Hello,?

unfortunately, received an email today regarding BigY-700, that the sample experienced a quality control failure at the end of its most recent run and they are starting a rerun immediately at the highest priority. Another couple of months I would say. Frustrating. I dont know will they do the analysis from the very beginning or only the last part, but was thinking whether that mistake had an impact on the fact that I don't have matches on Y 37, 67 and 111? Could that be the case?

Cheers,?
Dado

Connie, took me a couple of minutes to realize and remember you are one of the administrators for FTDNA U106 groups.? Below is Tatiana's response.? I will speak with FTDNA.

Hello Gene.

Unfortunately, SNP BY39679 is of poor quality and is found in other haplogroups. We had to remove it from the tree:?
Other SNPs of this subclade are negative in sample YF112399.

Best regards, Tatiana
YFull Team

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Hi Gene,

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I don't have much time to dig deep into the details tonight, but have you got the order right? R-Y31448 layers above R-BY39679, so a move from R-Y31448 to R-BY39679 would actually be a refinement of the haplogroup.

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Cheers,

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Iain.

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Hi Iain, I was quite surprised to see B move backward from R-BY39679 > R-Y31448.? The top tester L still has not finished the STR sorting.? When completed I will see if he also moves backwards.? There was no change in the other 7 T2T completed.? I have not asked Tatiana why the change backwards yet.

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Just to further Myles's comment: there are two conditions under which an STR can be reported as zero. The first is (as in Myles's example) if a mutation causes the STR to become unreadable by the primer used to measure it - there are many examples of this.

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The second is a true deletion, where the STR is entirely deleted from the Y chromosome. This is rarer, but does occasionally happen, and we have haplogroups within R-U106 that have entirely lost specific Y-STRs. In these cases, the Y-STRs can never "grow back" again. They will always remain completely deleted.

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- Iain.

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Razib Kahn's commentary.?

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Preprint from the Reich lab.?

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Hi Richard,

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The recombinations that Thomas Hunt Morgan discusses on the autosomes don't apply to the male-specific Y chromosome, because it doesn't recombine. For the autosomal DNA, I'll leave that to more experienced people on here.

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For the Y chromosomal mutations, there is no specific evidence to suggest that they are not random. However, there is a murky world down there that operates on much longer timescales than individual mutations. There do seem to be some "preferred" values for some STRs, whether this is due to structural stability of folding on the chromosome or something similar, I don't think is known. At some point, STR lengths have to be non-zero, otherwise the STRs disappear. The STR mutation rates do also seem to have some variation between haplogroup, though this is mostly down to systematic differences in the average STR length in specific haplogroups, because longer STRs have more repeats to mutate. There is a lot of this stuff that we simply haven't had the opportunity or databases to look at in detail.

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Cheers,

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Iain.

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Hi folks,

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Mike's comments are spot on, but I thought I'd try to be a bit more pedantic *ahem* precise in the reasoning.

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The reason people appear and disappear from match lists at different levels comes down mostly to random chance. I mentioned the Time Estimate table on the Y-STR results: you can see from this that the nominal cutoff for individual matches is a little over 1000 years in each case.

Now we know that the number of mutations a family builds up over 1000 years on each Y-STR is random. Some families will get a mutation, others won't. But if you're only looking at a small number of STRs and a small number of mutations, you'll find some families have no mutations and others have loads. It's only by taking a large number of Y-STRs that this effect averages out, and we get a better consistency in the number of mutations a family has accured. If you have a match close to this boundary, you might find that they have few mutations in the first 37 markers, so they are a match at Y-37, but lots of mutations in the 38-67 marker set, so they don't match at Y-67, but fewer mutations in the 68-111 marker set, so they are a match again at Y-111. This is the main reason that matches can appear at higher levels that weren't at lower levels.

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However, it is also true that the first 37 markers are a bit special. They are not especially "jumpy" or "erratic" in the technical sense, but their unusual combination of mutation rates does cause them to behave differently. Markers 38-111 are a fairly typical set of Y-STR mutations. However, when FTDNA was putting together the first set of 37 Y-STRs, which now seems to have become something of an industry standard, they picked specific STRs for specific reasons.

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Those choices were based how effectively they could be used to group people into genetic families. The first 12 markers are mostly very slow-mutating markers (e.g. DYS426, DYS388, DYS392), which lets people be reliably grouped into major haplogroups (e.g. R-M269). Both the Y-25 and Y-37 upgrades brought in more slow markers, but also added a number of faster ones: e.g., DYS458 and DYS464 in Y-25 and CDY, DYS576 and DYS570 in Y-37. These fast-mutating markers give a much better chance of finding mutations within a closely related family, but are pretty useless at grouping people on older timescales because there are too many convergent and back mutations on them. This wide range of mutation rates means it's both very easy to build up a large genetic distance from someone quickly, and relatively easy for spurious matches with convergent mutations to enter your Y-12, Y-25 and Y-37 match lists.

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To give you a sense of scale, you're about 100 times more likely to get a mutation on one of the CDY markers as you are on DYS426. When dealing with a wide range of mutation rates and fast-mutating markers, the relationship between TMRCA and genetic distance quickly breaks down due to the hidden and back mutations: the probability of getting a convergent or back mutation in two families over 1000 years is about 66% and is most likely to occur on CDY, with each of its two markers mutating roughly every 40 generations.

However, FTDNA generally simply takes an average of the mutation rates when dealing with Y-STR markers. If you do this, then you'd predict that a convergent or back mutation only happens about 49% of the time. So, even if FTDNA's Time Estimates accounted for convergent and back mutations, and even if it accounted for the growth in the number of cousins with time, this simplification to an average mutation rate would cause their estimates to underestimate the full range of possible TMRCAs.

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Cheers,

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Iain.

What Jason said is right, this can happen that we "have matches that disappear at 1 level before reappearing at another"

Ian noted too that "If you don't have any matches beyond Y-12 and Y-25, then it's likely that either no-one in the FTDNA Y-DNA database is related to you via your male line within the last 1000 years or so, or you have an unusual number of mutations in your Y-DNA."

The issue he brings up "or you have an unusual number of mutations" is a real issue. It happens more often than we think that there are matches that appear at Y67 and Y111 that don't appear at Y37 or even Y25 or Y12.? It may be in yourself or in the "missing matches".

This is because the first 37 STR markers are a little more "jumpy" erratic than 38-67 or 68-111.? The additional markers tend to smooth things out for more refined matching. Here is a study about this phenomenon.

"The Strange Case of the Missing Y37 Match" related to the Owston surname concludes:
*** "Do not discount the possibility that match may exist at 67 markers but be absent at 37 markers." ***
"In analyzing the matches of 18 matching FTDNA Y-STR participants in the Owston/Ouston DNA study..
- 100% of the men who tested at 67 markers matched at least one individual who was not found in their 37-marker match list"
- "The percentage of non-matches at 37 within the 67-marker match list ranged from 3.6% to 35.3% of their total 67-marker matches.
- "An average of 14.1% of their 67-marker matches were absent from their 37-marker match list.
"The Strange Case of the Missing Y37 Match" Jim Owston, 2018

https://linealarboretum.blogspot.com/2018/02/the-strange-case-of-missing-y37-match.html

By the way, this happens with me. When my group first started with Big Y, four of my six Y111 matches did not appear at Y12, Y25 or Y37.? It turned out via Big Y testing that two of the four missing matches were related to me in the last 700 years, the other two in the last 1500 years. All four of these missing matches were instructive to me.

I encourage deeper testing, such as Big Y700, rather than relying on STR matching to build a tree.