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How to estimate the age of a SNP?

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  • How to estimate the age of a SNP?

    How do you estimate the age of a SNP? I often see SNPs referred to online as being say 3000 years old but I'm not sure how to work this out.

  • #2
    YFull has a documented system to estimate SNP ages. This is how to get their estimate:
    1) Go to YFull's SNP search page
    2) Enter a SNP name and click the Search button
    3) A green hyperlink, labeled with a haplotree branch name (e.g., "R-L47"), should be displayed. Click on it.
    4) You should now see a branch of the haplotree. Typically, this branch will have two dates:
    a) The "formed" date is an estimate of when this branch began to diverge from its surviving siblings. (Extinct siblings are unknowable and therefore ignored.)
    b) The "TMRCA" date is an estimate of when this branch's surviving children began to diverge from each other. (Again, extinct lineages are ignored.)

    If your SNP of interest has been discovered recently, of course, it may not appear in YFull's haplotree yet.

    Many experts assert, based partly on tests of ancient DNA, that YFull's age estimates are 10-20% too low. On the other hand, many of those same experts assert that a haplotree branch typically goes through a "gestation period" (growth inside the tribe) before a major expansion; this hypothesized gestation interval may effectively cancel out the alleged 10-20% error.
    Last edited by lgmayka; 7th July 2016, 09:34 AM.

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    • #3
      Unfortunately my terminal SNP is only shared with two other people who have not uploaded their data to YFull and the SNP above that sufferers from the same situation and then the one above that is R-L2 which is very old.

      Thanks for the reply though, it looks like I'll just have to get the others to send their data to YFull.

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      • #4
        It is important to remember that almost all of the Y chromosome SNP ages are estimates. Even if the average rates of mutation happen to be correct, which I think is far from certain, it does not follow that any particular mutation or series of mutations happened to conform to the "average". The order of branching of the Y chromosome SNP "tree" is likely mostly correct, but beyond that, I think the age estimates have to be treated with caution.

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        • #5
          Poznik et al. 2016 age estimates aren't that far off from what YFull has especially when you take in to consideration the ranges that they have. It does show them to be slightly older that the specific date that YFull shows and the Poznik et al. age estimations are closer to what another person that uses STR markers for age estimations. So in a general sense the dates aren't that far off. The ancient DNA specimens are proving that the SNPs are at least as old as the age estimates. More ancient specimens being tested should prove the same and maybe even come very close to the age estimates.

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          • #6
            The results and methodology used for determining ages from BIg-Y SNPs can also be found in Iain McDonald's U106 analysis. Read the PDF's at http://www.jb.man.ac.uk/~mcdonald/genetics.html which are updated several times a year.

            On the whole the Y-Full estimates agree with the U106 results but specific age estimates, especially for U106 based haplogroups, may be off due to the limited number of samples that have been submitted to Y-Full.

            Remember that there is no "TERMINAL SNP" unless you have specifically tested and ordered all of your novel SNPs. I know my "TERMINAL SNP" showed up in my great-grandfather.

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