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M* haplogroup technical questions

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  • M* haplogroup technical questions

    Family Tree DNA's mtDNA HVR-1 analysis puts me in the M* haplogroup. In particular, the CRS-relative mutations reported (-16000) are 223T, 319A, 519C. While there are no matches reported at the ftDNA site, there are several entries with 1-step mutation(-1 mutational difference) reported at mitosearch.org.

    Interestingly however all of these entries happen to belong to different haplogroups such as H, HV. For example, there is an entry for HVR1 mutations 223T, 519C reported as belong to the H haplogroup. Assuming mitosearch data can be trusted, how can this be explained ? Why can't it be assumed that my particular M* haplotype is a branch (319A) from the HV haplotype from mitosearch, contrary to what a "standard" mtDNA phylogenetic tree might suggest ?

  • #2
    >there are no matches reported at the ftDNA site,

    That's not surprising. Knowledge of the South Asian phylogeny is still in its infancy though several thousands sequences were published last years. Too many lineages, highest diversity of M* and R* haplogroups, too intricate phylogenies. Your nickname says you are a Chitpavan Brahman, are you?

    >there are several entries with 1-step mutation(-1 mutational difference) reported at mitosearch.org.

    I don't think this database is helpful to search for South Asian sequences. It seems to be too "eurocentric". In your particular case, you may have really close HVS matches that will appear to be very distant from your variant in the remaining portion of mt molecule.

    Nevertheless, you do have hvs1 matches in the published literature, most are SNP tested:

    Cordaux 2003, Kerala, Kuruman Mullu
    M*
    223-319
    (range: 16022–16391)
    3 samples

    Cordaux 2003, Tamil Nadu, Kurumba Mullu
    M*
    223-319
    (16022–16391)
    3 samples

    Kivisild 1999, Uttar Pradesh
    M*
    223-319
    (16024-16383)
    -447HinfI +10394DdeI +10397AluI
    2 samples

    Kashyap 2005 Western India
    M*
    223-319
    73-263-309.1C-315.1C
    (16050-16391; 48-408)
    +10394DdeI +10397AluI
    1 sample

    Quintana-Murci 2004
    Pakistan, Karachi
    M*
    223-319-519
    73
    (16000-00133)
    +10394DdeI +10397AluI -10871MnlI
    1 sample

    Chang Sun 2005, India
    M38
    223-319-519
    73-152-189-204-214-246-263-309.1C-309.2C-315.1C-489
    (complete sequence)

    btw, the latter example is the only one complete sequence that matches your hvs1 type exactly. I recommend you to take HVS2 test to see whether more reliable matches exist.

    Valery
    Last edited by vraatyah; 11 March 2006, 05:00 AM.

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    • #3
      Thanks for pulling up all this data. Are the last two papers (Quintana-Murci 2004 and San Chung 2005) public-domain, i.e. freely accessible ?

      And yes, I indeed am a Chitpavan brahman..

      Comment


      • #4
        So Nenechitpavan belongs to M38?, a sub branch of M4'30, defined by the 12007. Macro Haplogroup M4'30 is estimated at 33,000 years, and coincides with the Upper Palaeolithic, when the interior of the Indian Subcontinent was populated my Sapiens. Offshoots of M4'30 include M4, M30, M37, M38 and M18.

        I have a question for Vraatyah. Approximately what proportion of Indians M sequences belong to M4'30? Thanks.

        M Tree:

        http://img386.imageshack.us/my.php?image=hapm9ev.jpg
        Last edited by Kir; 11 March 2006, 01:39 PM.

        Comment


        • #5
          Originally posted by Kir
          So Nenechitpavan belongs to M38?
          Hi Kir!

          Take a look at the above list of the hvs1 matches. 223-319 hvs1 sequence doesn't seem to be "weighty" enough to make conclusions although this type was found only in Indians. 3 of 6 haplotypes don't have hvs2, one has hvs2 cut off, and only 2 have valid ones though unrelated. Were Nenechitpavan to have his (her) own hvs2 sequenced, we'd make more reliable conclusions, or the contrary, we would claim that this HVS type does not have close relatives among already published HVSs.

          Originally posted by Kir
          Approximately what proportion of Indians M sequences belong to M4'30?
          Judging by reliable hvs matches and rare cases where authors seem to assign haplogroups using RFLPs, the answer is: very little portion, about 200 out of total 4300 published. You see, it's not really so, the frequency should be a bit greater. The most substantial reason is homoplasy: many of the hvs types are full of "noisy" mutations that occur elsewhere in the global tree and particularly in other Indian clades. Sometimes authors subject for the complete sequencing samples with very unusual hvs variants that are interesting in their own, ie phylogenetically, however they don't help in population studies.
          Last edited by vraatyah; 11 March 2006, 03:06 PM.

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          • #6
            Once again thank you Vraatyah for your response. From what I understand some mutations are highly variable, and occur a lot on unrelated haplogroups, and therefore don’t make great defining mutations, so would you say that 12700 is highly variable or not? One last question about mtDNA, what determines the name of the haplogroup? Why are haplogroups named B while others are referred to as R10 or R11 or in M haplogroups some called G while others are called M7? Is there something behind the naming?

            Comment


            • #7
              Originally posted by Kir
              Once again thank you Vraatyah for your response. From what I understand some mutations are highly variable, and occur a lot on unrelated haplogroups, and therefore don’t make great defining mutations, so would you say that 12700 is highly variable or not?

              Unfortunately, 12007 site varies. It separates L0 mtDNAs from other ones and occurs as a back mutation in several N9, D5, A2 (where it's indicative of the whole subclade), J1 and R sequences.

              Originally posted by Kir
              Is there something behind the naming?
              nothing

              Comment


              • #8
                Originally posted by nenechitpavan
                Thanks for pulling up all this data. Are the last two papers (Quintana-Murci 2004 and San Chung 2005) public-domain, i.e. freely accessible ?

                And yes, I indeed am a Chitpavan brahman..
                I don't know what a Chitpavan Brahman is ,but I do have a few numbers in common with Sun Chang,India. So maybe I have a few genes from the Medi,or East ,maybe I'm a White Brahman. My MtDNA results listed me as an MtK from the German Alps.I did have 12 solid markers from Germany first and foremost.The rest of my markers were from all over Caucasia and 519.1C is found in the Mediterranean and haplogroup H,and in some people in India. But all of a persons markers have to match a specific region code.Even though I have a 519.1C I was not classed as a Mediterranesn or an Indic,because I don't have all of the same markers they have.Most of my markers matched people from the German alps,not that they all have 519.1C,BUT ALL OF MY CLOSE MATCHES DO..

                Comment


                • #9
                  Originally posted by Jambalaia32
                  I don't know what a Chitpavan Brahman is ,but I do have a few numbers in common with Sun Chang,India. So maybe I have a few genes from the Medi,or East ,maybe I'm a White Brahman. My MtDNA results listed me as an MtK from the German Alps.I did have 12 solid markers from Germany first and foremost.The rest of my markers were from all over Caucasia and 519.1C is found in the Mediterranean and haplogroup H,and in some people in India. But all of a persons markers have to match a specific region code.Even though I have a 519.1C I was not classed as a Mediterranesn or an Indic,because I don't have all of the same markers they have.Most of my markers matched people from the German alps,not that they all have 519.1C,BUT ALL OF MY CLOSE MATCHES DO..
                  seems like you confused transition 16519 T->C with the C-insertion after this site. The transition is very usual and has no significance in phylogeny at all because it arises in any haplogroup background independently. As to the insertions, they are not found at this position yet.

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                  • #10
                    Vraatyah - R*

                    Vraatyah,
                    Do you have any data about mtDNA R* in India and surroundings?
                    Thanks

                    Comment

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