Announcement

Collapse
No announcement yet.

mt-Tree Mutation Timeline

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    Originally posted by PeterLarsen View Post
    I thought it was an effect of the well known mechanics of evolution, like for example:
    Genetic drift
    Fixation
    Natural selection
    Population bottleneck effects
    Founder effects
    Migration

    Please explain the details in why you think it is an effect of natural disasters. In my world a natural disaster wipes off a random fraction of an isolated population, and as the number of non-mutaded individuals always outnumber the number of mutated individuals, since the mutationrate is less than 50%, I can't understand how a natural disaster like the blackdeath should impact the MtDNA-tree the way you are suggesting. If, for example, a disaster wipes off 80% of a population it will leave 20% individuals and statistically those 20% should represent the total population in the fraction-size of individuals with mutated contrary non-mutated MtDNA individuals.

    Anyway, I do not understand these things good, it takes scientists many years to come up with good theories on this subject, so please explain why you think it is like you say and not what the general science in this area suggests.
    Unless you have a better explanation for large number of defining mutations for a subclade with lack of many sister clandes and suddenly an explosion of large number of branches. No one has given any explanation for these patterns. These patterns can only indicate a survival story from a massive wipe off and thriving later.

    Comment


    • #17
      Originally posted by felix View Post
      Unless you have a better explanation for large number of defining mutations for a subclade with lack of many sister clandes and suddenly an explosion of large number of branches. No one has given any explanation for these patterns. These patterns can only indicate a survival story from a massive wipe off and thriving later.
      When I read your "theory", I read:

      1. A mtDna-three graph visualized with a different X-axis.
      2. ?
      3. ?
      4. ?
      5. ?
      6. ?
      7. What you are looking at therefor must be black death.

      Where is the missing explaination and the details where you describe how you come to that conclusion?

      Comment


      • #18
        Originally posted by PeterLarsen View Post
        When I read your "theory", I read:

        1. A mtDna-three graph visualized with a different X-axis.
        2. ?
        3. ?
        4. ?
        5. ?
        6. ?
        7. What you are looking at therefor must be black death.

        Where is the missing explaination and the details where you describe how you come to that conclusion?
        I though I explained it, happy to explain further.

        Large number of defining mutations for a subclade with lack of many sister clandes and suddenly an explosion of large number of branches can explain only one thing - a disaster that is capable of wiping out all the sister clades of the subclade which had large number of defining mutations that survived and thrived after the disaster. This is because, the time taken for a subclade to have large number of mutations means, there should be other sister branches missing in the tree. Then, all of a sudden a large number of branches means, the population is growing exponentially, creating new mutations/branches. If you take the number of branches at each stage it is proportional to the world population, where extremely large amount of branches were seen only at the terminals - not at the roots or even intermediate. This can explain only one thing - most of the terminal clades with less than 5 mutations from the terminal are very recent. As I said, H timeline is a very good example for Black death.

        Comment


        • #19
          Originally posted by felix View Post
          I though I explained it, happy to explain further.

          Large number of defining mutations for a subclade with lack of many sister clandes and suddenly an explosion of large number of branches can explain only one thing - a disaster that is capable of wiping out all the sister clades of the subclade which had large number of defining mutations that survived and thrived after the disaster. This is because, the time taken for a subclade to have large number of mutations means, there should be other sister branches missing in the tree. Then, all of a sudden a large number of branches means, the population is growing exponentially, creating new mutations/branches. If you take the number of branches at each stage it is proportional to the world population, where extremely large amount of branches were seen only at the terminals - not at the roots or even intermediate. This can explain only one thing - most of the terminal clades with less than 5 mutations from the terminal are very recent. As I said, H timeline is a very good example for Black death.
          I thought you had done research and estimations on the different mechanics of evolutions impact on a haplotree, and used a method/methods to rule out every other possible reasons leaving black death as the only possible explaination. But you have done nothing like that right?

          I mean, for example, if a population with a 10 000 population limit constraint spend 100 generations isolated an island. In generation 101, 5 females escapes the island using a boat, they survive reaching the mainland without such strict population limit and the descendents straight female lines from those 5 individual females is extreamly many, and in the next 100 generations they are the maternal roots for 5 different groups of 10 000 females each. How are you suggesting the MtDNA-tree from such event whould look like and how do you separate it from the impact black death has on the MtDNA-tree?

          I mean, you explain absolutely nothing about how you came to your conclusion. If you say it is the cause of black death, then you must somehow have used a method to distinct the impact black death has on the MtDNA-tree from other mechanics of evolution, or else you can't know the cause, right?

          So please let me re-phrase my question a bit:
          1. What other mechanics of evolution have you studied and tried to estimate how they impact the MtDNA tree?
          2. What are the impacts? How do they "look" on the MtDNA tree if it is viewed and visualized the tree the way you did?
          3. Please explain the details in the method/methods you have used to separate black death from the other mechanics of evolution.
          4. Please list the results of the methods and investigations on the other mechanics of evolution. Visualize how, what impact, they have on the MtDNA-tree. I assume you know it already since you have ruled them all out.


          Thanks in advance! Don't forget to explain how my example with the isolated population on the island most probably is visualized on the MtDNA-tree.
          Last edited by PeterLarsen; 22 May 2014, 12:12 PM.

          Comment


          • #20
            Originally posted by PeterLarsen View Post
            I thought you had done research and estimations on the different mechanics of evolutions impact on a haplotree, and used a method/methods to rule out every other possible reasons leaving black death as the only possible explaination. But you have done nothing like that right?

            I mean, for example, if a population with a 10 000 population limit constraint spend 100 generations isolated an island. In generation 101, 5 females escapes the island using a boat, they survive reaching the mainland without such strict population limit and the descendents straight female lines from those 5 individual females is extreamly many, and in the next 100 generations they are the maternal roots for 5 different groups of 10 000 females each. How are you suggesting the MtDNA-tree from such event whould look like and how do you separate it from the impact black death has on the MtDNA-tree?

            I mean, you explain absolutely nothing about how you came to your conclusion. If you say it is the cause of black death, then you must somehow have used a method to distinct the impact black death has on the MtDNA-tree from other mechanics of evolution, or else you can't know the cause, right?

            So please let me re-phrase my question a bit:
            1. What other mechanics of evolution have you studied and tried to estimate how they impact the MtDNA tree?
            2. What are the impacts? How do they "look" on the MtDNA tree if it is viewed and visualized the tree the way you did?
            3. Please explain the details in the method/methods you have used to separate black death from the other mechanics of evolution.
            4. Please list the results of the methods and investigations on the other mechanics of evolution. Visualize how, what impact, they have on the MtDNA-tree. I assume you know it already since you have ruled them all out.


            Thanks in advance! Don't forget to explain how my example with the isolated population on the island most probably is visualized on the MtDNA-tree.
            The timeline is a contribution for people who want to visualise the MtDNA tree in mutation scale. It is not for people who looking for black death. Just because it is my opinion based on what I found does not mean you have to agree with it.

            Comment


            • #21
              Originally posted by felix View Post
              I though I explained it, happy to explain further. Large number of defining mutations for a subclade with lack of many sister clandes and suddenly an explosion of large number of branches can explain only one thing - a disaster that is capable of wiping out all the sister clades of the subclade which had large number of defining mutations that survived and thrived after the disaster. ... As I said, H timeline is a very good example for Black death.
              That's an unreliable assumption - constant or slow population growth and population drift is a more likely explanation. And your H timeline is off by more than 10,000 years because you don't accept the theory of evolution, i.e., that humans and the great apes descend from a common ancestor who lived around 6 to 8 million years ago.

              Comment


              • #22
                Originally posted by GST View Post
                That's an unreliable assumption - constant or slow population growth and population drift is a more likely explanation. And your H timeline is off by more than 10,000 years because you don't accept the theory of evolution, i.e., that humans and the great apes descend from a common ancestor who lived around 6 to 8 million years ago.
                Neither slow population growth nor population drift can be verified 10000 years back. So, lets use "methods" that can be verified for the patterns found. This way, it will be more scientific.

                Comment


                • #23
                  Originally posted by felix View Post
                  Neither slow population growth nor population drift can be verified 10000 years back. So, lets use "methods" that can be verified for the patterns found. This way, it will be more scientific.
                  Well, in fact we do have scientific evidence for very slow population growth in Europe during the Mesolithic, so population bottleneck and genetic drift is a plausible scientific theory for the lack of diversity in certain mtDNA subclades that date to that period. By contrast, your theory assumes dates that are extremely inconsistent with every published study of mtDNA. We also have mtDNA from ancient remains that are consistent with phylogenetic age estimates and that show that the major subclades of haplogroup H were present in Europe 8000 years ago. So it is simply not plausible to suggest that the genetic diversity of H arose within the last several hundred years, when human remains show that the diversity of H began to evolve many thousands of years ago.

                  Comment


                  • #24
                    Originally posted by felix View Post
                    The timeline is a contribution for people who want to visualise the MtDNA tree in mutation scale. It is not for people who looking for black death. Just because it is my opinion based on what I found does not mean you have to agree with it.
                    Please don't get me wrong, I have nothing against either new theories, an alternative view of the MtDNA-tree or individuals suggesting new alternative conclusions. Actually, I love visualizing data and statistics in different ways. If you would have asked us, in my opinion with better knownledge in the field than you, in a less self confident way we would probably just have answered your questions and got you in the right direction, no questions are to dumb to ask.

                    But when you present your "guesses" like if you have a well thought through theory (when you obviously does not have that), such statements receives critique from us who knows better. I mean, the response you get is totally dependent on the way you present your theories, and in the way you respond to critique when your "theory"(/guesses) is questioned.

                    Back to topic, your visualization of the tree does not have a timeline on any axis; you have clearly stated it yourself; but you seems to be the only one that have not understand that. Well, it is not your fault, viewing the tree like you have introduce one to believe that the X-axis is related to the timeline, and yes it is, but very little. Looking at a random part can look like this:

                    Code:
                    47│          │   │        │      │       └L0a2■■■■
                    49│          │   │        │      │       │        └L0a2a
                    50│          │   │        │      │       │        │ └L0a2a1
                    51│          │   │        │      │       │        │ │└L0a2a1a
                    53│          │   │        │      │       │        │ │ └L0a2a1a1
                    53│          │   │        │      │       │        │ │ └L0a2a1a2
                    53│          │   │        │      │       │        │ └L0a2a2
                    54│          │   │        │      │       │        │     └L0a2a2a
                    57│          │   │        │      │       │        └L0a2b■■■■
                    58│          │   │        │      │       │        │         └L0a2b1
                    60│          │   │        │      │       │        └L0a2c■■■■■■■
                    49│          │   │        │      │       │        └L0a2d
                    53│          │   │        │      │       └L0a3■■■■■■■■■■
                    The first illusion, which is very important to note, is that you might get the impression that in some way the L0a2 cease to exists at a given period of time and at that time frame spawns out in the subclades: L0a2a, L0a2b, L0a2c and L0a2d. That is of course not correct. L0a2 lives on and L0a2* individuals are alive today.

                    The second misconception could be to believe that L0a2a, L0a2b, L0a2c and L0a2d was created in about the same time frame. Without looking at current knowledge about the subclades and only looking at your view of the tree that could look like it made sense. That is not true, since L0a2* people are alive today, and some female MtDNA can mutate today and create a future L0a2e subclade. There can be hundred of generations in time between "parallel" subclades. A local "group" in your visualization does not correspond to a given time frame. You have already said that, I know, but you also have to really understand that.

                    I think the best for anybody looking at a tree with an alternative X-axis is to at least have the tree - with the time frame included - handy in front of you where you can take a look once in a while when you study alternative visualizations, so that you don't get lost and draw faulty conclusions.

                    They say that imitation is the sincerest form of flattery and I actually like ascii fixed-width-font visualizations very much, so I think I will spend some minutes to replicate your visualization using Excel and hopefully I can implement the option to include an option to alternate the X-axis to a time frame value. I guess a 3D version would be best, but that is difficult to accomplish in text-format

                    Comment


                    • #25
                      Originally posted by PeterLarsen View Post
                      They say that imitation is the sincerest form of flattery and I actually like ascii fixed-width-font visualizations very much, so I think I will spend some minutes to replicate your visualization using Excel ...


                      I managed to somewhat imitate Felix visualization, not perfectly but close, and at the same time enable you to use a different setting for the X-axis. In addition to number of SNPs defining the subclades you have 3 custom columns that can be filled with whatever you want. As it it excel, one benefit is that you can filter and do other spread sheet stuff with the data.

                      The Excel spread sheet basically consists of two parts, first the input columns and a listbox above where you can choose what X-axis you want (orange cells is input):



                      Over at column Z and AA we have the generated output trees, Z is Felix style (almost) and AA is supposed to best visualize the tree where X is time from past to present:



                      The content output trees in column Z & AA can be copy pasted into notepad and should look something like this:

                      Code:
                               0│├|MtEVE                                                                         [   0]	    0│├|MtEVE────────────────────────────────────────────────────────────────────────────────────────────────────────[   0]
                               0│ ├mtDNAPhylogeny                                                                [   0]	    0│ ├mtDNAPhylogeny───────────────────────────────────────────────────────────────────────────────────────────────[   0]
                              10│ │├L0▄▄▄▄▄▄▄                                                                    [  10]	    5│ │├────┬L0─────────────────────────────────────────────────────────────────────────────────────────────────────[   5]
                              14│ ││         ├L0a'b'f'k                                                          [   4]	   10│ ││    ├────┬L0a'b'f'k─────────────────────────────────────────────────────────────────────────────────────────[   5]
                              23│ ││         │   ├L0a'b'f▄                                                       [   9]	   15│ ││    │    ├────┬L0a'b'f──────────────────────────────────────────────────────────────────────────────────────[   5]
                              30│ ││         │   │        ├L0a'b▄                                                [   7]	   20│ ││    │    │    ├────┬L0a'b───────────────────────────────────────────────────────────────────────────────────[   5]
                              38│ ││         │   │        │      ├L0a▄▄▄▄                                        [   8]	   25│ ││    │    │    │    ├────┬L0a────────────────────────────────────────────────────────────────────────────────[   5]
                              39│ ││         │   │        │      │       ├L0a1'4                                 [   1]	   30│ ││    │    │    │    │    ├────┬L0a1'4────────────────────────────────────────────────────────────────────────[   5]
                              40│ ││         │   │        │      │       │├L0a1                                  [   1]	   35│ ││    │    │    │    │    │    ├────┬L0a1─────────────────────────────────────────────────────────────────────[   5]
                              42│ ││         │   │        │      │       ││├L0a1a                                [   2]	   40│ ││    │    │    │    │    │    │    ├────┬L0a1a───────────────────────────────────────────────────────────────[   5]
                              43│ ││         │   │        │      │       │││ ├L0a1a NL                           [   1]	   45│ ││    │    │    │    │    │    │    │    ├────┬L0a1a NL───────────────────────────────────────────────────────[   5]
                              44│ ││         │   │        │      │       │││ │├L0a1a1                            [   1]	   60│ ││    │    │    │    │    │    │    │    │    ├──────────────┬L0a1a1──────────────────────────────────────────[  15]
                              45│ ││         │   │        │      │       │││ │├L0a1a2                            [   2]	  100│ ││    │    │    │    │    │    │    │    │    ├──────────────────────────────────────────────────────┬L0a1a2──[  55]
                              44│ ││         │   │        │      │       │││ │└L0a1a3                            [   1]	   80│ ││    │    │    │    │    │    │    │    │    └──────────────────────────────────┬L0a1a3──────────────────────[  35]
                              41│ ││         │   │        │      │       ││├L0a1 NL                              [   1]	   36│ ││    │    │    │    │    │    │    ├┬L0a1 NL─────────────────────────────────────────────────────────────────[   1]
                              44│ ││         │   │        │      │       │││├L0a1b                               [   3]	   37│ ││    │    │    │    │    │    │    │├┬L0a1b──────────────────────────────────────────────────────────────────[   1]
                              45│ ││         │   │        │      │       ││││  ├L0a1b NL                         [   1]	   45│ ││    │    │    │    │    │    │    ││├───────┬L0a1b NL───────────────────────────────────────────────────────[   8]
                              46│ ││         │   │        │      │       ││││  │├L0a1b1                          [   1]	   46│ ││    │    │    │    │    │    │    │││       ├┬L0a1b1────────────────────────────────────────────────────────[   1]
                              47│ ││         │   │        │      │       ││││  ││├L0a1b1a                        [   1]	   47│ ││    │    │    │    │    │    │    │││       │├┬L0a1b1a──────────────────────────────────────────────────────[   1]
                              48│ ││         │   │        │      │       ││││  │││└L0a1b1a1                      [   1]	   48│ ││    │    │    │    │    │    │    │││       ││└┬L0a1b1a1────────────────────────────────────────────────────[   1]
                              48│ ││         │   │        │      │       ││││  │├L0a1b2                          [   3]	   55│ ││    │    │    │    │    │    │    │││       ├─────────┬L0a1b2───────────────────────────────────────────────[  10]
                              50│ ││         │   │        │      │       ││││  ││  └L0a1b2a                      [   2]	   56│ ││    │    │    │    │    │    │    │││       │         └┬L0a1b2a─────────────────────────────────────────────[   1]
                              45│ ││         │   │        │      │       │││├L0a1c                               [   4]	   63│ ││    │    │    │    │    │    │    │├──────────────────────────┬L0a1c────────────────────────────────────────[  27]
                              44│ ││         │   │        │      │       │││└L0a1d                               [   3]	   55│ ││    │    │    │    │    │    │    │└──────────────────┬L0a1d────────────────────────────────────────────────[  19]
                              55│ ││         │   │        │      │       │└L0a4▄▄▄▄▄▄▄▄▄▄▄                       [  16]	   32│ ││    │    │    │    │    │    └─┬L0a4────────────────────────────────────────────────────────────────────────[   2]
                              47│ ││         │   │        │      │       ├L0a2▄▄▄▄                               [   9]	   22│ ││    │    │    │    │    ├L0a2───────────────────────────────────────────────────────────────────────────────[   0]
                              49│ ││         │   │        │      │       │        ├L0a2a                         [   2]	   40│ ││    │    │    │    │    │├─────────────────┬L0a2a───────────────────────────────────────────────────────────[  18]
                              50│ ││         │   │        │      │       │        │ ├L0a2a1                      [   1]	   42│ ││    │    │    │    │    ││                 ├─┬L0a2a1────────────────────────────────────────────────────────[   2]
                              51│ ││         │   │        │      │       │        │ │├L0a2a1a                    [   1]	   60│ ││    │    │    │    │    ││                 │ ├─────────────────┬L0a2a1a─────────────────────────────────────[  18]
                              53│ ││         │   │        │      │       │        │ ││├L0a2a1a1                  [   2]	   85│ ││    │    │    │    │    ││                 │ │                 ├────────────────────────┬L0a2a1a1───────────[  25]
                              53│ ││         │   │        │      │       │        │ ││└L0a2a1a2                  [   2]	   92│ ││    │    │    │    │    ││                 │ │                 └───────────────────────────────┬L0a2a1a2────[  32]
                              53│ ││         │   │        │      │       │        │ ├L0a2a2                      [   4]	   50│ ││    │    │    │    │    ││                 ├─────────┬L0a2a2────────────────────────────────────────────────[  10]
                              54│ ││         │   │        │      │       │        │ │   └L0a2a2a                 [   1]	   94│ ││    │    │    │    │    ││                 │         └───────────────────────────────────────────┬L0a2a2a───[  44]
                              57│ ││         │   │        │      │       │        ├L0a2b▄▄▄▄                     [  10]	   70│ ││    │    │    │    │    │├───────────────────────────────────────────────┬L0a2b─────────────────────────────[  48]
                              58│ ││         │   │        │      │       │        │         └L0a2b1              [   1]	   75│ ││    │    │    │    │    ││                                               └────┬L0a2b1───────────────────────[   5]
                              60│ ││         │   │        │      │       │        ├L0a2c▄▄▄▄▄▄▄                  [  13]	   40│ ││    │    │    │    │    │├─────────────────┬L0a2c───────────────────────────────────────────────────────────[  18]
                              49│ ││         │   │        │      │       │        └L0a2d                         [   2]	   24│ ││    │    │    │    │    │└─┬L0a2d───────────────────────────────────────────────────────────────────────────[   2]


                      The source data for now is for the L haplogroup only, and the time column is just random without any scientific thought behind it.
                      I believe it serves to demonstrate that a tree using a timeline as x-axis could look very different.

                      Anyone may use it for whatever you find interesting!

                      You may download the spreadsheet from here (it is macro-free):
                      http://artificial.se/DNA/MtDNATreeViewer.xlsx

                      Comment


                      • #26
                        Originally posted by PeterLarsen View Post
                        Back to topic, your visualization of the tree does not have a timeline on any axis; you have clearly stated it yourself; but you seems to be the only one that have not understand that. Well, it is not your fault, viewing the tree like you have introduce one to believe that the X-axis is related to the timeline, and yes it is, but very little. Looking at a random part can look like this:

                        Code:
                        47│          │   │        │      │       └L0a2■■■■
                        49│          │   │        │      │       │        └L0a2a
                        50│          │   │        │      │       │        │ └L0a2a1
                        51│          │   │        │      │       │        │ │└L0a2a1a
                        53│          │   │        │      │       │        │ │ └L0a2a1a1
                        53│          │   │        │      │       │        │ │ └L0a2a1a2
                        53│          │   │        │      │       │        │ └L0a2a2
                        54│          │   │        │      │       │        │     └L0a2a2a
                        57│          │   │        │      │       │        └L0a2b■■■■
                        58│          │   │        │      │       │        │         └L0a2b1
                        60│          │   │        │      │       │        └L0a2c■■■■■■■
                        49│          │   │        │      │       │        └L0a2d
                        53│          │   │        │      │       └L0a3■■■■■■■■■■
                        The chart is more like Gantt chart and the X-Axis is number of mutations.

                        Originally posted by PeterLarsen View Post
                        The first illusion, which is very important to note, is that you might get the impression that in some way the L0a2 cease to exists at a given period of time and at that time frame spawns out in the subclades: L0a2a, L0a2b, L0a2c and L0a2d. That is of course not correct. L0a2 lives on and L0a2* individuals are alive today.
                        Yes, they do live with further mutations which must be around 60 from Y-Adam, but lack of population/samples make their defining mutations not as a separate branches. The point here is the pattern where all branches were branching out during the a period when it's ancestor clade had the same defining mutations.

                        Originally posted by PeterLarsen View Post
                        The second misconception could be to believe that L0a2a, L0a2b, L0a2c and L0a2d was created in about the same time frame. Without looking at current knowledge about the subclades and only looking at your view of the tree that could look like it made sense. That is not true, since L0a2* people are alive today, and some female MtDNA can mutate today and create a future L0a2e subclade. There can be hundred of generations in time between "parallel" subclades. A local "group" in your visualization does not correspond to a given time frame. You have already said that, I know, but you also have to really understand that.
                        No, it is not created at the same time, but after the disaster when the population is thriving and growing.

                        Comment


                        • #27
                          Originally posted by PeterLarsen View Post


                          I managed to somewhat imitate Felix visualization, not perfectly but close, and at the same time enable you to use a different setting for the X-axis. In addition to number of SNPs defining the subclades you have 3 custom columns that can be filled with whatever you want. As it it excel, one benefit is that you can filter and do other spread sheet stuff with the data.

                          The Excel spread sheet basically consists of two parts, first the input columns and a listbox above where you can choose what X-axis you want (orange cells is input):



                          Over at column Z and AA we have the generated output trees, Z is Felix style (almost) and AA is supposed to best visualize the tree where X is time from past to present:



                          The content output trees in column Z & AA can be copy pasted into notepad and should look something like this:

                          Code:
                                   0│├|MtEVE                                                                         [   0]	    0│├|MtEVE────────────────────────────────────────────────────────────────────────────────────────────────────────[   0]
                                   0│ ├mtDNAPhylogeny                                                                [   0]	    0│ ├mtDNAPhylogeny───────────────────────────────────────────────────────────────────────────────────────────────[   0]
                                  10│ │├L0▄▄▄▄▄▄▄                                                                    [  10]	    5│ │├────┬L0─────────────────────────────────────────────────────────────────────────────────────────────────────[   5]
                                  14│ ││         ├L0a'b'f'k                                                          [   4]	   10│ ││    ├────┬L0a'b'f'k─────────────────────────────────────────────────────────────────────────────────────────[   5]
                                  23│ ││         │   ├L0a'b'f▄                                                       [   9]	   15│ ││    │    ├────┬L0a'b'f──────────────────────────────────────────────────────────────────────────────────────[   5]
                                  30│ ││         │   │        ├L0a'b▄                                                [   7]	   20│ ││    │    │    ├────┬L0a'b───────────────────────────────────────────────────────────────────────────────────[   5]
                                  38│ ││         │   │        │      ├L0a▄▄▄▄                                        [   8]	   25│ ││    │    │    │    ├────┬L0a────────────────────────────────────────────────────────────────────────────────[   5]
                                  39│ ││         │   │        │      │       ├L0a1'4                                 [   1]	   30│ ││    │    │    │    │    ├────┬L0a1'4────────────────────────────────────────────────────────────────────────[   5]
                                  40│ ││         │   │        │      │       │├L0a1                                  [   1]	   35│ ││    │    │    │    │    │    ├────┬L0a1─────────────────────────────────────────────────────────────────────[   5]
                                  42│ ││         │   │        │      │       ││├L0a1a                                [   2]	   40│ ││    │    │    │    │    │    │    ├────┬L0a1a───────────────────────────────────────────────────────────────[   5]
                                  43│ ││         │   │        │      │       │││ ├L0a1a NL                           [   1]	   45│ ││    │    │    │    │    │    │    │    ├────┬L0a1a NL───────────────────────────────────────────────────────[   5]
                                  44│ ││         │   │        │      │       │││ │├L0a1a1                            [   1]	   60│ ││    │    │    │    │    │    │    │    │    ├──────────────┬L0a1a1──────────────────────────────────────────[  15]
                                  45│ ││         │   │        │      │       │││ │├L0a1a2                            [   2]	  100│ ││    │    │    │    │    │    │    │    │    ├──────────────────────────────────────────────────────┬L0a1a2──[  55]
                                  44│ ││         │   │        │      │       │││ │└L0a1a3                            [   1]	   80│ ││    │    │    │    │    │    │    │    │    └──────────────────────────────────┬L0a1a3──────────────────────[  35]
                                  41│ ││         │   │        │      │       ││├L0a1 NL                              [   1]	   36│ ││    │    │    │    │    │    │    ├┬L0a1 NL─────────────────────────────────────────────────────────────────[   1]
                                  44│ ││         │   │        │      │       │││├L0a1b                               [   3]	   37│ ││    │    │    │    │    │    │    │├┬L0a1b──────────────────────────────────────────────────────────────────[   1]
                                  45│ ││         │   │        │      │       ││││  ├L0a1b NL                         [   1]	   45│ ││    │    │    │    │    │    │    ││├───────┬L0a1b NL───────────────────────────────────────────────────────[   8]
                                  46│ ││         │   │        │      │       ││││  │├L0a1b1                          [   1]	   46│ ││    │    │    │    │    │    │    │││       ├┬L0a1b1────────────────────────────────────────────────────────[   1]
                                  47│ ││         │   │        │      │       ││││  ││├L0a1b1a                        [   1]	   47│ ││    │    │    │    │    │    │    │││       │├┬L0a1b1a──────────────────────────────────────────────────────[   1]
                                  48│ ││         │   │        │      │       ││││  │││└L0a1b1a1                      [   1]	   48│ ││    │    │    │    │    │    │    │││       ││└┬L0a1b1a1────────────────────────────────────────────────────[   1]
                                  48│ ││         │   │        │      │       ││││  │├L0a1b2                          [   3]	   55│ ││    │    │    │    │    │    │    │││       ├─────────┬L0a1b2───────────────────────────────────────────────[  10]
                                  50│ ││         │   │        │      │       ││││  ││  └L0a1b2a                      [   2]	   56│ ││    │    │    │    │    │    │    │││       │         └┬L0a1b2a─────────────────────────────────────────────[   1]
                                  45│ ││         │   │        │      │       │││├L0a1c                               [   4]	   63│ ││    │    │    │    │    │    │    │├──────────────────────────┬L0a1c────────────────────────────────────────[  27]
                                  44│ ││         │   │        │      │       │││└L0a1d                               [   3]	   55│ ││    │    │    │    │    │    │    │└──────────────────┬L0a1d────────────────────────────────────────────────[  19]
                                  55│ ││         │   │        │      │       │└L0a4▄▄▄▄▄▄▄▄▄▄▄                       [  16]	   32│ ││    │    │    │    │    │    └─┬L0a4────────────────────────────────────────────────────────────────────────[   2]
                                  47│ ││         │   │        │      │       ├L0a2▄▄▄▄                               [   9]	   22│ ││    │    │    │    │    ├L0a2───────────────────────────────────────────────────────────────────────────────[   0]
                                  49│ ││         │   │        │      │       │        ├L0a2a                         [   2]	   40│ ││    │    │    │    │    │├─────────────────┬L0a2a───────────────────────────────────────────────────────────[  18]
                                  50│ ││         │   │        │      │       │        │ ├L0a2a1                      [   1]	   42│ ││    │    │    │    │    ││                 ├─┬L0a2a1────────────────────────────────────────────────────────[   2]
                                  51│ ││         │   │        │      │       │        │ │├L0a2a1a                    [   1]	   60│ ││    │    │    │    │    ││                 │ ├─────────────────┬L0a2a1a─────────────────────────────────────[  18]
                                  53│ ││         │   │        │      │       │        │ ││├L0a2a1a1                  [   2]	   85│ ││    │    │    │    │    ││                 │ │                 ├────────────────────────┬L0a2a1a1───────────[  25]
                                  53│ ││         │   │        │      │       │        │ ││└L0a2a1a2                  [   2]	   92│ ││    │    │    │    │    ││                 │ │                 └───────────────────────────────┬L0a2a1a2────[  32]
                                  53│ ││         │   │        │      │       │        │ ├L0a2a2                      [   4]	   50│ ││    │    │    │    │    ││                 ├─────────┬L0a2a2────────────────────────────────────────────────[  10]
                                  54│ ││         │   │        │      │       │        │ │   └L0a2a2a                 [   1]	   94│ ││    │    │    │    │    ││                 │         └───────────────────────────────────────────┬L0a2a2a───[  44]
                                  57│ ││         │   │        │      │       │        ├L0a2b▄▄▄▄                     [  10]	   70│ ││    │    │    │    │    │├───────────────────────────────────────────────┬L0a2b─────────────────────────────[  48]
                                  58│ ││         │   │        │      │       │        │         └L0a2b1              [   1]	   75│ ││    │    │    │    │    ││                                               └────┬L0a2b1───────────────────────[   5]
                                  60│ ││         │   │        │      │       │        ├L0a2c▄▄▄▄▄▄▄                  [  13]	   40│ ││    │    │    │    │    │├─────────────────┬L0a2c───────────────────────────────────────────────────────────[  18]
                                  49│ ││         │   │        │      │       │        └L0a2d                         [   2]	   24│ ││    │    │    │    │    │└─┬L0a2d───────────────────────────────────────────────────────────────────────────[   2]


                          The source data for now is for the L haplogroup only, and the time column is just random without any scientific thought behind it.
                          I believe it serves to demonstrate that a tree using a timeline as x-axis could look very different.

                          Anyone may use it for whatever you find interesting!

                          You may download the spreadsheet from here (it is macro-free):
                          http://artificial.se/DNA/MtDNATreeViewer.xlsx
                          I don't understand what you are doing. The timeline I provided is based on number of mutations. If you add time to each mutation, then the tree should remain the same and must not change.

                          Comment


                          • #28
                            Originally posted by felix View Post
                            I don't understand what you are doing. The timeline I provided is based on number of mutations. If you add time to each mutation, then the tree should remain the same and must not change.
                            That is my whole point, the amount of defining mutation does not order parallel subclades in a ordered timeline on the X-axis in your tree. Only the tree "structure" is correct. Take a look at Kenneth Nordvedts powerpoints, for example, to get the idea how parallel subclades is spawn out of the parent during a long period of time:

                            http://knordtvedt.home.bresnan.net/BigYP109.pptx

                            There are more that can be found here:
                            http://knordtvedt.home.bresnan.net/

                            My spredsheet allows you to enter alternative X-axis for the subclade "spawns" and visualize it so parent clades isn't "chopped off" the X-axis, it is nothing complicated.

                            Comment


                            • #29
                              Originally posted by PeterLarsen View Post
                              That is my whole point, the amount of defining mutation does not order parallel subclades in a ordered timeline on the X-axis in your tree. Only the tree "structure" is correct. Take a look at Kenneth Nordvedts powerpoints, for example, to get the idea how parallel subclades is spawn out of the parent during a long period of time:

                              http://knordtvedt.home.bresnan.net/BigYP109.pptx

                              There are more that can be found here:
                              http://knordtvedt.home.bresnan.net/

                              My spredsheet allows you to enter alternative X-axis for the subclade "spawns" and visualize it so parent clades isn't "chopped off" the X-axis, it is nothing complicated.
                              Why do you want to destroy the actual mutations from my tree with just garbage/random numbers to create an alternative X-axis? Do you think my X-axis is wrong? My X-Axis is based on number of mutations from mt-Eve directly taken from mt-Tree. It's unit it in mutations.

                              For chopping off, yes it does chops off and people still live today under that clade - because, it exists as private mutations and there will not be enough population to create/declare a new branch. This does not mean new branches don't exist. It means, there are no people living today having only those defining mutations for that parent clade.

                              If you feel you can extend it and provide an alternative versions, feel free to post it in another thread, not this - as I want to stick with OP.

                              Comment


                              • #30
                                Originally posted by GST View Post
                                Well, in fact we do have scientific evidence for very slow population growth in Europe during the Mesolithic, so population bottleneck and genetic drift is a plausible scientific theory for the lack of diversity in certain mtDNA subclades that date to that period. By contrast, your theory assumes dates that are extremely inconsistent with every published study of mtDNA. We also have mtDNA from ancient remains that are consistent with phylogenetic age estimates and that show that the major subclades of haplogroup H were present in Europe 8000 years ago. So it is simply not plausible to suggest that the genetic diversity of H arose within the last several hundred years, when human remains show that the diversity of H began to evolve many thousands of years ago.
                                I already mentioned to you it's my "opinion" and I am not here to argue with you. Based on the evidences which I had analyzed, H or some of its branches like H1c which has 22 branches, esp., "the patterns" which I found are very recent in origin.

                                Comment

                                Working...
                                X