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Thread: SNP Counting and Estimating the Age of R1b

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    Question SNP Counting and Estimating the Age of R1b

    What is the latest on the SNP-counting method of estimating the age of R1b and its subclades?

    Where can one access a relatively complete list of SNPs that excludes SNP designators that are merely different names for the same SNP (to prevent over counting)?
    Last edited by rms2; 08-02-2014 at 03:10 PM.

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    I noticed most of the discussions on this have not been on this site. I am very interested in this too and it would be nice if anyone weighed in with some thoughts on this here.

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    I posted about the long lifespan and habit of having many wives in sequence of Medieval Irish kings strongly suggesting that any top-down expansion of y lineages from kings may well have involved people who help positions of power into old age. I believe something of a pattern of a longer inter-generation average than some suspect is appropriate for similar top-down expansions in the past. Leaders may have had sons over a span of 20 years or more and lived much longer than the poor. It seems pretty likely from the whole shape of P312 that a similar process was going on much earlier - perhaps from immediately after P312 itself. It looks like a top down push rather like Medieval Ireland. If so then I wouldnt hesitate to suggest 30 years or more as an average span between the birth of a male and his father on these apparently privileged lineages.

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    I'm in process of compiling such a list combining 1KGP, 23andMe, and FGC & YFull data via Ybrowse; several of these are recurrent, having at most 10 different occurrences on the tree. So far I've counted approximately 220 SNPs spanning from the top of the R-M343 branch (i.e. at the R1a-R1b split) down to the bottom of the R-L11 branch. If I presume that the U106-P312 split took place approximately 4500 ybp, and these SNPs accumulate once per approximately 70 years on average (faster than using FGC's estimate of ~89 years/SNP using their filtered data and rejection of recurrent SNPs), I end up at circa 19,900 ybp.

    But I may be on the high side here. The rate may be slightly faster and the ages slightly more recent.

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    Why did you go for 70 years per SNP instead of 89?

    Quote Originally Posted by VinceT View Post
    I'm in process of compiling such a list combining 1KGP, 23andMe, and FGC & YFull data via Ybrowse; several of these are recurrent, having at most 10 different occurrences on the tree. So far I've counted approximately 220 SNPs spanning from the top of the R-M343 branch (i.e. at the R1a-R1b split) down to the bottom of the R-L11 branch. If I presume that the U106-P312 split took place approximately 4500 ybp, and these SNPs accumulate once per approximately 70 years on average (faster than using FGC's estimate of ~89 years/SNP using their filtered data and rejection of recurrent SNPs), I end up at circa 19,900 ybp.

    But I may be on the high side here. The rate may be slightly faster and the ages slightly more recent.

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    Quote Originally Posted by VinceT View Post
    I'm in process of compiling such a list combining 1KGP, 23andMe, and FGC & YFull data via Ybrowse; several of these are recurrent, having at most 10 different occurrences on the tree. So far I've counted approximately 220 SNPs spanning from the top of the R-M343 branch (i.e. at the R1a-R1b split) down to the bottom of the R-L11 branch. If I presume that the U106-P312 split took place approximately 4500 ybp, and these SNPs accumulate once per approximately 70 years on average (faster than using FGC's estimate of ~89 years/SNP using their filtered data and rejection of recurrent SNPs), I end up at circa 19,900 ybp.

    But I may be on the high side here. The rate may be slightly faster and the ages slightly more recent.
    How many of those are known triangulated lineages where you can say you have 1 every 70 years or whatever?

    George

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    I calibrated to the reckoning of Dr. Nortdvedt and Dr. Klyosov that P312 and U106 split approximately 4,000 to 4,200 ybp, but up-scaled for Dr. Tim Janzen's reckoning of up to 5500 ybp, and acknowledgement that sample variances tend to underestimate true population variances slightly, so presumed 4,500 ybp.

    Below R-L11 (i.e. typical R-U106 and R-P312 branches), there appear to be a range of roughly 45 to 65 SNPs per sub-branch.

    65/4500 = ~69, bumped up to 70.

    Going with the high end: (220 + 65) * 70 = 19,950. This is more than Dr. Karafet's max 18,500 ybp estimate for R-M343, but I was looking for the upper end.

    We can take the median of approximately 55 SNPs from present day to the U106-P312 split: 4500/55 = ~82 years per SNP. (220 + 55) * 82 = 23,370 ybp, which is a bit more than Karafet's 18,500 ybp. I'm leaning away from this, because I suspect that the occurrence of highly recurrent SNPs due to population expansion in recent times likely filters out a decent percentage of the true SNP count, somewhat akin to the Birthday Paradox problem.

    Obviously, it's still pretty loosy-goosy at this point. And of course, finding and successfully sequencing an LGM-era R1(b?) sample would be pretty nifty.
    Last edited by VinceT; 08-03-2014 at 01:54 AM.

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    Quote Originally Posted by George Chandler View Post
    How many of those are known triangulated lineages where you can say you have 1 every 70 years or whatever?

    George
    I don't know of any projects that employ high resolution and high coverage (i.e. FGC's 'Elite' product, not FTDNA's 'BigY' product) full sequencing of family members with proven deep-rooted pedigrees.

    SNP rates would be inversely proportional to breadth of coverage, presuming a random distribution. BigY's coverage implies a rate closer to 137 years per SNP identified among the ~10 million bases sequenced by that test, according to several reports.

    I still yet need to sift through that count of 220 SNPs to see how many of them are identifiable through BigY's coverage.
    Last edited by VinceT; 08-03-2014 at 02:17 AM.

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    Quote Originally Posted by VinceT View Post
    I don't know of any projects that employ high resolution and high coverage (i.e. FGC's Elite, not FTDNA's BigY) full sequencing of family members with proven deep-rooted pedigrees.

    SNP rates would be inversely proportional
    We're getting ~45-60 under DF13 in our group but what will differ is the number of Sanger verified SNP's. Of the 32 Sanger verified SNP's under DF13 for me only 2 have happened in the past 12 generations (one every 189 years). When I look at the other Chandler who is 10 generation to out MRCA he discovered another 5 which were culled and primers can be made (yet to be retested). I'm going to retest those as well for consistency sake. Personally I don't like using STR calculations much anymore as they have been so wrong when you actually look at the SNP results.

    George

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    Quote Originally Posted by George Chandler View Post
    We're getting ~45-60 under DF13 in our group but what will differ is the number of Sanger verified SNP's. Of the 32 Sanger verified SNP's under DF13 for me only 2 have happened in the past 12 generations (one every 189 years). When I look at the other Chandler who is 10 generation to out MRCA he discovered another 5 which were culled and primers can be made (yet to be retested). I'm going to retest those as well for consistency sake. Personally I don't like using STR calculations much anymore as they have been so wrong when you actually look at the SNP results.

    George
    Of my own list of 52 SNPs below R-U106, Z2265, (that count does not including recurrent SNPs aside from L199) only 32 are testable and validated by Sanger sequencing. At least 9 of those happened within the last 1250 years or so.
    Last edited by VinceT; 08-03-2014 at 02:51 AM.

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