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SNP Testing

Posted: Sun, 2021-Mar-28 3:51 am
by Mark Monroe
*** Up for general discussion ***

I belong to a project where a knowledgeable member suggests limited SNP testing in lieu of in depth SNP testing and then riding on the shirt tails of close matches with Big-Y results to get an assumed confirmed terminal haplogroup to save money. One of my closest matches in the Y111 STR level has appeared to have taken his advice and has a Terminal Haplogroup of R-M222 which to me would be worthless information. I was given the same advice four years ago but did not take it. It appears he has taken the YSEQ R-M222 test and nothing else for SNP testing. I have reached out to him to upgrade to WGS400 or at least the Big-Y700. His results indicate we are a millennium apart even though I believe we are a lot closer.

Was I wrong in my suggestion?

Did he get bad advice?

How or should I convince him to upgrade?

To date, crickets...

Re: SNP Testing

Posted: Sun, 2021-Mar-28 12:54 pm
by Webmaster
Mark,

In essence, yes, testing to just R1b-M222 is not particularly useful. To ride the coattails of BigY or other NGS/WGS tests would mean to test against the unique/private variants of someone you think you are closely related to. That is what we did for my father and 2 McDonough men. There was another particular man who had done a BigY 500 test and his results were on The Big Tree. We did Wish-A-SNPs at YSEQ for his unique/private variants and were positive for several of them. That actually helped establish the R1b-FGC65253 clade.

That to me is a perfectly acceptable way to get close to a terminal clade and save money. But to only test to a high-level like R1b-M222 and then to use STR data to "match" below that is foolish. From the ISOGG website:
Convergence (also known as evolutionary convergence) is a term used in genetic genealogy to describe the process whereby two different genetic signatures (usually Y-STR-based haplotypes) have mutated over time to become identical or near identical resulting in an accidental or coincidental match.

One can think of convergence as producing misleading matches – two men appear to be more closely related than they actually are. The same situation may result (very occasionally) if there is an exceptional lack of divergence. In other words, so few mutations occurred in the descendants of a common ancestor over the course of time that the common ancestor may appear to have lived only a few hundred years ago when in fact he lived much further back than that, perhaps several thousand years ago.

Parallel mutations and back mutations in individual STR marker values are the mechanisms by which convergence occurs.

Convergence is likely to be a particular problem within haplogroups R1b and I1 which both have a more recent origin but expanded very rapidly. The haplotypes which are most affected are likely to be those which are closest to the modal haplotype for the haplogroup, such as people who match the Western Atlantic Modal Haplotype or the so called Niall of the Nine Hostages haplotype. The presence of matches with a large number of different surnames is a possible indicator that convergence has occurred. Convergence is more likely to be a problem with low-resolution 12-marker and 25-marker matches, but does also occur with 37-marker matches. It is less likely to occur at 67 markers, though a case has been reported of two 67-marker haplotypes with a genetic distance of 6, which were found to be in different R1b subclades. If convergence is a possibility then it is recommended to upgrade to a minimum of 67 markers and to order SNP testing to help rule out the coincidental matches which will have no genealogical relevance.

The incidence of convergence is not known, in part because the majority of people in the Family Tree DNA database have not ordered any SNP testing. Robert Casey has estimated that perhaps only 5% to 10% of genetic families or groups in surname DNA projects are affected by the problems of convergence but for the people in such groups perhaps 20% to 90% of their matches might be false positives.
That is about as plain and clear as it gets as to why depending on STR matching without corroborating detailed SNP testing for R1b-M222+ men in particular is just foolish. Another way is to look at the DCG STR Analyzer. It quickly becomes apparent that men in quite widely different clades have closer haplotypes (STR matching) than men in close clades.

I blame testing companies like FTDNA for propagating the "myth" that STR matching alone is meaningful, when it has been known for years now that for R1b+ men it is not. Rather than waste money on an FTDNA Y-STR111 test or similar, the SNP panel tests from YSEQ offer a far better value. For men who have a good idea they are R1b-DF49+, which is upstream of R1b-M222, the R1b-DF49 SNP Panel test for US$88 is a great test that will get you down to a near terminal clade, based on published Y-Haplotrees/Cladograms like FTDNA's, YFull's, The Big Tree's, and the DCG's.

For someone who has no idea of their location on the Y-Haplotree, the YSEQ TOP Panel for US$159 is a fantastic test. It literally works down all known clades to find a near terminal clade, again, based on published Y-Haplotrees/Cladograms like FTDNA's, YFull's, The Big Tree's, and the DCG's.

Compare those prices to an FTDNA Y-STR111 test for US$119, which again, leaves you with matching ambiguity due to STR Convergence versus knowing your near terminal clade. Let common sense rule...

As a final note, the one caveat to ANY SNP Panel testing is the possibility that a man may belong in an undiscovered-as-yet clade, and wind up with a fairly high-level terminal clade. In this situation, ONLY a WGS test like the WGS400 will uncover the actual terminal clade.