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mt-Tree Mutation Timeline

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  • mt-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 maternal 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. I made this view first for Y-DNA. Then, I decided why not for mtDNA?

    Below is a quick view of how the text file will look. The first column is the number of mutations from mt-Eve and the tree haplogroup width is relative to the number of defining mutations - thus giving a visual timeline.



    The entire mt-Tree (based on 19 Feb 2014 on mtDNA tree Build 16) is done. You can download it from here.

    Link: http://www.fc.id.au/2014/05/mt-tree-...-timeline.html

  • #2
    I will have to confess I have not got a clue what you are trying to say here about branches being wiped off. What do wars and disasters have to do with mutation timelines?

    Comment


    • #3
      Hallo Felix,

      thank you for sharing this overview. I can see the mutation steps for each Haplogroup back to the "original Eve".

      But I do not understand the "timeline" in this case. How will you define the number of years for each mutation step? How can I read this in your picture?

      Sorry for asking dump, but I thought it is still difficult to be sure, how old f.e. H1B1 is? The word timeline irritates me.

      Thank you ina dvance for your explanation.

      Comment


      • #4
        Originally posted by LynCra View Post
        I will have to confess I have not got a clue what you are trying to say here about branches being wiped off. What do wars and disasters have to do with mutation timelines?
        Because of the nature of how mtDNA is passed down from mother to children and daughters pass on to their children, when a haplogroup or subclade is having 'n' number of defining mutations, all these mutations are from 1 single ancestor before it branched out through her descendent. When her descendent have a new mutation, she starts a new branch. Based on this, when a haplogroup is having too many defining mutations but no sister branches, it means, only that lineage had survived (from some disaster?) to pass on the mutations to her descendent for creating new branches. However, when a haplogroup and it's descendents are having too less defining mutations, it means the population is growing (and having new branches as the population grows).

        Hence, in the graph, a long bar means, a haplogroup is having so many defining mutations (bar length is equal to the defining mutations), indicating only that lineage had survived and all it's sisters branches from the ancestor which must have existed, died out. It is like an entire town or a country gets destroyed and only one ancestor survived. Each of those long bars is having it's own story to tell. For mtDNA, I believe most of those disasters would be natural like famines, earthquake, flood, volcanic eruption etc rather than wars. Wars is a major factor for Y-DNA but may not be for mtDNA.

        For example, if you look at the below picture, H5j, J2, T,, U4, U7, K - these European haplogroups starts branching out at the same time after having lot of mutations, indicating a massive disaster wiping off several of it's sister branches/lineages in Europe leaving only these lineages - Could this be black death? I don't know. But, I am very sure Black death must have left it's signature in all European mtDNA (and YDNA) haplogroups. Then, when population grows, you will notice several subclades branching out all having very few defining mutations (indicating several quick branching as the population grew from that survived lineages).

        Attached Files

        Comment


        • #5
          Originally posted by Petra View Post
          Hallo Felix,

          thank you for sharing this overview. I can see the mutation steps for each Haplogroup back to the "original Eve".

          But I do not understand the "timeline" in this case. How will you define the number of years for each mutation step? How can I read this in your picture?

          Sorry for asking dump, but I thought it is still difficult to be sure, how old f.e. H1B1 is? The word timeline irritates me.

          Thank you ina dvance for your explanation.
          The scale is based on number of mutations which is relative to number of 'n' years. So, the graph is in scale 1:n, where 'n' is number of years.

          H1b1 is 51 mutations from mt-Eve and has the same age as the below subclades which range from 50-52 mutations from mt-Eve.

          L0a1b2a, L0a2a1, L0a2a1a, L1c1a1a, L1c2a, L1c2b, L1c2b1, L1c4b, L1c3b1, L2a1, NoLabel, L2a2'3'4, L2c, L6, L6b, L4a1, L4b2a, L3b1a, L3b1a1, L3b1a1a, L3b1a2, L3b1a3, L3b1a4, L3b1a5, L3b1b, L3b2, L3f1b, L3d1a1, L3d1c, L3e1a1, L3e1a1a, L3e1a3, L3e1c, L3e1d1, L3e2a1a, L3e3a, L3x2, L3x2a, L3h1b1a, M1a, M1a2, M1b, M1b2, M51a1, M2a3, M3c1a, M38c, M38d, M43b, M63, M64, M5a1a, M5a1b, M6a1, M6a2, M7a1, M7a1a, M7a2a, M7c1, M7c1a, M7c1d, M7c2, M7c2a, M7c2b, M7c3, M7c3c, M8a2, M8a3, M8a3a, C, Z, Z1, Z3, M9a1a1a, M9a1a1b, M9a1a1c, M9a1a1c1, M9a1a1c1a, M9a1b1, M9a1b1a, M9a1b1c, M9a1b2, M9b, E1, E1a, E1a1, E1a2, E2, E2a, E2b, M11a'b, M11a, M11b, M11c, M12a, M12b, G1a1, G1a2'3, G1a2, G2a, G2a1, G2b1b, G2b2a, G2b2b, G3a1, G3b1, M13a, M13b1, M15, M17a, M53, M75, M41c, M28, M29, Q2, Q3a, M31b2, M31c, M32a, M33a1a, M33b1, M34b, M57b, M35a1a, M36c, M36d1, M39a, M39a1, M39b1, M40a1a, M40a1b, M62, M62b, M42b1, M74a, M52a1, M60b, M71c, M73a, D1b, D1e, D1f1, D1g2, D1g3, D1j, D1j1, D4a, D4a1, D4a1a, D4a1b, D4a1c, D4a1d, D4a1f, D4a2, D4a3, D4b1, D4b1a, D4b1b'd, D4b2a, D4b2a2, D4b2b, D4b2b1, D4b2b2, D4b2b5, D4c1b, D4c2b, D4e1c, D2, D4e4a1, D4e4b, D4e5, D4e5b, D4f1, D4g1, D4g1c, D4g2a, D4g2a1, D4g2b1, D4h1a, D4h1b, D4h3, D4j1a, D4j1b2, D4j2, D4j2a, D4j3a1, D4j5, D4j7a, D4o2, D4m2, D4q1a, D5a, D5a3, D6a1, D6c, N2a, N9a1, N9a1a, N9a3, N9a2, N9a2a, N9a2a2, N9a2d, N9a4, N9a4a, N9a4b, N9a5, N9a10a, N9b1b, N9b1c1, Y1, N14, A3, A4, A4a, A4c, A11, A5, O1, S4, X2a'j, X2b'd, X2c, X2e, X2e1, X2e2, X2f, X2i, X2k, R0a, R0a1, HV0a1, V1, V1a, V1a1, V1b, V2, V2a, V2b, V2b1, V2c, V3, V3a, V3a1, V3b, V3c, V4, V5, V6, V7, V8, V9, V10, V10a, V10b, V11, V12, V13, V14, V15, V15a, V16, V17, V18, V19, V20, V21, HV0e, HV0f, HV1a1, HV1a2, HV1a2a, HV1a3, HV1b3, HV4a2a, HV6a, HV9a1, H1a, H1a1, H1a2, H1a3, H1a3a, H1a3b, H1a3c, H1a4, H1a5, H1a7, H1b, H1b1, H1b1e, H1b2, H1b3, H1b4, H1f, H1g, H1g1, H1g2, H1k, H1k1, H1y, H1z, H1aa, H1ab, H1ab1, H1ac, H1ad, H1c1, H1c1a, H1c1b, H1c2, H1c2a, H1c3, H1c4, H1c4a, H1c4b, H1c4b1, H1c5, H1c5a, H1c6, H1c7, H1c8, H1c9, H1c9a, H1c10, H1c11, H1c12, H1c13, H1c14, H1c15, H1c16, H1c17, H1c18, H1c19, H1c20, H1c21, H1c22, H1e1, H1e1a, H1e1a2, H1e1a3, H1e1b, H1e1b1, H1e2, H1e2a, H1e2b, H1e4, H1e4a, H1e5, H1e6, H1h1, H1h2, H1i, H1i1, H1i2, H1i2a, H1an, H1an1, H1an1a, H1an2, H1bb, H1j1, H1j1a, H1j1a1, H1j1a2, H1j1b, H1j1c, H1j2, H1j3, H1j4, H1j5, H1j6, H1j7, H1j8, H1m1, H1n1, H1n1a, H1n2, H1n3, H1n4, H1n5, H1n6, H1o, H1q1, H1q2, H1t1, H1t1a, H1t1a1, H1t2, H1u1, H1v1, H1v1a, H1v1b, H1x, H1ae1, H1ae2, H1ae3, H1ae3a, H1af1, H1af1a, H1af2, H1ag1, H1ag1a, H1ag1b, H1ah, H1ai1, H1aj1, H1ak1, H1ak2, H1am1, H1ao, H1ap1, H1aq1, H1ar, H1ar1, H1as1, H1as1a, H1as2, H1at1, H1at1a, H1au1, H1au1a, H1au1b, H1av1, H1av1a, H1aw, H1ax, H1bc, H1be, H1bf, H1bf1, H1bg, H1bh, H1bt1, H1bu, H1bv1, H1bx, H2a1, H2a1c, H2a1e, H2a1f, H2a1g, H2a2, H2a2a, H2a2b, H2a3, H2a3a, H2a3b, H2a4, H2a5, H2a5a, H2a5a1, H2a5b, H2a5b1, H2b, H2c, H3a, H3a1, H3a1a, H3g, H3g1, H3g2, H3g3, H3g4, H3i, H3i1, H3j, H3k, H3k1, H3k1a, H3b1, H3b2, H3b3, H3b4, H3c1, H3c2, H3c2a, H3c2b, H3c2c, H3c3, H3d, H3e, H3h, H3h1, H3h2, H3h3, H3h3a, H3h5, H3m, H3n, H3q1, H3r1, H3s, H3w, H3y, H3z1, H3ab, H3af, H3ak, H3ao1, H3at1, H3av, H4, H4a, H4b, H4c, H5a, H5a1, H5a1a, H5a1b, H5a1d, H5a1e, H5a1f, H5a1g, H5a1h, H5a1j, H5a1k, H5a2, H5a3, H5a4, H5a5, H5a7, H5b, H5b2, H5b3, H5c, H5c1, H5c1a, H5c2, H5d, H5e, H5e1, H5f, H5g, H5h, H5k, H5m, H5n, H5p, H5q, H5s, H6, H6a, H6b, H6c, H7a1, H7a1a, H7a1b, H7a1c, H7a2, H7b1, H7b2, H7b2a, H7b3, H7b4, H7b5, H7b6, H7c1, H7c2, H7c3, H7d1, H7d2, H7d2a, H7d3, H7d3a, H7e, H7i, H31, H31a, H31b, H11, H11b, H12, H9a, H32, H46a, H10a1, H10a1a, H10a1a1, H10b1, H10c, H10c1, H10e, H10e1, H10e1a, H10e2, H10e3, H10e3a, H10f, H10g, H10h, H13a1, H13a1a, H13a1a2, H13a1a3, H13a1a4, H13a1a5, H13a2, H13a2a, H13a2b, H13b1, H13c1, H14a, H14a2, H14b, H15, H15a, H15a1, H15b, H15b1, H16a, H16a1, H16c, H17a, H17a1, H17a2, H17b, H17c, H27, H27a, H27b, H27c, H27d, H21, H24a1, H24a2, H26a1, H26a1a, H26b, H26c, H28a, H28a1, H29, H30a, H30b1, H33b, H85, H39a, H39a1, H40b, H41a, H42a, H42a1, H44a, H44a1, H44b, H45a, H45b, H47a, H49a1, H49a2, H51a, H55a, H56a1, H63a, H65a, H67a, H72, H73a, H73a1, H74, J, R5a1, R6a1, R8a, R8a2, R9b1a, R9b1b, R9c1, F1, F4, B6a, B4a1c, B4a1c1, B4a1c1a, B4a1c4, B4a1c3, B4a1d, B4a2, B4a2a, B4a2b, B4a4, B4i, B4b, B4b1, B4b1b'c, B4d1'2'3, B4d1, B4c1a'b, B4c1a, R24, R22, P1d, P1d1, P2, P3, P4b, U1, U5, U5a, U6a, U6a1, U6a7, U6b, U6d, U2a, U2c, U3, U8b

          If you look at L0a, L0f, L0k, L0d1a, L0d1c, L0d3, L1b, L1c3, L5c, M, N haplogroups, all it's sister clades died out at the "same time" (as you can see in the graph). Try to find the heat maps of these haplogroups and look back in history to find what disaster is common to these places/people which could have wiped off all it's sister clades. You belong to N. Based on what you can find, and mapping it to a natural disaster, you will get a clear picture of how old is N. After N, your tree (female lineage) is not affected by any major wiping off type disasters.

          Attached Files

          Comment


          • #6
            V19a1

            Originally posted by felix View Post
            The scale is based on number of mutations which is relative to number of 'n' years. So, the graph is in scale 1:n, where 'n' is number of years.

            H1b1 is 51 mutations from mt-Eve and has the same age as the below subclades which range from 50-52 mutations from mt-Eve.

            L0a1b2a, L0a2a1, L0a2a1a, L1c1a1a, L1c2a, L1c2b, L1c2b1, L1c4b, L1c3b1, L2a1, NoLabel, L2a2'3'4, L2c, L6, L6b, L4a1, L4b2a, L3b1a, L3b1a1, L3b1a1a, L3b1a2, L3b1a3, L3b1a4, L3b1a5, L3b1b, L3b2, L3f1b, L3d1a1, L3d1c, L3e1a1, L3e1a1a, L3e1a3, L3e1c, L3e1d1, L3e2a1a, L3e3a, L3x2, L3x2a, L3h1b1a, M1a, M1a2, M1b, M1b2, M51a1, M2a3, M3c1a, M38c, M38d, M43b, M63, M64, M5a1a, M5a1b, M6a1, M6a2, M7a1, M7a1a, M7a2a, M7c1, M7c1a, M7c1d, M7c2, M7c2a, M7c2b, M7c3, M7c3c, M8a2, M8a3, M8a3a, C, Z, Z1, Z3, M9a1a1a, M9a1a1b, M9a1a1c, M9a1a1c1, M9a1a1c1a, M9a1b1, M9a1b1a, M9a1b1c, M9a1b2, M9b, E1, E1a, E1a1, E1a2, E2, E2a, E2b, M11a'b, M11a, M11b, M11c, M12a, M12b, G1a1, G1a2'3, G1a2, G2a, G2a1, G2b1b, G2b2a, G2b2b, G3a1, G3b1, M13a, M13b1, M15, M17a, M53, M75, M41c, M28, M29, Q2, Q3a, M31b2, M31c, M32a, M33a1a, M33b1, M34b, M57b, M35a1a, M36c, M36d1, M39a, M39a1, M39b1, M40a1a, M40a1b, M62, M62b, M42b1, M74a, M52a1, M60b, M71c, M73a, D1b, D1e, D1f1, D1g2, D1g3, D1j, D1j1, D4a, D4a1, D4a1a, D4a1b, D4a1c, D4a1d, D4a1f, D4a2, D4a3, D4b1, D4b1a, D4b1b'd, D4b2a, D4b2a2, D4b2b, D4b2b1, D4b2b2, D4b2b5, D4c1b, D4c2b, D4e1c, D2, D4e4a1, D4e4b, D4e5, D4e5b, D4f1, D4g1, D4g1c, D4g2a, D4g2a1, D4g2b1, D4h1a, D4h1b, D4h3, D4j1a, D4j1b2, D4j2, D4j2a, D4j3a1, D4j5, D4j7a, D4o2, D4m2, D4q1a, D5a, D5a3, D6a1, D6c, N2a, N9a1, N9a1a, N9a3, N9a2, N9a2a, N9a2a2, N9a2d, N9a4, N9a4a, N9a4b, N9a5, N9a10a, N9b1b, N9b1c1, Y1, N14, A3, A4, A4a, A4c, A11, A5, O1, S4, X2a'j, X2b'd, X2c, X2e, X2e1, X2e2, X2f, X2i, X2k, R0a, R0a1, HV0a1, V1, V1a, V1a1, V1b, V2, V2a, V2b, V2b1, V2c, V3, V3a, V3a1, V3b, V3c, V4, V5, V6, V7, V8, V9, V10, V10a, V10b, V11, V12, V13, V14, V15, V15a, V16, V17, V18, V19, V20, V21, HV0e, HV0f, HV1a1, HV1a2, HV1a2a, HV1a3, HV1b3, HV4a2a, HV6a, HV9a1, H1a, H1a1, H1a2, H1a3, H1a3a, H1a3b, H1a3c, H1a4, H1a5, H1a7, H1b, H1b1, H1b1e, H1b2, H1b3, H1b4, H1f, H1g, H1g1, H1g2, H1k, H1k1, H1y, H1z, H1aa, H1ab, H1ab1, H1ac, H1ad, H1c1, H1c1a, H1c1b, H1c2, H1c2a, H1c3, H1c4, H1c4a, H1c4b, H1c4b1, H1c5, H1c5a, H1c6, H1c7, H1c8, H1c9, H1c9a, H1c10, H1c11, H1c12, H1c13, H1c14, H1c15, H1c16, H1c17, H1c18, H1c19, H1c20, H1c21, H1c22, H1e1, H1e1a, H1e1a2, H1e1a3, H1e1b, H1e1b1, H1e2, H1e2a, H1e2b, H1e4, H1e4a, H1e5, H1e6, H1h1, H1h2, H1i, H1i1, H1i2, H1i2a, H1an, H1an1, H1an1a, H1an2, H1bb, H1j1, H1j1a, H1j1a1, H1j1a2, H1j1b, H1j1c, H1j2, H1j3, H1j4, H1j5, H1j6, H1j7, H1j8, H1m1, H1n1, H1n1a, H1n2, H1n3, H1n4, H1n5, H1n6, H1o, H1q1, H1q2, H1t1, H1t1a, H1t1a1, H1t2, H1u1, H1v1, H1v1a, H1v1b, H1x, H1ae1, H1ae2, H1ae3, H1ae3a, H1af1, H1af1a, H1af2, H1ag1, H1ag1a, H1ag1b, H1ah, H1ai1, H1aj1, H1ak1, H1ak2, H1am1, H1ao, H1ap1, H1aq1, H1ar, H1ar1, H1as1, H1as1a, H1as2, H1at1, H1at1a, H1au1, H1au1a, H1au1b, H1av1, H1av1a, H1aw, H1ax, H1bc, H1be, H1bf, H1bf1, H1bg, H1bh, H1bt1, H1bu, H1bv1, H1bx, H2a1, H2a1c, H2a1e, H2a1f, H2a1g, H2a2, H2a2a, H2a2b, H2a3, H2a3a, H2a3b, H2a4, H2a5, H2a5a, H2a5a1, H2a5b, H2a5b1, H2b, H2c, H3a, H3a1, H3a1a, H3g, H3g1, H3g2, H3g3, H3g4, H3i, H3i1, H3j, H3k, H3k1, H3k1a, H3b1, H3b2, H3b3, H3b4, H3c1, H3c2, H3c2a, H3c2b, H3c2c, H3c3, H3d, H3e, H3h, H3h1, H3h2, H3h3, H3h3a, H3h5, H3m, H3n, H3q1, H3r1, H3s, H3w, H3y, H3z1, H3ab, H3af, H3ak, H3ao1, H3at1, H3av, H4, H4a, H4b, H4c, H5a, H5a1, H5a1a, H5a1b, H5a1d, H5a1e, H5a1f, H5a1g, H5a1h, H5a1j, H5a1k, H5a2, H5a3, H5a4, H5a5, H5a7, H5b, H5b2, H5b3, H5c, H5c1, H5c1a, H5c2, H5d, H5e, H5e1, H5f, H5g, H5h, H5k, H5m, H5n, H5p, H5q, H5s, H6, H6a, H6b, H6c, H7a1, H7a1a, H7a1b, H7a1c, H7a2, H7b1, H7b2, H7b2a, H7b3, H7b4, H7b5, H7b6, H7c1, H7c2, H7c3, H7d1, H7d2, H7d2a, H7d3, H7d3a, H7e, H7i, H31, H31a, H31b, H11, H11b, H12, H9a, H32, H46a, H10a1, H10a1a, H10a1a1, H10b1, H10c, H10c1, H10e, H10e1, H10e1a, H10e2, H10e3, H10e3a, H10f, H10g, H10h, H13a1, H13a1a, H13a1a2, H13a1a3, H13a1a4, H13a1a5, H13a2, H13a2a, H13a2b, H13b1, H13c1, H14a, H14a2, H14b, H15, H15a, H15a1, H15b, H15b1, H16a, H16a1, H16c, H17a, H17a1, H17a2, H17b, H17c, H27, H27a, H27b, H27c, H27d, H21, H24a1, H24a2, H26a1, H26a1a, H26b, H26c, H28a, H28a1, H29, H30a, H30b1, H33b, H85, H39a, H39a1, H40b, H41a, H42a, H42a1, H44a, H44a1, H44b, H45a, H45b, H47a, H49a1, H49a2, H51a, H55a, H56a1, H63a, H65a, H67a, H72, H73a, H73a1, H74, J, R5a1, R6a1, R8a, R8a2, R9b1a, R9b1b, R9c1, F1, F4, B6a, B4a1c, B4a1c1, B4a1c1a, B4a1c4, B4a1c3, B4a1d, B4a2, B4a2a, B4a2b, B4a4, B4i, B4b, B4b1, B4b1b'c, B4d1'2'3, B4d1, B4c1a'b, B4c1a, R24, R22, P1d, P1d1, P2, P3, P4b, U1, U5, U5a, U6a, U6a1, U6a7, U6b, U6d, U2a, U2c, U3, U8b

            If you look at L0a, L0f, L0k, L0d1a, L0d1c, L0d3, L1b, L1c3, L5c, M, N haplogroups, all it's sister clades died out at the "same time" (as you can see in the graph). Try to find the heat maps of these haplogroups and look back in history to find what disaster is common to these places/people which could have wiped off all it's sister clades. You belong to N. Based on what you can find, and mapping it to a natural disaster, you will get a clear picture of how old is N. After N, your tree (female lineage) is not affected by any major wiping off type disasters.

            I know I am V19a1, and I have 35 mutations, counting (2) heteroplasmies in my coding region, and another 22 mutations in my HVR1 & HVR2 regions, so I guess thats correct. I think that V19 subclade is a more recent subclade of V haplogroup, which occurred in the British Isles.

            Best regards, Douglas W. Fisher, Kit#122883

            Paternal: U106+Z18+Z14+Z372+
            Maternal: V19a1

            Comment


            • #7
              Originally posted by DWFlineage View Post
              I know I am V19a1, and I have 35 mutations, counting (2) heteroplasmies in my coding region, and another 22 mutations in my HVR1 & HVR2 regions, so I guess thats correct. I think that V19 subclade is a more recent subclade of V haplogroup, which occurred in the British Isles.

              Best regards, Douglas W. Fisher, Kit#122883

              Paternal: U106+Z18+Z14+Z372+
              Maternal: V19a1
              There is no V19a1 in mtDNA tree. Either you are V19 (or) V9a1. Is there a typo?

              Comment


              • #8
                Spreadsheet

                Originally posted by felix View Post
                There is no V19a1 in mtDNA tree. Either you are V19 (or) V9a1. Is there a typo?

                I have been assigned V19a1 subgroup by the V project, because I have 2 heteroplasmies, which puts me on a different branch then my closest matches who are assigned V19a subgroup, because they have a few mutations different from V19 folks.

                Best regards, Doug

                Comment


                • #9
                  Originally posted by felix View Post
                  The scale is based on number of mutations which is relative to number of 'n' years. So, the graph is in scale 1:n, where 'n' is number of years.
                  mtDNA mutation rates are highly variable, so you cannot assume that the age of the subclade is proportional to the number of mutations that define it. You would have to analyze the average number of mutations for all of the members of each subclade to estimate its age, similar to the analysis that Behar et al. performed in their 2012 paper.

                  Small sample size is also a concern. We have not identified all of the surviving mtDNA subclades, and many are represented by just a few samples. The diversity within the tree will increase as more samples becomes available.

                  Comment


                  • #10
                    Originally posted by GST View Post
                    mtDNA mutation rates are highly variable, so you cannot assume that the age of the subclade is proportional to the number of mutations that define it. You would have to analyze the average number of mutations for all of the members of each subclade to estimate its age, similar to the analysis that Behar et al. performed in their 2012 paper.

                    Small sample size is also a concern. We have not identified all of the surviving mtDNA subclades, and many are represented by just a few samples. The diversity within the tree will increase as more samples becomes available.
                    The assumption is based on what mutation rate itself is and how it had been used for all these years by every scientist in this field. So, I don't think that's a problem.

                    I agree that the mtDNA tree itself is not complete and it will get updated when new data comes in. So, if the tree changes, so does the timeline represented. I will try to update when the tree changed.

                    Comment


                    • #11
                      Originally posted by felix View Post
                      The assumption is based on what mutation rate itself is and how it had been used for all these years by every scientist in this field. So, I don't think that's a problem.
                      The scientists who have published on this have used fairly sophisticated analysis methods to address variability in the mutation rate and have found cases where the molecular clock performs poorly. Quoting from Behar et al. 2012 where they discuss the clock violations:
                      We are currently unable to offer well-founded explanations for these findings, which remain the scope of future studies. As the clock violation was observed only in a restricted number of specified cases, we applied the best available tools for estimating the ages of ancestral nodes. We adopted a conventional calculation approach and mutation rate and used PAML 4.4 to generate maximum likelihood estimates for internal node ages under a molecular clock
                      assumption.
                      This problem is apparent for H5j which you compared to U4, U7, T, J2 and K. H5j is defined by a set of 6 mutations, and a simple molecular clock assumption would imply that the ancestor of H5j lived more than 16,000 years without any branching, yet we know that H5j must be younger than H5 which Behar estimated to be about 10,000 years old. So H5j is a case which appears to have accumulated a large number of mutations very rapidly. Perhaps environmental stress or exposure to toxins caused the fast mutation rate in some maternal lines, or perhaps it is just a random process. I don't think anyone has been able to explain this yet, but it is a problem that we have to consider, as it complicates the analysis.

                      Comment


                      • #12
                        Originally posted by GST View Post
                        The scientists who have published on this have used fairly sophisticated analysis methods to address variability in the mutation rate and have found cases where the molecular clock performs poorly. Quoting from Behar et al. 2012 where they discuss the clock violations:


                        This problem is apparent for H5j which you compared to U4, U7, T, J2 and K. H5j is defined by a set of 6 mutations, and a simple molecular clock assumption would imply that the ancestor of H5j lived more than 16,000 years without any branching, yet we know that H5j must be younger than H5 which Behar estimated to be about 10,000 years old. So H5j is a case which appears to have accumulated a large number of mutations very rapidly. Perhaps environmental stress or exposure to toxins caused the fast mutation rate in some maternal lines, or perhaps it is just a random process. I don't think anyone has been able to explain this yet, but it is a problem that we have to consider, as it complicates the analysis.
                        Which is one of the reasons I try to refine myself from giving any age and the unit for the timeline is mutations .

                        The other reason for doing this is to compare mt-DNA tree (also Y-DNA trees) with actual natural disasters with known dates. This way there will be an accurate age for clades. One thing that I am more confident is that we must find the signature of Black death. Europe literally grew from a shrunk population of 50 million (some estimates give only 30 million) around 1350s to >700 million today. Which means, there must be these surviving subclades in mt-tree with more mutations (signifying the loss of it's sister clades in Black death) and suddenly a huge number of branches (signifying the huge exponential population growth).

                        And ofcourse it can be seen clearly. Take H for example, the most common mtDNA haplogroup in Europe: H haplogroup itself has 68 branches (H1c has 22 branches) and several others have ~8 branches. Could this signify the exponential population growth event after Black Death? I believe so.

                        Comment


                        • #13
                          Originally posted by felix View Post
                          Take H for example, the most common mtDNA haplogroup in Europe: H haplogroup itself has 68 branches (H1c has 22 branches) and several others have ~8 branches. Could this signify the exponential population growth event after Black Death? I believe so.
                          There is uncertainty in age estimates, but Behar's estimate for H is about 14,000 years, while other have estimated that H is significantly older than this. Assuming Behar is correct, the explosive growth in H is likely associated with the development of agriculture in the Near East. The extremely rapid growth in some of the H subclades (H1, H2, etc) could be associated with the expansion of those groups into Europe in the Neolithic. The mtDNA mutation rate is too slow to resolve events on the scale of a several hundred years, but you can use this approach for much more ancient events.

                          Comment


                          • #14
                            Originally posted by GST View Post
                            There is uncertainty in age estimates, but Behar's estimate for H is about 14,000 years, while other have estimated that H is significantly older than this. Assuming Behar is correct, the explosive growth in H is likely associated with the development of agriculture in the Near East. The extremely rapid growth in some of the H subclades (H1, H2, etc) could be associated with the expansion of those groups into Europe in the Neolithic. The mtDNA mutation rate is too slow to resolve events on the scale of a several hundred years, but you can use this approach for much more ancient events.
                            Behar's estimate is still based on human/chimp split which cannot be verified and it is a conflict of interest to me for various other scientific reasons/experiments which Behar (or any scientist in this particular field) cannot give an explanation.

                            Given the fact that some of the direct branches of H itself haven't mutated yet to create new further branches (or not enough population to declare as new branch), I doubt the 14,000 year estimate.
                            Last edited by felix; 21 May 2014, 01:40 AM.

                            Comment


                            • #15
                              Originally posted by felix View Post
                              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 maternal 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. I made this view first for Y-DNA. Then, I decided why not for mtDNA?

                              Below is a quick view of how the text file will look. The first column is the number of mutations from mt-Eve and the tree haplogroup width is relative to the number of defining mutations - thus giving a visual timeline.



                              The entire mt-Tree (based on 19 Feb 2014 on mtDNA tree Build 16) is done. You can download it from here.

                              Link: http://www.fc.id.au/2014/05/mt-tree-...-timeline.html
                              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.

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