Y-DNA testing to determine if a male is related

Question

My father has done both the Y-111 test and the Big-Y test at FTDNA. His father (my grandfather) was adopted and I'm trying to determine who his birth parents were. Through atDNA testing and research, I've been able to determine (with reasonable certainty) one set of my grandfather's grandparents. Out of their many children, their are potentially 5 children who could be my grandfather's parent: two daughter and three sons.

I have had conversations with a descendant and fellow genealogist from that family and they have identified a direct male descendant who would be willing to do a DNA test.

I believe testing one male for a Y-DNA match is the most efficient/affordable way to narrow down my list. With my Big-Y test results, I have positive SNPs for a line that many others have (mutation ~800 years ago) and my Big-Y test has also found new positive SNPs for which there are no other matches for yet.

My thoughts are to order both the SNP from ~800 years ago and the SNP that is unique from YSeq.net. If both are negative then I can rule out the sons. If both are positive then it would be very likely that its one of the sons and I can continue with an atDNA test. If one is positive and one is negative then I probably haven't learned very much since its possible that the "new SNP" is a very recent mutation.

Is ordering these two SNP tests ($17.50 x 2) the most affordable way to accomplish my objectives? My thoughts are the Y-37 test is $169 and would likely provide similar information.

I'm fairly new to Y-DNA testing so if I'm overlooking something, please let me know!

Thanks!

Answer 1

I don't think that Big Y testing will give you the results and answers you seeking.

My haplogroup (including subclade) is extremely rare in Europe, and only a few examples found in the British Isles, and most of those are in the northern counties, mostly Yorkshire, there are over 40 matches at varying genetic distances in America, but they all descend from the same immigrant ancestor (migrated to Jamestown in 1618)/

About six of us in the project have tested Big Y.. Previous to testing we were R-Z93, subsequent to testing we are R-Z93>YP5578 of that group two (including myself) are further mutated to R-Z93>YP5578>YP5904

The two that are R-YP5904 are separated at a genetic distance of 1, but that doesn't tell the story either, because our common ancestor was born 1637.

Point is that Big Y has revealed that our R-Z93 has mutated/evolved into subclades and subclades and even sub sub clades (we both have what are called novel SNP's, that is SNP's that until someone else tests Big Y and has the same SNP's will be reclassified as confirmed.

I share with this distant cousin 45 Novel Variants. However I share 58 novel variants with an even more distant cousin, one's whose common ancestor with me was born in the British Isles between 350 and 1300 C.E., yet his DNA is R-Z93>YP5578 and he does not have YP5904.

This means that although all of us share the same ancestor born between 350-1300, and He does not share the same More Recent Common Ancestor as my cousin who shares with me the man born in the Virginia Colony.

It is not known yet when the subclade R-YP5904 mutated into existence.It could have been before the migration of our common ancestor or after the mutation of our common ancestor.

That analysis is being done by the BigY R1a project and should be available in summer 2017 (The admin of the Yfull groups are volunteers)

Comments

Update: No sooner had I posted the above, than I received email from Yfull. They have updated their tree. And my common YP5578 ancestor was born circa 750 ybp.

That means that his son YP5904 was born even more recent, either just before my ancestor migrated to Virginia (1618) or after, it will take more Big Y testers to make that determination.

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I think he's asking whether he should test 2 SNPs at YSEQ, not do a BigY on his potential cousin. He's already done BigY on his father.

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Yseq does not have tests for all SNP's. Especially new ones.

However if he can cross reference his YFULL tree with his known terminal SNP (provided it is Big Y) then check Yseq.net and see if they offer that SNP, if so then you will save a bunch of money.

I admit to binocular vision. I have (distant) cousins who share with me R-Z93>YP5578 but not Z93>YP5578>YP5904 and if they  wanted to test YP5904 (which Yseq.net does not have). they would be frustrated because it is not offered by yseq.net,  nor is YP5578, only the older established Z93.

So before deciding to test YSeq versus Big Y, first check Yseq and see if they even offer the test.

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You can order "Wish a SNP" from YSEQ for $1 per SNP, and they'll figure out the needed primers. Then it'll be on their regular list of $17.50.ea. offerings. I've done this myself. But I don't think MD is asking about doing a BigY at all.

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Wish a SNP.  I just signed in to my yseq account. Yep they have Wish a list, but they require information that I don't have, or know how to obtain

Anyone have an idea?

As follows:

Then enter the name of your desired SNP, its position (hg19) on ChrY, the ancestral/derived mutation bases and the haplogroup where it’s been observed in the “Add Comments About Your Order” field. 

 

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Yes, I can definitely tell you how to obtain that information for most any SNP (rarely, one will turn out to have a complicated story). It'd be best if I did that using an example. Can you name a SNP you are interested in that YSEQ doesn't already have in their catalog?

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There would be two. SNP YP5578 and YP5904. These two are new SNP's at least from the aspect of the YFULL tree.

Here they are: I am YF07529

https://www.yfull.com/tree/R-YP5578/

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Terrific! Here's my process for researching the SNP YP5578:

1. Go to Ybrowse.org -- which is the largest database of Y-SNPs and is maintained by Thomas Krahn, co-owner of YSEQ. Ybrowse uses the hg19 human reference genome (which is equal to GRCh37 aka "build 37," as opposed to hg18,GRCh38 or hg38 for example) so the locations it gives you don't need to be converted.
2. In the search box under "Search Landmark or Region" replace the text with the name of your SNP, YP5578, and click the Search button. Don't include the haplogroup branch ("R") just the SNP name.
3. The page will reload and show you a chrY overview map, with YP5578 on it, and below that a number of tracks each showing information about that region if its known. On first view, the region is only 1 letter/basepair wide, but you can expand that if you wish with scroll zoom. But to continue, all you need to do is look for the SNPs track, where you'll find YP5578 highlighted in yellow-glowing red. Click on it.
4. A new page/tab will come up showing the database's detailed info about that SNP. You need its position ("ChrY:2861870"). You need the ancestral ("allele_anc") and derived ("allele_der") bases, which in this case are A & G respectively. And you already know that "R" is the major haplogroup it's found in. You are ready to "Wish a SNP."
5. Optionally check your work by viewing the YFull record for that SNP (or do this first and use Ybrowse to confirm). This will only work for SNPs in the YFull database. Go to the YFull tree and in the top right click the "YFull Y-SNPs" link.
6. In the page that comes up, go to the top right and click the "SEARCH" link. In the next page that comes up, enter your SNP name YP5578 and then click the Search button.
7. The YFull database info for that SNP is shown. It shows the build 37 (aka GRCh37 aka hg19) reference genome location for the SNP, the ancestral and derived alleles, and a link to the SNP's location on their tree (R-YP5578) that shows the major branch. These all match the info from Ybrowse, so you are good to go.

 

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Bonus research, for people really into it... Use the big DNA research NCBI Genome Data Viewer to see more details about the chrY around your SNP, which the Ybrowse database doesn't include. They only have names (in "rsXXXX" format) for SNPs that have been submitted to dbSNP (another SNP database, for scientists), but since you know the location "ChrY:2861870" you can enter that into the Search field in the left sidebar. Make sure the "Pick Assembly" selector at the top of the left sidebar shows the GRCh37 reference genome. Click on the right-arrow search button in the Search field and the page will update to show the region around the SNP. Zoom out to see nearby SNPs (from the dbSNP database), genes, and other chrY features, with links to more info about them.

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I followed your instructions. Went to ybrowse.org, typed in YP5578, hit search and it reloaded with the default information.

I then tried Z93, hit search and got a different result.

I don't think that ybrowse or yseq can handle newly found SNP's like YP5578 and YP5904.

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William, I just checked right now and YP5578, Z93 , and YP5904 are all in that database with full information. So YBrowse can definitely handle new SNPs, including those specific ones you are interested.

I remembered a quirk in the search field that's confused me in the past: If there is a space before or after the SNP name in the Search field, then the search won't work. So if the SNP info doesn't come up, that's the first thing I check. After you click the Search button and the page reloads, check below in the "Details" section for the "SNPs" line, and your SNP name will be there with a yellow-glowing red box. Click on that box for details about the SNP.

I hope you'll try again and let me know if it works for you. Once you have the needed SNP info, YSEQ can handle the testing for a new SNP that isn't in their catalog yet, using their "Wish A SNP" catalog item. As I mentioned, I've done exactly that thing. And just in the last few weeks, too.

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So that you can see what a search result is supposed to be, here is a direct link to the page that comes up if you do a search for "P5578" ...

http://ybrowse.org/gb2/gbrowse/chrY/?name=P5578

Answer 2

I'm working out the logic to make sure I understand correctly. You've identified a family with whom you have a 2nd-great grandparent couple in common, so your same-generation relatives on their side are your 3rd cousins. For your father, his same-generation cousins would be 2nd cousins. If you've done atDNA testing, then that will have been confirmed, because 3rd cousins match 98% of the time and 2nd cousins essentially 100% of the time by atDNA matching, and the amount of shared DNA should be large (see the Shared cM Project for numbers). So with atDNA testing you've identified (or hope to identify) one of your grandfather's two grandparental couples, either his maternal or paternal grandparents.

If they are his paternal grandparents, then since you and your father are a patrilineal descendant of the man in that couple, then you two will share a Y-chromosome with all his patrilineal descendants. If they are his maternal grandparents, then comparing your or your father's chrY to that couple's patrilineal descendants will give no match (unless there are a lot of cousin marriages going on). So if you do see a matching chrY then you immediately know your grandfather's father was one of the sons of that common root couple. If you don't see a match, then either it was one of their daughters who was your grandfather's mother, or that root couple was your grandfather's maternal grandparents. Is that the logic of how the Y-test will narrow things?

If you have NOT done atDNA testing on a member of that other family yet, and are hoping to use a couple of YSEQ SNP tests as a less expensive alternative than auDNA testing to confirm the common ancestral root couple between the families, then it seems to me Y-testing is too likely to not confirm anything. That root couple might really be in common with your families, but a Y-DNA match depends on their being both your grandfather's paternal (vs. maternal) grandparents (50%) and his descent from one of their sons rather than a daughter (50% if they had an equal number of each). So it's most likely a Y-DNA will tell you little to nothing, and a 25%-ish chance you'll learn that your grandfather's father was one of the root couple's sons.

My call would be to do the $99/$79 auDNA test to confirm your other research, and only if it's confirmed then do the $35 Y-DNA test you described.