Are you interested in Y-DNA, but only have an autosomal DNA test?

+16 votes
1.5k views

-then you should try Yseq's new Cladefinder. It takes autosomal files from 23andMe, Ancestry, and My Heritage and returns a qualified guess on your haplogroup. 

It is still a beta version, but it worked OK for me with autosomal files from Ancestry and 23andMe and returned haplogroup I-L22. My haplogroup found with BigY I-Y47236 is a 6th subhaplogroup to I-L22.

There are also links to the haplogroup's position on the Yfull tree and to PhyloGeographer, a data-driven project that calculates approximate male line migrations from YFull and other ancient samples with links to relevant projects and Facebook groups.

Besides, it will give you a recommendation for further SNP testing at Yseq.

EDIT to avoid confusion Men only!

in The Tree House by Ole Selmer G2G6 Mach 2 (27.1k points)
edited by Ole Selmer
A key thing to understand is that the provided haplogroup predictions are of SNPs first seen 4000 years ago, about 3000-3500 years before surnames existed.
Question:  Is this only male autosomal tests?  Could it find a suggestion for a female’s autosomal test?
Some positions on the Y chromosome are read by the "autosomal test". This predictor depends on that data entirely.

It apparently doesn't work for autosomal tests done by females. I didn't really think it would. I got this error:  

Warning: Possible female or corrupted sample  

25218 X reads, 0 Y reads  

unable to determine clade due to no positive SNPs

Some positions on the Y chromosome are read by the "autosomal test". This predictor depends on that data entirely.

Not really, I just wanted to see if my autosomal DNA test would match the haplogroup of my brother's YDNA test.  This cladefinder is not for autosomal tests done by females.
Females do not have a Y chromosome.
Yes, of course.  I just wondered if the autosomal DNA carried some bit of the father's yDNA.  Nope.  Live and learn.
As I tried to explain earlier, the predictor depends entirely on Y DNA. Y DNA is only found in the Y chromosome.
It is not quite correct to label the YSEQ y cladefinder as being based upon an "autosomal test", since it uses y SNPs that are included in the ancestryDNA, 23andme, or Myheritage tests (but not ftdna familyfinder which is strictly autosomal). That might help people understand why it only works for males. One could have a mitochondrial cladefinder tool as well; unfortunately, there just aren't many mitochondrial snps in the ancestryDNA results, so it would be of limited use.

7 Answers

+3 votes
I’m new to the dna stuff, can you dumb it down for me lol by looking at the link it tells the side of your father?
by Alice Glassen G2G6 Mach 3 (31.5k points)
edited by Alice Glassen
I shall try although others may explain it in more fluent English

The Y chromosome is transferred nearly intact from father to son with a SNP mutation now and then. Depending on how much of the Y chromosome you look at, you can expect a SNP mutation every 80 to 150 years. The mutations are stable and will not mutate back again, so you can put up a tree for males when you know the mutations.

The examination of Y-DNA at the Y-chromosome is expensive and mostly done by FTDNA and not by Ancestry, 23andMe or My Heritage. But now Yseq has found a way of finding the defining mutations in the autosomal files, but of course only in men's autosomal files. I don't think FTDNA is happy about it.
Competition should drive the price down at FTDNA.

Ole, these chips provide some coverage of the Y chromosome (and X), but it's very sparse and only useful for ruling out matches as the data is literally bronze-age prehistoric. 23andMe already provided both Y and mtDNA haplogroup predictions for quite some time.

==== This is what I got from my 2018 Ancestry atDNA file ====

Most specific position on the YFull YTree is R-M222 Link to R-M222 on YFull View theoretical migration on PhyloGeographer image
 

R-M222  FGC8023/S7815(?) Y2596/FGC449/S7072($) Y2606(?) Z2955/S653($) Z2959/S656(?) Z2960(?) Z2962(?) Z2963(?) Z2964(?) Z2967/S634(?) Z2968/S635($) Z2970/S637(?) Z2971($) Z2972/S640($) Z2973/S641(?) Z2974/S642(?) Z2975/S643(?) Z2982/S648(?) Z2984(?) Z2988/S651(?) Z2989/S652(?) Z2990/S6152(?) Z2991/S6141(?) Z2992/S655(?) M222/PAGE84/USP9Y+3636/PAGES00084+
┣━R-A7362  A7360($) A7361($) A7362($) A7363($) A7364/BY3340($) A7365/BY3341(?) Y146139/BY42873(?) Y23821($) Y24086(?) Y30427($)
┣━R-S568  S568/FGC451($)
┗━R-Y2605  Y2605/FGC4124(?)


Available Panels

  • R1b-DF49 Panel Predicted R-M222 is downstream of the panel root. This panel may be applicable if it tests subclades below R-M222. Please verify and check with YSEQ customer support.



Next best prediction (scored 198 compared to 199) 

Mike, I am not talking about finding matches or the age of haplogroups. I just asked if someone was interested in Y-DNA and then showed a cheap and in my opinion secure way of finding out in which haplogroup they belong. You don't give any names or email addresses, but I don't know if the zipfile contains any personal information.

In your case, the price would have been $39 on sale at My Heritage for an autosomal test plus the R1-DF49 panel at Yseq at $88 to know the haplogroup R-DF105. BY153644 is not in the panel yet with only 2 testers, but you can wish that SNP for $1 and I think it will be included in the R-DF49 panel later on.  

 I think you have paid several times more for let us say a Y37, Y67, Y111, BigY500, and BigY700?
Most people are using haplogroups for matching as the context is genealogy - migrations, common ancestry, surnames. The panel tests would refine the haplogroup to maybe 1500-1800 years ago. That is the age of DF105. If say you were DF85 you'd get that also. But these are still quite old.

Since you brought it up, in my case, I ordered a Y67 but cancelled after I was told it was not sufficient for surname matching. So I ordered a Y111. I then upgraded to Y500 then to Y700 w/ double the SNPs between my terminal and DF105. This is the only way to define potential branch points with useful granularity.

I don't understand why you'd be stressing cost difference, as a Y700 doesn't have equivalent application and value. Not even remotely. The difference is info from literally hundreds of YDNA positions vs tens of thousands.

The predictor+panel provides an ancient haplogroup shared by potentially millions of men. Useful but obviously limited. With a Y700 (or equivalent) perhaps 10-20 additional, newer, undiscovered terminal SNPs are provided with an age down to 83 years. 83 years per 10-20 terminal SNPs vs a 1500 year old haplogroup (in my case 1800).

90+%  of people are indeed using these tests to help match. Take a random sample of G2G posts with YDNA tag.
That’s a lot of people! I’ve been considering doing a mitochondrial test, still on the fence on it.

When I uploaded my dna to the two places to get my matches here, one gave me a ton of relatives, the other, not one. I’d hate to spend the money and not get any matches again.
For matching purposes, mtDNA is only good for determining perhaps common maternal ancestors that lived past 2500 years ago. The YDNA equivalent would be something like the old Y12 test. So a mtDNA test would provide many matches for sure. However, it'd be mainly suitable for ruling out a common, direct-maternal ancestor rather than for determining one.

My post was only meant as an appetizer and piece of service information for Y-DNA testing

I agree with you that Y700 will find a useful branch point. In my case, I tested a not-related Selmer at least back to mid-1600 and myself and found our haplogroup estimated to be formed 2000 years ago with an MRCA 550 years ago. So now I have a "Selmer" branch point that I can use to prove or disprove a match with 100 %. Besides I have tested a 7th cousin for 2 of my private variants and found that he was derived for them, and now I have another branch point. 

I see 4 ways of examining Y-DNA

  1. Y700 (or WGS) will give all known SNPs plus your private variants. Will increase our knowledge of haplogroups and the test will stay relevant with new testers. In my opinion the best choice.
  2. YSEQs Top Level Orientation Panel. Will only find known SNPs, so you have to supplement when new SNPs are found downstream. In my opinion an OK choice
  3. Autosomal test at Ancestry, 23andMe or My Heritage - Cladefinder and then the relevant SNP panel at YSEQ. You have to supplement when new SNPs are found downstream. In my opinion an OK choice
  4. Y37, Y67, Y111 In my opinion waste of money.

A good example of a situation where Y37 is not a waste of money is when you want to determine if a candidate cousin could share your paternal line in a genealogical timeframe.

Since nothing else remotely exists in comparison for the price, it's a great starting point. 

Exactly my point!

I test candidates for my "Selmer" branch point Y47236 for $18 at YSEQ with 100 % certainty compared to a Y37 on sale today for $99 with a variable Genetic Distance but with a possibility of a TIP report with a probability of x % that I shared a common ancestor within the last y generations .
+2 votes

A small note for those concerned about DNA privacy, especially given that it is a security risk to upload your data to other sites. This site offers the best possible solution. The software is open source and can be downloaded (cloned) from GitHub: 

https://github.com/hprovyn/clade-finder

It also means that the process used here isn't a "black box", but rather something where a person with sufficient skill can go in and see how it works... and even consider making a personalized version. 

by anonymous G2G6 Pilot (128k points)
+5 votes

Please enter your Y haplogroup estimated by Cladefinder at https://www.wikitree.com/wiki/Special:DNATests

by selecting Other yDNA test under Add New Test Information.  In the "free space note field" enter that your Y haplogroup was estimated by Cladefinder using your AncestryDNA, 23andMe, or MyHeritage (also enter the date you ran Cladefinder).

If you don't use Cladefinder then you can also use https://geneticgenealogist.net/2017/08/updated-method-to-get-ydna-haplogroup.html .  An alternative to PhyloGeographer is http://scaledinnovation.com/gg/snpTracker.html

by Peter Roberts G2G6 Pilot (546k points)
edited by Peter Roberts

I got unable to find FGC41245 on the YFull tree from them. 

From where do you have FGC41245? See Ybrowse 

I don’t think I did it right. I just uploaded my raw data  from Ancestry. What do you put in the top line?

Eta it’s all for guys lol
You can't use female DNA data in the cladefinder as male only has a Y-chromosome. The top line is another option to be used with SNPs from FTDNA - and men only.
Lol that’s what I figured. If I want to go further back I going to have to do the bigger buck stuff. Just not in the budget right now.
@Peter (& @Ole) - Thanks for that. The instructions for adding this additional indirect measure provides some utility for male WikiTree users who have done autosomal testing, alone, to at least potentially match others of their "ancient" haplogroup. Similarly, persons who have done the more advanced Y tests can enter their data and see how positive markers and deletions get mapped.
+3 votes
Is what you are suggesting similar to the 23&Me haplogroup suggestions?  In my case, 23&Me suggested a Y-chromosome haplogroup based (I presume) on my autosomal test results.  I found another male with my surname who matches my 23&Me haplogroup.  Genealogy strongly supports the idea that we both stem from a male with our surname born about 1800.  So, for a crude mapping of haplogroup, the info from autosomal DNA seems to work.  Even if the "granularity" of the prediction at 23&Me is not nearly as good as proper Y-DNA testing--why is it so often ignored?  It seems to work fine as a first draft. Is there a risk of false positives or negatives?
by Michael Schell G2G6 Mach 2 (27.7k points)
Yes, I think the Cladefinders results are similar to 23andMe suggestions and also done in the same way and I don't think there are risks of neither false positives nor negatives.

But as Mike has pointed out the haplogroups are often old. In your case is J-M241 supposed to have been formed 12.800 years ago with a TMRCA of 9.700 years. But with 1.264 positive J-M241 out of a total of 184.314 BigY testers as of today, I think it is a good first draft and indication for further testing.

I would recommend Y700 for one of you two and the most distant cousin in the male line you can find and then, when the results are ready to test the other of you two for the found terminal SNP at YSEQ. An alternative will be for one of you to take the recommended SNP Panel and then test the other for the found terminal SNP.
Thanks Ole, that was also my understanding, with the caveats you mentioned.  Basically, a "match" at that level of granularity is not proof-positive--but a non-match at that granularity IS a strong refutation.  Despite the fact that J-M241 diverged roughly 10,000 years ago, the number of people in this clade is relatively small compared to the total number of clades.  On Wikitree, a number of other Schell/Shell males have taken Y-DNA tests.  All of them (so far) are definitely NOT M241, so I can eliminate them as close relatives.  By contrast, the one male I found who is also predicted to be M241 on 23&Me is indeed my relative, as supported by genealogy and sources. Thus, my conclusion is that autosomal-based haplogroup prediction is a great first step (and it costs nothing) because in research, the strongest result one can obtain is a refutation.
0 votes

Just to inform you, that the cladefinder yesterday went from a beta version to version 1.0. 

Now you can also use VCF files from BigY or similar. It automatically unzips the files and convert them to hg38 The VCF files are free to download from your BigY result. 

by Ole Selmer G2G6 Mach 2 (27.1k points)
+1 vote
It is frustrating that this is only for the Y chromosome. My father died 4 years ago and I have no living brothers, male uncles or male cousins. I only have one mother, one sister (both of whom have done DNA tests - these were done in 2018 & 2019) and female cousins still living.

I only did an autosomal test - cannot afford the mtDNA test - and thus I still do not know what my haplogroup is.

Since my original DNA test was with FT DNA, would I still have to pay the full (or sale)  price of an mtDNA test or would I just need to pay for an "upgrade" which would hopefully be less than the full or sale price?

I am curious.  Wondering if the upgrade price (if there is one) might be possible.
by Robynne Lozier G2G6 Pilot (886k points)
Robynne,

If you only have the family finder test with FTDNA you would now need to pay full (or sale) price for the MTDNA.

An upgrade would only be possible if you had already taken what was called the MTDNA-Plus and now wanted to upgrade to the MTDNA full sequence. I don't think they offer the MTDNA-Plus anymore.
Y-DNA haplogroups and mtDNA haplogroups are two quite different things. Only men have Y-DNA haplogroups, and both men and women have mtDNA haplogroups, but only women can pass it on to their descendants. mt stands for mitochondria, which are the "power plants" in the cell and in sperm cells situated in the tail. The tail is left outside the egg cell so your mtDNA has been passed down in your mother's mothers line.

I don't think there are upgrade prices at FTDNA now and I am afraid you just missed FTDNA's Mother Days Sale at $139 for mtDNA Full Sequence. The normal price is $159 and the price at YSEQ for mtDNA complete is $145.
Thanks Karen.
+4 votes

My results at Big-Y were:

  • R-M207 > M173 > M343 > L754 > L389 > P297 > M269 > L23 > L51 > P310 > L151 > P312 > Z290 > L21 > DF13 > FGC11134 > BY60917 > R-BY102750

The result found by YSEQ is hereunder. It found the 6th right superhaplogroup (Panels): P312

I would say this is a reliable tool!

by Melle van der Heide G2G Crew (440 points)

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