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  • M30, M*

    Hi there,

    Can anyone please help me with this - in what frequencies do any of these additions / deletions occur in other population groups & in which other haplogroups are they present):

    HVR1 = 223T, 278T, 304C, 311C, 391A, 519C

    HVR2 = 044.1C, 073G, 152C, 195A, 263G, 309.1C, 315.1C, 489C, 522-, 523-

    It seems that am the only member of the database confirmed as M30 through full sequence testing. Am from India.

  • #2
    memaker:

    the paper "The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes" by Sun et al. has a tree with some M30 sequences.

    Also, some are reported in Ian logan's website under M4:
    http://www.ianlogan.co.uk/discussion/hap_M4.htm

    I think M30 is the branch with 195 and 15431 (see the link to the tree in that page). None of the sequences though seem to match your HVR1.

    cacio

    Comment


    • #3
      Cacio,

      That's what is confusing me. Am told that my signature is unique in this database at this time.

      NatGeno has put me in as M* (they do not recognize M30 as yet?).

      Would like to know in which countries / linguistic groups do these HVR 1 and 2 mutations show up? Shd i try a DNAtest print? From where can I get it done?

      How different is mtDNA H with 16311C mutation from mtDNA M30 / M* with 16311C mutation?

      Am told that 16278T, 16311C are typical of haplogroup R1. Is that correct?

      16223T obviously is an old African mutation. What does it mean?

      Are there any mutations here linked to any diseases..

      Thanks very much.
      Last edited by ; 26 March 2008, 01:20 AM.

      Comment


      • #4
        memaker:

        I don't think the gen project uses many of the more recently discovered haplogroups like M30. There are very many haplogroups, especially in places like India, that have been only recently defined and studied, and the gen project has not yet incorporated them into their standard analysis.

        Mutations can happen entirely independently in unrelated haplogroups. As you say, 16311 is found in other haplogroups as well, but there is no relation between your 16311 and that of, say, haplogroup H. (In fact, I think 16311 is a mutation that pops up in many haplogroups - it is simply a very volatile location, like 16519).

        16223 is a slightly different case, because your 16223 is actually not a mutation, it is the ancestral value. In other words, the ancestral value is 16223T. However, there was a mutation along the line leading to haplogroup R, and all descendants of R have 16223C. However, M is not a descendant of R. Descendants of R include also (for instance) H. However, pretty much everybody else has 16223T, and this includes not only Africans, but also most Indians and Asians and a few Europeans too.

        When thinking about your mtdna, you should think about the genealogical tree of haplogroups, not about single mutations. You are close to the other M30's, which in turn is a sister group of other M4 groups. Going backwards, you are part of the big M family. Most Europeans belong to the N family. However, India is divided about equally between M and N. As far as I know, M30 has been found only in India, however, I am not an expert on this. And unfortunately, because Indians have not tested much, it is common for an Indian person not to have any matches. The situation may change when more people of Indian origin start testing in large numbers, but this hasn't happened yet.

        Incidentally, none of the HVR1 is related to any disease, simply, it is a junk part of the mtdna. (In principle, there can be deleterious mutations in the coding region of the mtdna, but these mutations are extremely rare.)

        cacio

        Comment


        • #5
          Thanks much Cacio. That solves a good many things for me. And I really hope more number of Indians get into this. It feels disappointing to remain unmatched

          Which of these HVR mutations are characteristic of M30? If I were to go thru several of the M* haps present in the db and try and figure out which of those cud be M30, what shd I be looking for?

          Comment


          • #6
            memaker:

            according to the tree in the Sun paper cited above and to Ian Logan's webpage, M30 is characterized by coding region mutations 12007, 15431, and by HVR2 mutation 195A.

            So if you are looking at mitosearch, if the person has HVR2 you can see whether he or she has 195A. But few people have tested HVR2. Other than that, there's little you can do. Of course, if you find a person who has an HVR1 similar to yours, then he's probably also M30. But you need a match on many mutations, not just one or two. As said, _all_ M have 16223, many people also have 16519, and a few 16311 as well, so these three are not particularly informative.

            Anyway, I would assume that the sequences present in the Sun paper or in Logan's website are pretty much most of what we have for M30. If you have tested your whole mtdna, you can also have it submitted to Genbank (anonymously, of course).

            cacio

            Comment


            • #7
              M30

              Cacio,

              1) According to this paper: http://www.pubmedcentral.nih.gov/art...?artid=1945034

              "M30 has a broad geographic, ethnic and linguistic range in India. It has been detected in northern and southern India, in Australoids and Caucasoids, and in Dravid and Indo-European speakers".

              Its presence in Palestinians was attributed to a probable recent gene flow from India into the middle-east.

              Unfortunately am not able to get info on which Indian linguistic groups report M30 presence. Is there some place I can get this info from?

              So far am only aware it was detected in Orissa / Oriya speaking people: http://www3.interscience.wiley.com/c...TRY=1&SRETRY=0


              2) Could you please help me understand the dating of M30 expansion (which seems contradictory in these 2 papers - perhaps am not understanding it well):

              a) According to this -- http://www.biomedcentral.com/content...2164-7-151.pdf -- M30 branched out from M4′30 superclade and dates to 15400+/-6300 ybp.

              (Since M4′30 super-clade shares an intermediate lineage between 2 haplogroups, should I be looking at possible matches from the M4 group as well ?)

              b) According to this -- http://genomebiology.com/2004/6/2/P3 -- the age of M30 lineage was estimated at 33,042 YBP.

              Comment


              • #8
                Cacio,

                I did find a lady on Mitosearch that has the same HVR 1 as mine. She plans to test for HVR 2. Lets see how it goes.

                Yes I will submit the mtDNA seq with GenBank.

                Am curious, how many Indians have had their whole mtDNA sequenced?

                Thanks much for the replies...am grateful for your guidance.

                Comment


                • #9
                  memaker:

                  very interesting links.

                  I am no expert on mtdna, so I don't know how to evaluate age computations (which I guess depends on the assumed rate of mutation). However, note that the two papers define M30 in different way. What Rajkumar (which is an earlier paper) calls M30, Thangaraj calls M4'30. M30 in Thangaraj is a subgroup of M4'30. So it makes sense that a subgroup is younger that the bigger group. Th. says M30 is about 15K years old.

                  There is indeed some discrepancy, because Thangaraj gives an age of 60K years for M4'30. I don't know the reason for this discrepancy. Thangaraj's paper is newer, and it also has more observations, so perhaps it has more information. Or perhaps he uses a different mutation clock.

                  Anyway, if you know you're M30, you shouldn't look for matches among people who belong to M4'30, but not M30 itself, as the two groups have diverged at least 15K years ago, possibly more. Your HVR1 match in mitosearch belongs very likely to your own haplogroup.

                  Thangaraj also defines a few subgroups of M30 (M30a etc.), and since you have your own full sequence, you can check whether you belong to any of those subgroups.

                  Perhaps the scientific articles have additional files with the data used in the paper, and perhaps these files also say the origin of the observations. But I don't know, and in general, according to the first article, M30 is found all over India. Indeed, as far as I know, it is in general true that mtdna haplogroups have no particular geographic relation within India.

                  cacio

                  Comment


                  • #10
                    Originally posted by cacio
                    Perhaps the scientific articles have additional files with the data used in the paper, and perhaps these files also say the origin of the observations. But I don't know, and in general, according to the first article, M30 is found all over India. Indeed, as far as I know, it is in general true that mtdna haplogroups have no particular geographic relation within India.
                    Cool! that makes all indian women true blue Indians, not region-specific, found everywhere - this pleases me to no end

                    If Thangaraj says M30 is about 15K years old, then this expansion is indeed very recent...will check if i belong to any of those sub-groups.

                    15K is earlier than the known neolithic expansion times in india.....so they were still hunting then...interesting.

                    Comment


                    • #11
                      Good point- the women were all local. It's probably many of the men who came from outside later on (Aryans? or what else).

                      15K years ago is still paleolithic. But note that there are always large confindence intervals. The other M4'30 groups have even earlier estimates, so perhaps even M30 is more ancient too. Anyway, these are all clearly Indian-specific haplogroups. Stuff that came with the neolithic later on is probably more like the typical Middle Eastern-European haplogroups, of which there is just a little in the area.

                      cacio

                      Comment


                      • #12
                        Cacio,

                        Yeah so its the men who have been perpetuating class and caste probs in India not the women There were so many waves of men people coming into India, its so hard to say which were Aryans...

                        Please hv a look at this: You had mentioned abt looking for 195A and this person is the only other person in the entire db apart from me that has it (from what hv searched so far). :

                        KIT 77257
                        M* Hap
                        HVR 1 = 189C,223T,278T,519C 73G,143A,152C,
                        HVR2 = 195A,263G,309.1C,315.1C,489C,522-,523-

                        Its a near perfect match. Only one mutation in HVR 1 and 2 do not match (in HVR 2 this person has 143A and I have 44.1C and in HVR 1 this person has 189C, while I have 304C, 311C, 391A).

                        Can I contact him / her?

                        Comment


                        • #13
                          Why not? However, there are significant differences. 3 mutations is a lot, this probably implies that the two of you separated basically at the beginning of M30 (if this person is indeed M30, which is likely given the 195A)..

                          also, I forgot to say, you can as well contact the authors of the papers on Indian M which you cited in a previous post, telling them about your sequence and asking them for suggestions. They may or may not answer. Still, it's worth a try.

                          cacio

                          Comment

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