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New PhyloTree and Me

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  • New PhyloTree and Me

    FTDNA has had me at H1 since I tested last year and here are my results:

    HVR1 DIFFERENCES FROM rCRS 16519C

    HVR2 DIFFERENCES FROM rCRS
    152C
    195C
    263G
    315.1C
    523.1C
    523.2A

    CODING REGION DIFFERENCES FROM rCRS
    750G
    1438G
    3010A
    4769G
    8860G
    11864C
    15326G

    I have been looking over the new phylotree with great interest and of course 3010 is for H1 but then I noticed that 1438 is with H2 and then 4769 is for H2a. So my question is, am I going to be a better fit, if you will, for H2 or H2a then for H1?

    I used this nifty tool: http://vps1.jameslick.com/dna/mthap/mthap.cgi and my 'fit's' are H1, H(195), H and H2.

  • #2
    The new revision puts the estimated ages (emergence) at:
    H2 11905.3 years ago
    H2a 10531.8 ya
    H1 9888.6 ya

    So I guess that puts you in H1 as that is your most recent polymorphism.
    Last edited by Jomid59; 15th April 2012, 01:45 PM. Reason: typo

    Comment


    • #3
      Not sure why the more recent mutation would mean your in that group? Just curious what you base that on?

      Comment


      • #4
        Originally posted by RondaMiller View Post
        FTDNA has had me at H1 since I tested last year and here are my results:
        ...
        I have been looking over the new phylotree with great interest and of course 3010 is for H1 but then I noticed that 1438 is with H2 and then 4769 is for H2a. So my question is, am I going to be a better fit, if you will, for H2 or H2a then for H1?

        H1 is correct -- this is a bit confusing, but FTDNA lists our results as differences from the Cambridge Reference Sequence (CRS) which is H2a2a. As a result, mutations at sites specific to H2a2a are listed in the results for everyone who is NOT H2a2a. If you compare your results to Phylotree, you will see that H2 is defined by G1438A, while you have the ancestral value at this site, A1438G.

        Comment


        • #5
          Originally posted by GST View Post
          H1 is correct -- this is a bit confusing, but FTDNA lists our results as differences from the Cambridge Reference Sequence (CRS) which is H2a2a. As a result, mutations at sites specific to H2a2a are listed in the results for everyone who is NOT H2a2a. If you compare your results to Phylotree, you will see that H2 is defined by G1438A, while you have the ancestral value at this site, A1438G.
          Oh ok I see now - thank you.

          Comment


          • #6
            This is the part that threw me however (from: http://vps1.jameslick.com/dna/mthap/mthap.cgi) :

            3) H2

            Defining Markers for haplogroup H2:
            HVR2: 263G
            CR: 750G 4769G 8860G 15326G
            HVR1:

            Marker path from rCRS to haplogroup H2 (plus extra markers):
            H2a2a(rCRS) ⇨ 263G 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 152C 195C (315.1C) 524.1A 524.2C 1438G 3010A 11864C (16519C)

            Good Match! Your results also had extra markers for this haplogroup:
            Matches(5): 263G 750G 4769G 8860G 15326G
            Extras(7): 152C 195C (315.1C) 524.1A 524.2C 1438G 3010A 11864C (16519C)

            Comment


            • #7
              Originally posted by thetick View Post
              Not sure why the more recent mutation would mean your in that group? Just curious what you base that on?
              Temporal logic.

              It would appear to be a coincidence that it was correct.

              RhondaMiller understands and is happy with the explanation given by GST and that is the important thing.

              Comment


              • #8
                Look out for age estimates in the "new revision". Behar et al do not date H1 to 10,000 BC. They date it to 8,000 BC. Then they insist that, even though it originated in the Middle East or southeatern Europe, H1 spent the ENTIRE last ice age in Spain, which could not have happened even if it originated in 10,000 BC.

                Also, now, if my maternal line ancestor was from southern England, and most H1 inflow to southern England was from post-ice age Spain, why is my coding region partial match from Finland? I don't think so!

                Not to mention why does Basque DNA pretty closely match that of Sardinia, and their languages have much in common as well. That's the Mediterranean Neolithic, not the last ice age. Mediterranean Neolithic was in 6,000 BC, between the emergence of H1 and its arrival in Basque country, following the Mediterranean Neolithic path of migration which both circled the coast of Spain and cut directly across through Basque territory.

                If Behar et al want to insist that H1 spent the last ice age in Basque country, they have to date it to atleast 20,000 BCE, and pretty much noone still puts it that far back. Basque country spent the last ice age completely isolated from the eastern refugia.

                Interesting. I researched it and took it apart, at http://freepages.genealogy.rootsweb..../MitoLine.html

                Dora

                Comment


                • #9
                  I didn't read all of this thread. It appears you differ from H1 by at most one mutation. It is possible you do not appear on the phylotree because noone else shares this mutation for you.

                  Make sure you use the search feature in your browser to check the right portion of the phylotree for your mutation.

                  Comment


                  • #10
                    One other thing. You could not make it onto the current phylotree unless you either submitted your sequence to Genbank, or gave Family Tree DNA permission to use your sequence for research, or possibly both. One may have been more important than the other.

                    Alot of people are keeping their complete mitochondrial sequences deep dark secrets, because certain "experts" have been propounding from on high. that in case of the highly unlikely event that you have a coding region mutation that has a serious adverse effect on health, that you did not already know about, it would be highly unethical to allow anyone in your entire mitochondrial lineage to know they need to seek medical care. The more I say bunk, as well as point out that it's unethical by all the standards I learned in graduate school, not to share knowledge that could save someone else's health, the more high and mighty and regal people like that get.

                    If you want to be on the phylotree, you have to release your sequence. Otherwise it will be forever private, your maternal line relatives will not find you, and you wno't possibly help build the new clade that you eventually fall into.

                    I belong to a new clade that consists entirely of my own sequence (plus that of a likely 10th cousin from New England), and one of Dr. Behar's research subjects. If I had not contributed to the research the knowledge that enabled me to learn anything about the ancestral whereabouts of this lineage could not have been constructed, so I wouldn't find anything. The probable 10th cousin has already learned alot about her ancestry that she didn't already know because her complete mitochondrial sequence match found me - not possible if I'd kept my sequence a secret.

                    Dora

                    Comment


                    • #11
                      Originally posted by villandra View Post
                      Look out for age estimates in the "new revision". Behar et al do not date H1 to 10,000 BC. They date it to 8,000 BC. Then they insist that, even though it originated in the Middle East or southeatern Europe, H1 spent the ENTIRE last ice age in Spain, which could not have happened even if it originated in 10,000 BC.
                      I agree, the Behar et al Basque paper is oddly inconsistent with the Behar et al paper with the Phylotree updates. One possible explanation is that the Basque paper took a long time to get through peer review (which would not surprise me because it is a very flawed paper) so pehaps they didn't have the benefit of the more recent analysis in the Phylotree paper.

                      While nothing is certain, many people have theorized since at least the 2009 Bramanti et al paper that many H daughter groups were neolithic migrants to Europe. I have not seen any data to support the theory that H was in Europe during the last glacial maximum, and yet many respected academics seem to believe this is true. I think we are seeing an old theory dieing slowly and that migth explain the strange inconsistencies.

                      Comment


                      • #12
                        How do you work out age of H31 or H31a?

                        So far most of H31a known place of origin seems to be Scotland (4 out of 5) It probably predates setlement of Scotland, but this is where it seems to be clustering for now.

                        There are 39 HVR1 and HVR2 "Exact matches" and as the defining markers seem to be located on these is it safe to assume that if these folks can be convinced to part with their hard earned cash for a not inexpensive FMS test that their, regional coding markers could also define additional clades/supgroups?
                        Or would it just confirm them as H31a or whatever designation that ends up with?

                        Comment


                        • #13
                          Originally posted by Colin View Post
                          How do you work out age of H31 or H31a?
                          I let others work it out, Behar et al estimates;
                          H31 3965.8
                          H31a 2127.4

                          Comment


                          • #14
                            So about 107 20 year generations?

                            Comment


                            • #15
                              Originally posted by villandra View Post
                              One other thing. You could not make it onto the current phylotree unless you either submitted your sequence to Genbank, or gave Family Tree DNA permission to use your sequence for research, or possibly both. One may have been more important than the other.

                              Alot of people are keeping their complete mitochondrial sequences deep dark secrets, because certain "experts" have been propounding from on high. that in case of the highly unlikely event that you have a coding region mutation that has a serious adverse effect on health, that you did not already know about, it would be highly unethical to allow anyone in your entire mitochondrial lineage to know they need to seek medical care. The more I say bunk, as well as point out that it's unethical by all the standards I learned in graduate school, not to share knowledge that could save someone else's health, the more high and mighty and regal people like that get.

                              If you want to be on the phylotree, you have to release your sequence. Otherwise it will be forever private, your maternal line relatives will not find you, and you wno't possibly help build the new clade that you eventually fall into.

                              I belong to a new clade that consists entirely of my own sequence (plus that of a likely 10th cousin from New England), and one of Dr. Behar's research subjects. If I had not contributed to the research the knowledge that enabled me to learn anything about the ancestral whereabouts of this lineage could not have been constructed, so I wouldn't find anything. The probable 10th cousin has already learned alot about her ancestry that she didn't already know because her complete mitochondrial sequence match found me - not possible if I'd kept my sequence a secret.

                              Dora
                              My sequence was released prior to the new Phylotree I believe in sharing information, especially to help science along. I went back and re-read, I went from H1 to H1bb.

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