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  #1  
Old 24th April 2018, 02:34 PM
clintonslayton76 clintonslayton76 is offline
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Please comment - SNP vs STR

Below is a segment from a book I am preparing about my one-name study. I would be interested in any comments you might have regarding these ideas:

If SNP testing could result in projects where samplers could see surname pools as clearly as STR testing, then I would recommend nothing but SNP testing.

For another opinion: here is a paraphrase of a recommendation of a SNP analyst whose name I protect, illustrating the divergence between an expert focusing on haplos instead of male-to-male lineage:

Haplotype predictions for the cost of a Y-67 STR test are no different from a far cheaper 12 or 25 STR test, which is why I have been recommending men to test 12 STRs to get their haplogroup, then focus on testing SNPs, either testing an appropriate SNP Pack, or sequencing a Y genome.
From the standpoint of the analyst, this is perfectly logical, from both a cost and data point-of-view. But it means that interpretation is entirely in the hands of the analyst who is almost certainly not interested in your surname or family history.

Comments about yDNA STR testing as being a waste of money or somehow “second-class” coming from those who are biased toward SNP testing are not helpful: the idea that surname students should leave DNA research to the experts who can interpret SNPs totally misses the point. The estimates of aging and branching from a particular haplogroup are possible with large-scale SNP testing, but it is questionable that the most extensive SNP sequencing might lead to something of interest to those of us who are tracing males for genealogical surname purposes. A 2012 British publication about genealogical “brick walls” actually advises against yDNA STR testing until costs come down for genomic sequencing. I consider this hare-brained advice. To discourage any STR testing in the hopes of less expensive SNP sequencing in the future risks the loss of the sample altogether. Repeating myself: if SNP testing could result in projects where samplers could posit surname pools as clearly as with STR testing, then I would recommend nothing but SNP testing.
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  #2  
Old 24th April 2018, 02:50 PM
J Honeychuck J Honeychuck is offline
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To see this issue in practice, compare Family Tree DNA with 23andMe. The former uses STRs and the latter only SNPs. I ask (rhetorically) which is better for surname research?
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  #3  
Old 24th April 2018, 05:21 PM
dna dna is offline
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I do not have time until Friday or Saturday, so just a short comment since the issue is a very important one.

I am acutely aware that this is not the best solution money-wise, but I am trying to get to a point when there is at least one man, but preferably two, with Y-DNA67 (or Y-DNA111) and Big Y results in each patriline I am researching.

My views might have been different a couple of years ago, but the SNPs help us (my family) to find out who the real matches at Y-DNA67 level are. Some haplotypes are clearly shared among the lines that diverged thousands of years ago, the net result being many (for example more than 50!) matches with 67 markers or many thousands of matches with 12 markers.

On the other end of spectrum, there are men with no matches at all when using 12 markers (and while having no null values!). In such cases, Big Y offers some reassurance that one is not alone.


So Y-DNA111 (as I am not aware of any false positives on that level). Possibly only supplemented with Big Y, if either nothing comes out at first or conversely too many matches start appearing. (And Big Y only when the budget is permitting such an investment.)


Mr. W.
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  #4  
Old 24th April 2018, 11:01 PM
dna dna is offline
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More...

How possibly SNPs alone could be used for a surname project, today?

Sometime in a future? That cannot be excluded. However, one should notice that FTDNA has just bundled Y-DNA111 with the original Big Y (but Y-DNA111 is still available alone). Did FTDNA think that SNPs have to be supplemented by STRs ? ! ?


Yes, SNPs can be very useful, when trying to investigate a possibly extremely distant cousin - like one from 4000+ years ago . Otherwise, one could correctly(!) interpret the inherently limited TiP results as a non-zero chance of being related in the last 400 years (16-20 generations). If we tested our SNPs (SNP pack might be enough), just one glance tells us that our branches had Most Recent Common Ancestor 4300-5300 years ago (95% confidence interval provided by YFull). But that is all in addition to STRs.


Mr. W.


P.S.
The above is a real life example from the kits I manage here. Your mileage may vary. Past performance is not indicative of future results. Etc.
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  #5  
Old 25th April 2018, 11:48 AM
Svein Davidsen Svein Davidsen is offline
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For what it is worth: I would emphasis that both SNPs and STRs are essential. SNP mutations place you firmly on specific locations on the phylogentic tree, not necessarily on your final position, as the tree sprouts branches and twigs as the knowledge increases.

Within each tree position the STR mutations help identification of possible genealogical relationships. The more markers tested the better the predictions are. However, be acutely aware of false positives with STR matching.

One of the other replies indicates that he has not seen a false positive with 111 markers. I dont't know how he defines a false positive, but on my YFull STR match page my 3de and 4th closest matches, both 0.122 (45/370 and 28/229) are false positives in that they are 7-8 SNPs away from my sub-branch, i.e they are useless in predicting any sort of genuine relationship.

Good luck in writing you study.
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  #6  
Old 25th April 2018, 01:33 PM
dna dna is offline
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@Svein Davidsen

Quote:
Originally Posted by Svein Davidsen View Post
For what it is worth: I would emphasis that both SNPs and STRs are essential. SNP mutations place you firmly on specific locations on the phylogentic tree, not necessarily on your final position, as the tree sprouts branches and twigs as the knowledge increases.

Within each tree position the STR mutations help identification of possible genealogical relationships. The more markers tested the better the predictions are. However, be acutely aware of false positives with STR matching.

One of the other replies indicates that he has not seen a false positive with 111 markers. I dont't know how he defines a false positive, but on my YFull STR match page my 3de and 4th closest matches, both 0.122 (45/370 and 28/229) are false positives in that they are 7-8 SNPs away from my sub-branch, i.e they are useless in predicting any sort of genuine relationship.

Good luck in writing you study.
I meant specifically matches with FTDNA Y-DNA111.

And what is the difference to those two men, when you limit yourself to 111 markers used by FTDNA Y-DNA111 test? I mean the difference counted like FTDNA counts? (It is OK for some STRs to be not reported.)

In my opinion, there is a very good chance that the matches you gave as examples would not show as matches with Y-DNA111 test.


Mr. W.
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  #7  
Old 25th April 2018, 02:32 PM
Svein Davidsen Svein Davidsen is offline
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Quote:
Originally Posted by dna View Post
I meant specifically matches with FTDNA Y-DNA111.

And what is the difference to those two men, when you limit yourself to 111 markers used by FTDNA Y-DNA111 test? I mean the difference counted like FTDNA counts? (It is OK for some STRs to be not reported.)

In my opinion, there is a very good chance that the matches you gave as examples would not show as matches with Y-DNA111 test.


Mr. W.
You are quite correct of course, they don't show up on my STR 111 match page, but then again I don't know if they have taken the 111 test.

In fact I don't have a single match that meets the FTDNA match criteria for 111 markers. One recent tester have the same terminal SNP as me, N-Y17416, but he has only taken the 67 marker test, so no result for 111 markers, but neither does he show up on my 67, 37 or 25 marker comparison! We match 54/67, on my count, and as our ancestries are thousands of miles/kilometers apart we are not "kissing cousins"!

EDIT
Sorry, disregard the above paragraph - I mixed up two results. The 67 marker tester is 1 SNP downstream from me. This obviously is what is reflected in the STR difference between us!
End Edit.

With excuses to clintonslayton76 for hijacking his thread, does anyone know how the new 450 FTDNA's additional STR markers compare with the 4 - 500 markers used by YFull? Is there much of an overlap?

Last edited by Svein Davidsen; 25th April 2018 at 02:57 PM.
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  #8  
Old 25th April 2018, 03:24 PM
dna dna is offline
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In the Y-DNA111 test none of the STRs used is named FTY*, my guess FTY* are STRs discovered at FTDNA and not necessarily read by the other labs.

Most of the new ones are FTY*. I had counted that 55 of the new STRs are not FTY*:

DYF392, DYF398A, DYF398B, DYF405, DYS389B,
DYS453, DYS466, DYS474, DYS475, DYS476,
DYS477, DYS480, DYS483, DYS484, DYS488,
DYS489, DYS493, DYS499, DYS502, DYS507,
DYS508, DYS512, DYS514, DYS516, DYS523,
DYS530, DYS538, DYS539, DYS541, DYS542,
DYS543, DYS544, DYS551, DYS569, DYS573,
DYS574, DYS577, DYS580, DYS581, DYS583,
DYS584, DYS585, DYS598, DYS602, DYS608,
DYS615, DYS616, DYS618, DYS620, DYS623,
DYS624, DYS631, DYS637, DYS642, DYS645

I have no idea whether they happen to be the ones used by YFull.


Mr. W.


P.S.
Please also find included the full list of STRs reported by FTDNA (from my CSV download). And the same STRs sorted alphabetically.
Attached Files
File Type: txt all_FTDNA_reported_STRs_1-561.txt (3.7 KB, 2 views)
File Type: txt sorted_FTDNA_reported_STRs_1-561.txt (4.3 KB, 1 views)
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  #9  
Old 27th April 2018, 03:03 AM
Svein Davidsen Svein Davidsen is offline
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Thank you dna/Mr.W.

I guess I should ask on the YFull FB page if there is a list of the YFull markers.
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  #10  
Old 27th April 2018, 03:41 AM
dna dna is offline
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Quote:
Originally Posted by Svein Davidsen View Post
Thank you dna/Mr.W.

I guess I should ask on the YFull FB page if there is a list of the YFull markers.
According to their FAQ https://yfull.com/faq/str-interpretations/ if you download your STR results with the option All you will get all of them, just some might be low confidence results.


Mr. W.


P.S.
A comparison might be easier than expected. It is possible that YFull has all or most of STRs beyond first 111 as either DYF* or DYR*. FTDNA does not have a single DYR and only the following DYFs: DYF392, DYF398A, DYF398B, DYF405, DYS389B.

My above guess is based on a low quality JPEG screenshot that does not include all of the YFull STRs.

Last edited by dna; 27th April 2018 at 03:58 AM. Reason: +P.S.
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