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  • Large Y descent clusters

    I was just studying an interesting paper that first appeared last summer and has been noted here.

    Y-chromosome descent clusters and male differential reproductive success
    http://www.ncbi.nlm.nih.gov/pubmed/25585703

    They looked at 5000 samples from Turkey to East Asia for SNPs and 8-STR haplotypes, and then focused on haplotype clusters that occurred in a large number of people. Haplotypes were only included in a cluster if they were in the same SNP haplogroup. Most haplotypes occurred only once, but 15 occurred in 9-71 samples. They then looked at haplotypes closely related to those 15 clusters and they grouped down to 11 descent clusters.

    This kind of thing has been seen before in an Irish M222 cluster and 2 Central Asian clusters which these guys found again.

    The idea in all this is that unusually large clusters of men in closely related haplotypes may reflect the descendants of patriarchs who were dominant males, like the proposed Ghengis Khan descent cluster. They detected that cluster - it was the most numerous with 71 samples. They mapped the clusters geographically and estimated regions of origin by STR variance. Also estimated time to MRCA of each. Some clusters localized to a defined region - others were spread in a way suggesting a migration - the "Khan" was one of these.

    The one I found interesting was a J1 cluster that fits by time of expansion and locale to the era of the Assyrian and Neo-Babylonian Empires. It could be the offspring of a royal line of one of these Empires. This leads to one of my favorite silly songs, The Mesopotamians. by They Might Be Giants, which I find to be a real earworm. The video still cracks me up at the 50th view.

    They Might Be Giants - The Mesopotamians (official TMBG video)
    https://www.youtube.com/watch?v=jAMRTGv82Zo

    It seems likely that large descent clusters could be found and TMRCA determined in the large haplogroup projects using SNPs alone. My little clade (FGC12346) is definitely not one of them at <0.2% of U106.
    Last edited by PNGarrison; 14 March 2015, 05:05 PM. Reason: Forgot something.

  • #2
    Originally posted by PNGarrison View Post
    I was just studying an interesting paper that first appeared last summer and has been noted here.

    Y-chromosome descent clusters and male differential reproductive success
    http://www.ncbi.nlm.nih.gov/pubmed/25585703

    They looked at 5000 samples from Turkey to East Asia for SNPs and 8-STR haplotypes, and then focused on haplotype clusters that occurred in a large number of people. Haplotypes were only included in a cluster if they were in the same SNP haplogroup. Most haplotypes occurred only once, but 15 occurred in 9-71 samples. They then looked at haplotypes closely related to those 15 clusters and they grouped down to 11 descent clusters.

    This kind of thing has been seen before in an Irish M222 cluster and 2 Central Asian clusters which these guys found again.

    The idea in all this is that unusually large clusters of men in closely related haplotypes may reflect the descendants of patriarchs who were dominant males, like the proposed Ghengis Khan descent cluster. They detected that cluster - it was the most numerous with 71 samples. They mapped the clusters geographically and estimated regions of origin by STR variance. Also estimated time to MRCA of each. Some clusters localized to a defined region - others were spread in a way suggesting a migration - the "Khan" was one of these.

    The one I found interesting was a J1 cluster that fits by time of expansion and locale to the era of the Assyrian and Neo-Babylonian Empires. It could be the offspring of a royal line of one of these Empires. This leads to one of my favorite silly songs, The Mesopotamians. by They Might Be Giants, which I find to be a real earworm. The video still cracks me up at the 50th view.

    They Might Be Giants - The Mesopotamians (official TMBG video)
    https://www.youtube.com/watch?v=jAMRTGv82Zo

    It seems likely that large descent clusters could be found and TMRCA determined in the large haplogroup projects using SNPs alone. My little clade (FGC12346) is definitely not one of them at <0.2% of U106.
    I think that there is another reason which the scientists don't fully understand yet for this phenomenom.

    Comment


    • #3
      1798, why don't you speak your mind?

      Comment


      • #4
        Originally posted by MikeP View Post
        1798, why don't you speak your mind?
        I did.

        Comment


        • #5
          Oh, come on Ciaran. Enlighten us. Telling us that you know the answer, but you won't say what it is, is not exactly speaking you mind.

          Comment


          • #6
            Originally posted by 1798 View Post
            I did.
            Ciaran has spoken! All further scientific knowledge or questions are futile since the world's leading authority has decided the question. If only the oracle of Delphi were around, we would know what Ciaran's judgement is, since he won't tell us himself.

            Comment


            • #7
              Originally posted by PNGarrison View Post
              Oh, come on Ciaran. Enlighten us. Telling us that you know the answer, but you won't say what it is, is not exactly speaking you mind.
              I did not say that I knew the answer. I may have a few ideas about dna but if I shared them I would be accused of being a crackpot.

              Comment


              • #8
                Originally posted by PNGarrison View Post
                Oh, come on Ciaran. Enlighten us. Telling us that you know the answer, but you won't say what it is, is not exactly speaking you mind.
                Can the female have a role in the number of mutations on the Y chromosome?

                Comment


                • #9
                  Originally posted by 1798 View Post
                  Can the female have a role in the number of mutations on the Y chromosome?
                  Try searching Google Scholar - http://scholar.google.com/?hl=en - for something like "y chromosome mutations" and review the results. Then, if you do find something that supports your idea, report back to us. If you do, please provide a link and also quote the relevant text that backs up your idea.

                  Comment


                  • #10
                    The number of new mutations occurring in any part of the genome will depend on the genetic background of genes coding for DNA replication and repair, and those genes are all over the autosomes, so yes the chromosomes a man gets from his mother will have an effect on mutations that occur in the DNA that he passes on, if that's what you mean.

                    Comment


                    • #11
                      Originally posted by PNGarrison View Post
                      The number of new mutations occurring in any part of the genome will depend on the genetic background of genes coding for DNA replication and repair, and those genes are all over the autosomes, so yes the chromosomes a man gets from his mother will have an effect on mutations that occur in the DNA that he passes on, if that's what you mean.
                      A lot of the M222 group are very close at 67 markers and they have a very strong genetic signature. Why do you think that is?

                      Comment


                      • #12
                        Originally posted by PNGarrison View Post
                        The number of new mutations occurring in any part of the genome will depend on the genetic background of genes coding for DNA replication and repair, and those genes are all over the autosomes, so yes the chromosomes a man gets from his mother will have an effect on mutations that occur in the DNA that he passes on, if that's what you mean.
                        FMS can be sequenced from Big Y results. Why is that? What part does the female play in the Y.

                        Comment


                        • #13
                          Originally posted by 1798 View Post
                          FMS can be sequenced from Big Y results. Why is that? What part does the female play in the Y.
                          Can you reference the source for that please.

                          My understanding was that Mitochondrial DNA is only found in Mitochondria.
                          Autosomal and sex DNA are only found in cell nuclei.

                          Comment


                          • #14
                            Originally posted by Jomid59 View Post
                            Can you reference the source for that please.

                            My understanding was that Mitochondrial DNA is only found in Mitochondria.
                            Autosomal and sex DNA are only found in cell nuclei.
                            The FMS results are in the Bam file that comes with the Big-Y results.

                            Comment


                            • #15
                              Originally posted by 1798 View Post
                              The FMS results are in the Bam file that comes with the Big-Y results.
                              Thank you. Did not know that.

                              Comment

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