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Full mtDNA match (or only HVR1 & HVR2 match)?

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  • Full mtDNA match (or only HVR1 & HVR2 match)?

    Looking at the list of "Full matches" (rather than simply the HVR1 & HVR2 matches) for someone who is H1a1, I get 18 pages of matches, with about 12 pages being exact matches and the rest 1 or 2 mis-matches.

    Is this truly matching all of the mtDNA, including the coding region (which is private), or is it only matching the HVR1 & HVR2 regions?

  • #2
    When the matches page is showing Genetic Distance 0, 1, 2 and 3 matches, those are your full sequence matches. There is a drop down tab you can use to select HVR1 matches or HVR1,HVR2 matches.

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    • #3
      Originally posted by GST View Post
      When the matches page is showing Genetic Distance 0, 1, 2 and 3 matches, those are your full sequence matches. There is a drop down tab you can use to select HVR1 matches or HVR1,HVR2 matches.
      Yes, they are your Full Sequence matches. However, are they matching the entire mtDNA (including the Coding Region) or are they only matching the HVR1 & HVR2 section for your Full Sequence matches.

      I believe they are matching the entire mtDNA (including the Coding Region) but I have a hard time believing their are absolutely no mutations within the whole mtDNA for several centuries. I have Full Sequence matches from folks from a variety of Countries on the European Continent as well as innumerable matches whose MDKA was from "the (British) Isles".

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      • #4
        Difference in size between mtDNA and Y-DNA

        A big issue I personally have is the fact I am used to working with Y-DNA (being a co-administrator for the R-U106 Haplogroup Project).

        The Y-DNA contains 58 MILLION base-pairs (bp), and even if we only include the ?20%? which is currently testable, it still leaves us with over 10 MILLION bp where we are able to track mutations.

        The mtDNA has only 16,569 bp in total. This is roughly 1/500th the size of the currently readable Y-DNA bp. While the HVR regions of the mtDNA mutate much more frequently than chromosomal DNA, the much smaller size of the mtDNA means some haplogroups are VERY old and cannot be broken down further.

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        • #5
          The answer to your question from the FAQ is:

          "Higher testing levels (mtDNAPlus and mtFullSequence) include matching from lower testing levels. This means that someone who tests at the mtFullSequence testing level will have matching at the HVR1 level, the HVR1 & HVR2 level, and the HVR1, HVR2, & Coding Region level."

          Comment: "will have matching" does not mean "do match". Thus, I have many matches at a genetic distance of more than 0 on the setting "HVR1, HVR2, Coding Region" which do not appear on my "HVR1" and "HVR1, HVR2" lists.

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          • #6
            Originally posted by Wing_Genealogis View Post
            Yes, they are your Full Sequence matches. However, are they matching the entire mtDNA (including the Coding Region) or are they only matching the HVR1 & HVR2 section for your Full Sequence matches.I believe they are matching the entire mtDNA (including the Coding Region) but I have a hard time believing their are absolutely no mutations within the whole mtDNA for several centuries.
            Yes - they are showing differences for the entire mtDNA genome, so you have 18 pages of matches who have identical results in the full mtDNA genome. As you noted, the mutation rate is slow because of the small size of the mtDNA genome. In a 2010 paper Soares et al. estimated that the average mutation rate is about 1 mutation in 3600 years, but it is also highly variable. For example, some people might have no mutations in 8000 years while another person might have 10 or more mutations in that same time period. If your maternal line has not had any mutations in several thousand years, you can have a very large number of identical matches.

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            • #7
              What is your haplogroup, and do you have any "extra" mutations when you run your mtDNA through James Lick's utility?

              http://dna.jameslick.com/mthap/

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              • #8
                Originally posted by Ann Turner View Post
                What is your haplogroup, and do you have any "extra" mutations when you run your mtDNA through James Lick's utility?

                http://dna.jameslick.com/mthap/
                This is not my personal mtDNA, but the calculated mtDNA for a Mayflower passenger, Elizabeth (Tilley) Howland, coming from multiple "umbilical" descendants of Elizabeth via two different daughters.

                Up until recently, I did not have direct access to the Coding Region mutations. I finally do have access, and checking with James Lick's utility, it is a perfect match for mtDNA H1a1 with no extra mutations (besides the flaky 315.1C and 16519C).

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                • #9
                  H1a1 a very old haplogroup

                  I was hoping to be able to use mtDNA results to help with answering some long-standing questions regarding the spouses & families of a couple of maternal granddaughters (and great-granddaughters) of Elizabeth.

                  According to the mtDNA H1 Haplogroup Project, H1a1 originated roughly 2500 BC, and can be found in multiple locations on the European Continent as well as spread out widely in the (British) Isles.

                  Thus, mtDNA testing cannot conclusively prove whether these girls were maternal (great-)grandchildren, but it could conclusively disprove the relationship (if their mtDNA descendants are of a different haplogroup).

                  As I said before, I am used to working with Y-DNA results and have become "spoiled" regarding how often one can expect a mutation.

                  The mitochondria DNA is so small, mutations a much rarer than working with chromosomal DNA.

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                  • #10
                    Originally posted by Wing_Genealogis View Post
                    This is not my personal mtDNA, but the calculated mtDNA for a Mayflower passenger, Elizabeth (Tilley) Howland, coming from multiple "umbilical" descendants of Elizabeth via two different daughters.

                    Up until recently, I did not have direct access to the Coding Region mutations. I finally do have access, and checking with James Lick's utility, it is a perfect match for mtDNA H1a1 with no extra mutations (besides the flaky 315.1C and 16519C).
                    So when you say there at twelve pages of exact matches, you're referring to some specific instance where a descendant has the consensus sequence for Elizabeth Tilley Holland?

                    I looked at the H1a1 sequences deposited in GenBank. There are 69 (not including subclades) out of ~32,999 records. Twelve of those have retained the core haplotype, there are two sets of two identical haplotypes, and there are 53 singletons. The mutation rate for mtDNA is much higher than Y SNPs, so you can get a lot of diversity with all the possible combinations of mutations scattered over the molecule.

                    I'm still surprised that you see twelve pages of exact matches, though. The FTDNA database much be enriched with Elizabeth's descendants

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                    • #11
                      The mtDNA signature is an exact match to Haplogroup H1a1 with no extra markers (with the exception of the flippy 315C & 16519C). According to the H1 mtGenome Project, Haplogroup H1a1 dates back about 2500 B.C.E. Thus the mtDNA "signature" is not limited to descendants of Elizabeth (Tilley) Howland, but predate her by several millennia.

                      Doing an exact count of mtDNA matches within all of FTDNA, there were 155 matches with a GD of 0, 151 matches with a GD of 1, 81 matches with a GD of 2 and 39 matches with a GD of 3. I know two of the matches definitely come down from Elizabeth (Tilley) Howland, but almost all of the rest certainly came down from other ancestral lines.

                      The MDKA for the exact mtDNA matches come from several locations on the European Continent as well as being spread out across the (British) Isles.

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