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  • Y-Tree Mutation Timeline

    Irrespective of how long does each mutation takes, I always wanted a view of each haplogroup based on number of mutations. Why do I want that? That's because, when a haplogroup or subclade is having so many defining mutations, then, the other branches from the ancestor of that clade just wiped off, leaving behind just this lineage which appears on the tree. In other words, when a haplogroup or subclade is having many defining mutations, it means, a major war, invasion, natural disaster or holocaust like events. If a haplogroup or clade is having so many sister branches, then those are peaceful times or having a population explotion when no lineages are wiped off.

    Take a look at the below Y-Tree graphed based on mutation timeline.



    As you can see, A0-T branches out after 30 mutations. It means, from Y-Adam till 30 mutations of A0-T, only 2 lineages survived. At this time or during this time, some disaster might have happened, that wiped out all other sister branches. Again after 33 mutations from A0, both A00 and A0 sister clades are wiped out exactly at the same time. Similarly for other clades.

    Similar to the above diagram, the entire Y-Tree (based on 10-Marth 2014 on ISOGG Tree) is also done. You can download it from here. The first column is the number of mutations from Y-Adam and the haplogroup/subclade is expanded based on number of defining mutations (thus giving a timeline based on mutation count).

    Through this, we can trace black death, invasions and battles, severe famines etc.

    Example: Black Death
    It is impossible for Black death to leave a mark on Y-Tree which shrunk the Europe population so drastically and then the population exploded.

    Below, the first column is the haplogroup, second is the number of defining mutations, third is the number of mutations from Y-Adam and finally, the tree itself with mutation timeline.


    E-Haplogroup


    I-Haplogroup


    J-Haplogroup


    R-Haplogroup

    The yellow line signifies Black death, as there are numerous branches at that line, signifying a population explosion from a few lineages, which means, other lineages were wiped out.


    G-Haplogroup
    I feel something wrong with G because, if 281 mutations are defining it, then it means, there was a catastrophic large scale disaster where it completely wiped out it's sister clades, and only 1 lineage survived. But, I got some confirmation that G indeed has so many defining mutations - exact comment was their ancestor slept over uranium deposit and R has minimum number of mutations from Y-Adam confirmed from various sources.

    Please comment and let me know if this model can be used to trace catastrophic events like natural disasters, invasions and battles, holocaust like events etc where most of the population got wiped out leaving behind a a very few lineages.

    Link: http://www.fc.id.au/2014/05/y-tree-m...-timeline.html
    Last edited by felix; 18 May 2014, 10:18 PM.

  • #2
    Originally posted by felix View Post
    Please comment and let me know if this model can be used to trace catastrophic events like natural disasters, invasions and battles, holocaust like events etc where most of the population got wiped out leaving behind a a very few lineages.
    I do not think this thin data can be used to draw any such conclusions without combining the data with other related data-sets for reasons I have suggested in the corresponding thread about the MtDNA-tree:

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    • #3
      Originally posted by PeterLarsen View Post
      I do not think this thin data can be used to draw any such conclusions without combining the data with other related data-sets for reasons I have suggested in the corresponding thread about the MtDNA-tree:
      @PeterLarsen, Y-DNA is very different from mtDNA, unless you have actually looked into data and know what you are talking about.

      Do you know the entire defining mutations from Y-Adam to any terminal in R is much less than the defining mutation for just G haplogroup (even excluding it's branches) alone?
      Given the fact 1 mutation every 125 years based on BigY results, the age of that line calculated from the terminal can only be black death.

      Just to myself: I keep forgetting Pro 26:4 esp., with posting on online forums. No offence intended.

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      • #4
        Originally posted by felix View Post
        @PeterLarsen, Y-DNA is very different from mtDNA, unless you have actually looked into data and know what you are talking about.

        Do you know the entire defining mutations from Y-Adam to any terminal in R is much less than the defining mutation for just G haplogroup (even excluding it's branches) alone?
        Given the fact 1 mutation every 125 years based on BigY results, the age of that line calculated from the terminal can only be black death.

        Just to myself: I keep forgetting Pro 26:4 esp., with posting on online forums. No offence intended.
        Felix you are too clever for most of the people on this forum.

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        • #5
          Originally posted by felix View Post
          Just to myself: I keep forgetting Pro 26:4 esp., with posting on online forums. No offence intended.
          Felix, you and I have had our disagreements. While I don't agree with a number of your theories and positions, you have a right to have them. I feel that you have good analytic skills and appreciate the work you do in this area.

          I feel that all of that gets destroyed when you post things like this.

          This is my opinion, stick to what you are good at adding lines like this only cheapens the good work that you have done.

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          • #6
            Originally posted by felix View Post
            Do you know the entire defining mutations from Y-Adam to any terminal in R is much less than the defining mutation for just G haplogroup (even excluding it's branches) alone?
            Is your analysis accounting for the fact that the GRCh37 reference is not Y-Adam, but an amalgamation of G and R1b males? http://archiver.rootsweb.ancestry.co...-12/1387331004
            Last edited by JimKane; 28 May 2014, 06:13 AM.

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            • #7
              Originally posted by JimKane View Post
              Is your analysis accounting for the fact that the GRCh37 reference is not Y-Adam, but an amalgamation of G and R1b males? http://archiver.rootsweb.ancestry.co...-12/1387331004
              Yes indeed. The context is Y-Tree from Y-Adam. Based on my conversation with Ray Banks, he said, R is indeed having very less mutations from Y-Tree which was confirmed by various sources and G seems to have slept over a uranium ore (too many mutations and so abnormal) and repeated checking did confirm G does indeed have too many mutations - so huge that a G terminal person have 3 times more mutations from Y-Adam than R and twice as much as all other terminals. These are new developments since March 2014. If you compare R with H, R terminals are having around 220 mutations from Y-Adam while my terminal (H3a2a1) is having more than 30 mutations than R from Y-Adam. Not only this, I have 400+ Novel Variants while a person from R have around 50-100 Novel Variants.

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              • #8
                Since all aspects of the DNA replication, repair, and recombination processes are themselves under genetic control, both because of variants of the enzymes involved and probably because of variants in the DNA sequences that control those enzymes or that those enzymes bind to, I think we have to expect to see this sort of variation.

                I have always worried about the great leaps of faith involved in using the accumulation of mutations as an evolutionary clock. Yes, I do expect mutations to accumulate over time, but I question whether this clock necessarily runs at the same rate over vast spans of time and throughout a complicated and unknown genetic history. Perhaps we have an example of the difficulties of this idea in the Big Y results.

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                • #9
                  Originally posted by John McCoy View Post
                  Since all aspects of the DNA replication, repair, and recombination processes are themselves under genetic control, both because of variants of the enzymes involved and probably because of variants in the DNA sequences that control those enzymes or that those enzymes bind to, I think we have to expect to see this sort of variation.

                  I have always worried about the great leaps of faith involved in using the accumulation of mutations as an evolutionary clock. Yes, I do expect mutations to accumulate over time, but I question whether this clock necessarily runs at the same rate over vast spans of time and throughout a complicated and unknown genetic history. Perhaps we have an example of the difficulties of this idea in the Big Y results.
                  Like you say, the expected variance should be very high. There are only a very small fraction of all straight male lines that survive in the long run. We see the ones that actually survived, but we know nothing about all lines that died out. The amount of parallel subclades sharing a parent clade depends on the impact of various mechanics of evolution. If one parent clade has numerous subclades that could be a big clade (in amount of parallel male line) that "produce" a lot of mutated subclades over a small period of time, or it could be a fairly small parent clade that "produce" a lot of mutated subclades over a much much longer period of time. As long as there are males with the parent clade alive, more subclade branches can still be produced. The parallel subclades sharing the same parent can be separated by tens of thousands of years.

                  Felix; isn't my idea suggested in the corresponding mtDNA-thread, where we instead align the tree to the right and have the present vertically aligned, a better idea? The present is better known than the hypothetical past.

                  Example mtDNA-version looks like this:



                  Doing it like that keeps the tree-structure, while also visualize a more realistic view where parallel subclades sharing the same parent isn't visualized strict vertically but spawns along the x-axis from the parent.

                  Such a model suffers from the same disadvantage though, the thin data a tree structure combined with the SNP count provides. Still, going from hypothetical root all the way until present and end up at with the present visualized all over the x-axis and not lined up vertical is not a good timeline visualization in my opinion. How should one be able to draw any conclusions from such an odd version when it is so much easier to get a more realistic overview if you line the present vertically?

                  Well, you loose the 1 character = 1 mutation = x number of years, but that is so unrealistic anyways. Look at the clades today, how many unique mutations they have and try to combine them into the tree structure and keep the 1 mutation timeline? It is impossible. there are almost none of even the youngest clades that one could combine into a the tree without added spaces where no mutations could have occured on the lines.

                  Same logic for both Y-DNA and mtDNA.

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                  • #10
                    Based on the comment in my blog, I think it is worthwhile here to be in context for the discussion - the reason for this differences between G and other haplogroups.

                    The reason so many have been posted in G is that it has been the pilot, the example haplogroup, in which they are starting to post all the mutations which have been found through Next-Gen sequencing. There will someday be correspondingly large numbers of SNPs shown for all haplogroups. ... So, for now, don't take too literally the numbers of SNPs shown on the ISOGG tree to draw conclusions about human population histories.
                    From what I understand, G has been the pilot, the example haplogroup, in which they are starting to post all the mutations which have been found through Next-Gen sequencing. So, very soon, all haplogroups will have as many mutations as G once they are placed in the tree. I personally think it will take some years for the tree to be complete with all haplogroups reaching the same level of mutations as G. So, atleast for now, we cannot relate SNPs/mutations to human population histories but wait until SNPs/mutations from Next-Gen sequencing data is placed into all haplogroups in Y-tree.

                    I also think it is not the right time for any conclusions on human population histories, esp about black death, but will revisit this topic once the tree is complete with Next-Gen sequencing data.
                    Last edited by felix; 30 May 2014, 11:14 PM.

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                    • #11
                      Y-Tree Mutation Timeline

                      G has such a big jump because it starts with a large indel which destroys a lot of SNPs. There are also indels in other haplogroups.

                      It's not proven that B descends from A or C from B (though they must have a common ancestor of course). Much of A is ancient biological sidelines, some of which likely pre-date homo sapiens.

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