I have used Y-STR testing to confirm that my immigrant ancestor was Robert Thompson who died 1697 in St. Mary's County, Maryland. I used my list of Y-DNA matches at Family Tree DNA and the results in the Thompson surname project to do this. You can read the story in Breaking through brick walls with Y-DNA. It was an amazing discovery that could not have been done without DNA.
Now I need to expand my search to find others who might be more distantly related and who can shed clues to the European origins of Robert Thompson. Some of these people will not share my surname. So I needed to conduct some SNP testing and join a haplogroup project. This story assumes that you have read my previous blog post about STRs, SNPs, SNP testing, haplogroups, haplotrees, and the Big Y test. If you haven't read it, please do so now so that the following procedure will make sense. See Y-DNA STRs, SNPs and haplogroups. You won't regret it.
I joined the R-FGC11134 haplogroup project, and so did one of my Thompson matches. In the image below, our test results are grouped with a man named Cairns.
I examined the STR patterns, and even though Cairns does not appear on my list of STR matches because he is not related closely enough to be considered a match by Family Tree DNA, it looks as though we might have shared a common ancestor sometime in the past. My Thompson match has already done SNP testing by taking a SNP Pack, so ordering any standard SNP test will not help us much. I notice, however, that Cairns has tested 111 STRs and has taken the Big Y SNP discovery test. I, on the other hand, have only tested 67 STRs and have relied on the SNP pack testing of my Thompson matches to determine that I belong in this haplogroup. I really believe that the project administrators are correct and that I am somehow related to Cairns. Cairns knows a specific parish in Scotland where his ancestors originated. If we are related, maybe Robert Thompson was Scottish, too.
The Big Y test was on sale, and I may not get any further with Robert Thompson's ancestry unless I order this test. I have been researching this family for decades. It's time to upgrade my STRs to 111 markers and order the Big Y test. Who knows? I might share a couple of new SNPs with Cairns. If so, these results may help me work forward in time from FGC11134 to the present.
To order the Big Y log into your FTDNA account and click Upgrade.
You will be taken to a screen that shows suggested upgrades. Here the Big Y is shown at its regular price. You can order this test at a much lower price if you wait, as I did, until it goes on sale. For example, Family Tree DNA has great sales in the month of December.
I clicked immediately on Big Y matches. Would Cairns be there? I certainly hoped so, but I was stunned by what I saw.
Cairns showed up as my closest match. There are many other matches not shown, but they are too distantly related to be relevant. My brother and Mr. Cairns shared 23 newly-discovered SNPs! I expected to see a few, but not 23! It took three screen shots to capture them. Here is screen 1:
When the results are initially reported, your haplogroup assignment will be for a known SNP that is already on the haplotree. FTDNA reported our common haplogroup as R-A9871. This new assignment automatically changed in our FGC11134 project results.
What does all this mean? How closely are Cairns and I related? After receiving the results I immediately began submitting them to multiple analysts. To share your results go to the Big Y results section and click Download Raw Data.
You will see options to access two different types of files. Some analysts want the VCF file, and some want the BAM file.
Full Genomes Corp (FGC) and YFull will analyze your results for a fee. They want the BAM file. A link to the BAM file will not appear until you request it. The file is very large so you will rarely download it. Instead you will click "Share BAM" to receive a link to the file. You will copy that link and share it with FGC, YFull, or any other analyst who uses that file.
One analyst who does remarkable work for my haplogroup, at no charge, is Alex Williamson. His "Big Tree" is for Haplogroup R-P312 and the various downstream SNPs. He is beginning to incorporate other groups into his tree as well. Alex wants the VCF file for his analysis. If you are within the R-P312 group, follow his instructions to submit the file. It is very important that you name your file EXACTLY as he suggests which is Haplogroup_KitNumber_AncestralSurname_BigY_RawData_YYYYMMDD.zip
My file was A9871_38962_Thompson_BigY_RawData_20170525.zip
The Thompson Big Y results have been submitted to FGC, YFull, Mike Walsh's L21 Tree, Iain McDonald's P312 Tree, Alex Williamson's Big Tree, and James Kane's Haplogroup R and Subclades Tree. We will take a look at Williamson's tree and Kane's tree in this post and examine these and the other analysts in more detail in future posts.
I clicked Download VCF to submit the file to my haplogroup projects and to Williamson's Big Tree. I shared the BAM file with FGC, YFull, and James Kane:
When my kit first appeared on Williamson's Big Tree it was immediately placed with Cairns who had been sitting on the tree in his own branch for more than a year. He now was forming a new group with Thompson. Only shared SNPs are shown on the tree. "Private" SNPs will not appear until shared by someone else. My Thompson results were highlighted to indicate that they had not yet been fully analyzed.
At that time Williamson had close to 400 kits that had not yet been analyzed, so it took several weeks before my results changed the tree. In the meantime two other Big Y results had been submitted, and our R-A9871 section now looks like this:
In the above image, some SNPs have been given names like BY9001 and BY12552. Others had not yet been named, so they appear as their position on the Y chromosome followed by the ancestral value and the value held by the tester (the derived value). For example, all of the SNPs in the Cairns-Thompson block had not yet been named. The number 4780182 in the first SNP tells its position on the Y chromosome. It is followed by the letters T-C. This means that the ancestors had a T in this position but in Cairns and Thompson the T has mutated to a C.
Notice how much one test can change the known Y-tree. In the first image Ferrel, Leonard, and Shalvoy were placed together. But Kelley shared one of the SNPs that had formerly been one of Leonard's "private" SNPs. Wakely shared seven SNPs with Leonard, including the one shared by Kelley. Because Kelley does not have the additional six SNPs, this means that the 23580583-G-A SNP occurred before the others. Leonard and Wakely are now forming a separate branch.
What about that Thomson who was placed with the Edgecombes in the FGC11134 project? [Review the first image in this blog post.] Should he have been placed with the Thompsons? If we extend this tree we can see in the image below that Thomson and one of the Edgecombes took the Big Y test and appear in the Big Tree. The FGC11134 project administrators were correct. Thomson is very distantly related to the Thompsons. They are in completely different haplogroups.
As mentioned before, new SNPs are not automatically named. This is a manual process that can be expedited if requested by a project administrator. All of the SNPs shared by Thompson and Cairns are now named by Family Tree DNA, and we form a new haplogroup under A9871. The haplogroup is named by the first SNP in the block, but all 23 are listed. When someone comes along who shares at least one of those SNPs, but not all of them, the Thompson-Cairns haplogroup will change. Below is our contribution to the Y-DNA haplotree:
The new haplogroup is now shown in the FGC11134 Project:
- Test yourself first. Don't wait until someone else has tested. When Cairns ordered the Big Y, no other Cairns had tested. But he took the test anyway because he wanted to find out what he could learn about his ancestry. I am forever grateful that he did! When he received his results he had no Big Y matches who were even remotely related. So he publicized his results and waited. Now he shares a long string of SNPs with my brother. I might not have done the test at all if I had not been curious about my relationship to Cairns. If everybody waits until they are assured they will get a match we'll all be waiting forever. Be a leader!
- Recruit others. You can wait until someone else shows up as a Big Y match, or you can recruit people. It was only after I took the Big Y test that another Thompson was willing to do so. But I had to notify the Thompsons of my results and explain how the test could help us with our ancestry. My list of Y-STR matches includes some people who do not share the Thompson surname. I need to encourage them as well.
- Publicize your results. In addition to recruiting people, you can help motivate people you don't even know to do DNA testing. Let others find your results by joining surname, haplogroup, and geographical projects. For example I have joined the Thompson surname project, the Maryland geographical project, and the R1b, P312, L21, and FGC11134 haplogroup projects as well as several others. You can learn more about surname projects in Surname projects: Examining my first Y-DNA match. You can learn more about haplogroup projects in Y-DNA STRs, SNPs, and haplogroups. My STR results are on YSearch.org with notations in the "Additional information" box about my Big Y results. To submit your STR results to YSearch log into your FTDNA account, go to your Y-DNA matches page, and click the orange "Take me to YSearch.org" button at the bottom of the page. I have also submitted Big Y results to Full Genomes Corp, YFull, and the other trees I mentioned earlier in this blog entry.
- Build an extensive online family tree. Trace up and down family lines to help others connect with you. One of the best sites for this is Ancestry.com because it has the most subscribers, but I use multiple sites because I want to have my ancestry in as many places as possible. See my 2014 blog post about Online Family Trees. If you have a tree at Ancestry.com you can easily transfer it to Family Tree DNA. See the section "Exporting a tree from Ancestry.com" in Setting up for great DNA matches. Be sure your family tree is public! By tracing descendants of your ancestors you will help other people who have not gotten back as far as you have. I am regularly contacted by people who see their grandparents and great-grandparents in my tree. I often look to see if these people would be good candidates for DNA testing to help break through another brick wall. For Y-DNA testing alone, I have recruited people for not only my Thompson line but many other lines as well. Y-DNA can help you find ancestors in a way that no other test can.
- Be sure that all of your account settings are set correctly so that you can make maximum use of your DNA results. See Setting up for great DNA matches.
- Take screen shots of your DNA results and post them to your online family tree(s). I take screen shots of my YSearch records, for example, and post them to every relevant ancestor in my online trees. You can see an example of this in the "Finding Family Members for DNA Testing" section of Setting up for great DNA matches. I have received emails from people wondering about Y-DNA testing and how they can do it.
- Take other DNA tests to expand your pool of family matches. Upgrade your Y-STR markers to a higher level. Order an autosomal DNA test from Ancestry DNA, Family Tree DNA, 23andMe, or My Heritage. Prove your ancestry by using as many resources as possible. You are leaving a lasting legacy for future generations.
Up next: We submitted our results to YFull.com. See What are the Benefits of YFull?
See the new changes to Big Y results and what they can reveal: Evaluating new Big Y changes