best resource you have to help identify where your Bray line might have come from. You may also need to test further. I1-Z138 is a relatively old marker, formed about 4,600 years ago.

      Hope this Helps

  4. Jim Bray says:

    Hi Phil,
    I am a member of the Bray y dna project at ftdna. I just found out today the I can download the ydna raw data as a separate file from my Living DNA account. I haven’t been able to upload my ydna because of some comflicts/compatibility with ftdna’s system; but I can get some info from the project. I have also looked at ftdna’s l1-z138 ydna project.

    Today I wrote to Neville Bray, admin for the Bray project, to see if I can upload my Living DNA file to the project.

    You mentioned upgrading my Living DNA raw data to see what new data has been added to Z138. What do you recommend? I have been to the YSEQ site and poked around a bit. I’ve exchanged a couple of emails with Astrid. She recommended I1 Superclade Panel. It is kind of pricey so I’ll hold off on that for awhile.

    Thanks for responding. Look forward to hearing from you.
    Jim

    • Phil Grass says:

      Hi Jim,

      I’m always a little careful to give recommendations as testing choices depend very much on what you want to know, your budget and your timescales. In “theory” the cheapest approach is to just do a test of your “complete” y chromosome with a test like the FamilyTreeDNA BigY-700. (I use the phrase “complete” as there are parts of the y chromosome that are unreadable with current technology). The downside of this is that it’s expensive (US $ 649 as of today), although prices should go down with time, competition from other firms and special offers.

      More focused testing depends very much on your goal. If you are more interested in your deep ancestry e.g. how, and possibly where, your fatherline came from, then the Z1 superclade pack from ySeq is probably the best value approach. If you are more interested in how you might be connected to other “Bray” males then it would probably help to take a yDNA STR (Short Tandem Repeat) test such as the yDNA 37 STR marker test from FamilyTreeDNA (see https://www.familytreedna.com/products/y-dna).

      Whichever way you choose I would follow the testing recommendations from the Admin(s) in either your Surname (Bray) or Haplogroup (I1-Z138) Project. They have way more experience than myself on such testing choices.

      You mentioned about transferring your data from your LivingDNA test to ftdna. I’m not aware that you can transfer your yDNA data to ftdna – only your autosomal DNA, but I may be wrong on this.

      I hope this helps and please let me know how your testing goes.
      Phil

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