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  • #16
    Originally posted by Ann Turner View Post
    I don't feel entirely comfortable with the original numbers, as they seem to be based on a rather high mutation rate. But I really don't have an alternative to propose. I've done a number of custom reports for people who have obtained their FGS, and there are some cases where the coding region is an exact match to the founder of a haplogroup, perhaps tens of thousands of years ago. On the other hand, there are cases where people have mutations that have never been observed before, so there's quite a range.
    Ann,
    Is there enough of a "handle" on this general subject matter that we have an idea how much is out there that has not yet surfaced? An example of what I am trying to say: from time to time I read reports that note that scientists estimate that there are hundreds or sometimes thousands of species that have not been discovered lyng out in the deep ocean. The recent discoveries at both poles buttress that. To day FT DNA is justifiably proud that it has 85,000 separate mt dna samples, but next to the number who have not submitted to testing that is a small number. At some point I would expect that an enterprizing statistician working with knowledgable genetists could start estimating the dimensions of what is out there undiscovered. Have we crossed that threshold yet? If so are there sources who have boiled that down into a form that even a liberal arts guy like me could "get it"?

    Comment


    • #17
      For the benefit of those reading this topic...
      Originally posted by Darren View Post
      ...A Full Sequence match would yield a 50% chance of a common ancestor within the past 5 generations and a 90% chance within the past 16 generations. There is a comparison table in the certificate packet that is mailed out with the results.
      In a follow-up email I asked Darren, "When a FTDNA FGS match occurs does that mean that the HVR1, HVR2, and CR mutations all match, and the individuals are in the same haplogroup? Does it also mean that there are in the same subclade?"

      He replied,
      For an Full Sequence match there must be an exact match in both HVR1 and 2. This would also indicate that the two would be in the same exact haplogroup and subclade.
      Although his reply did not state it included the CR mutations, I thought it might be implied because the haplogorup & subclades must also match.

      Comment


      • #18
        Originally posted by wighty44 View Post
        ...I asked Darren, "When a FTDNA FGS match occurs does that mean that the HVR1, HVR2, and CR mutations all match, and the individuals are in the same haplogroup? Does it also mean that there are in the same subclade? ... Although his reply did not state it included the CR mutations, I thought it might be implied because the haplogorup & subclades must also match.
        It is implied in the name of the test; a full genomic sequence must include the entire genome (of the mitochondrion), of which the hypervariable regions are a part.

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        • #19
          hmmmm

          touch confused here. I am sure it is the Liberal Arts mind trying to understand a technical field and not having had the benefit of the direct contact with Darren on topic. When I was in the business of doing my technical responses on the law, we used to tell our clients over and over, change the question you change the answer. I don't know exactly what this all means, but I know this for a fact: My FGS match who is classified into the same T1b as I am is not an exact match on HVR2. The 3 people who are exact matches on my HVR 1 and 2 and also T1b have, I know, taken the FGS, but to date are not popping up on my FGS matches. Now it may be theirs have not yet been reported out. It may be theirs are being held privately. Or it may be I just do not understand, but the facts in my case do not seem to square with the reply you received. I absolutely trust the source so am not trying to imply anyone is confused or has confused the issue other than me.

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          • #20
            Originally posted by Deirwha View Post
            ... I don't know exactly what this all means, but I know this for a fact: My FGS match who is classified into the same T1b as I am is not an exact match on HVR2. The 3 people who are exact matches on my HVR 1 and 2 and also T1b have, I know, taken the FGS, but to date are not popping up on my FGS matches. Now it may be theirs have not yet been reported out. It may be theirs are being held privately. Or it may be I just do not understand, but the facts in my case do not seem to square with the reply you received. I absolutely trust the source so am not trying to imply anyone is confused or has confused the issue other than me.
            The HVR2 difference with your FGS near-match is not a difference diagnostic of a haplogroup or subclade difference (according to current phylogeny) and the haplogroup and subclade classification shared with two HVR exact-matches is based entirely on HVR-based phylogeny (if these two exact HVR matches get FGS they may or may not be reclassified based on coding region results as there are also coding region differences that are/are not diagnostic of subclade differences under current phylogeny).
            Last edited by tomcat; 26 February 2009, 12:27 PM.

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            • #21
              Another thing or two ...

              Even though there is planet's worth of human mitochondria yet to be sequenced, FTDNA's rule-of-thumb about TRMCA for FGS does not seem to fit with results already in-hand (Turner).

              And while FTDNA may suggest phylogenetic and TRMCA revisions based on FGS results of it's clients, phylogenetic and TRMCA revisions might be facilitated with other sets of eyes on the problem:

              As of 2/26/09 FTDNA has 4,328 FGS in it's database.
              As of 2/21/09 FTDNA clients have posted 326 FGS to GenBank.
              As of 2/1/09 Total FGS at GenBank is 5,496.

              Hence the GenBank total would virtually double in size if the balance of FTDNA FGS were submitted to GenBank by FTDNA customers. Here's how:
              www.ianlogan.co.uk/

              Comment


              • #22
                Originally posted by tomcat View Post
                The HVR2 difference with your FGS near-match is not a difference diagnostic of a haplogroup or subclade difference (according to current phylogeny) and the haplogroup and subclade classification shared with two HVR exact-matches is based entirely on HVR-based phylogeny (if these two exact HVR matches get FGS they may or may not be reclassified based on coding region results as there are also coding region differences that are/are not diagnostic of subclade differences under current phylogeny).
                I correct myself:
                FTDNA does sample coding region SNP's for their determination of haplogroup/subclade based on HVR's so the HVR exact-matches would likely hold up in FGS as pertains to shared haplogroup/subclade.
                However, FTDNA is always conservative in its adoption of proposed phylogenetic changes so that shared haplogroup/subclade assignment might not endure.

                Comment


                • #23
                  Originally posted by Deirwha View Post
                  Ann,
                  Is there enough of a "handle" on this general subject matter that we have an idea how much is out there that has not yet surfaced? An example of what I am trying to say: from time to time I read reports that note that scientists estimate that there are hundreds or sometimes thousands of species that have not been discovered lyng out in the deep ocean. The recent discoveries at both poles buttress that. To day FT DNA is justifiably proud that it has 85,000 separate mt dna samples, but next to the number who have not submitted to testing that is a small number. At some point I would expect that an enterprizing statistician working with knowledgable genetists could start estimating the dimensions of what is out there undiscovered. Have we crossed that threshold yet? If so are there sources who have boiled that down into a form that even a liberal arts guy like me could "get it"?
                  I wish I could answer your question, but I can offer up an observation. The latest Genographic Project spreadsheet has a little over 50,000 HVR1 records (16001-16569). Only 344 of those bases show a mutation, in spite of the fact that there have been umpteen generations giving an opportunity for a mutation to occur. It does appear that there are "cold spots" as well as "hot spots" (like 16519C, for example).

                  Comment


                  • #24
                    Shock and awe, actually

                    Originally posted by Ann Turner View Post
                    I wish I could answer your question, but I can offer up an observation. The latest Genographic Project spreadsheet has a little over 50,000 HVR1 records (16001-16569). Only 344 of those bases show a mutation, in spite of the fact that there have been umpteen generations giving an opportunity for a mutation to occur. It does appear that there are "cold spots" as well as "hot spots" (like 16519C, for example).
                    Wow. With so little variation it would be very hard to project statistically the variety of life in the ocean, to retain analogy. I quickly run out on fumes when I deal with the technical, but statistics were a part of my "former life." So I can apprieciate your point. How, with so little variance, have projections been made as to the age of mt groupings like T and JT etc?

                    Comment


                    • #25
                      Originally posted by Deirwha View Post
                      touch confused here. ... My FGS match who is classified into the same T1b as I am is not an exact match on HVR2...
                      I doubt it has anything to do with LA... Just when I think I'm beginning to understand something I find conflicting information.

                      On One hand, I have Darren's reply to my email questions about FGS matches (also posted here); and yet, I read that an FTDNA customer has a FGS match except for HVR2...

                      Either something in the matching criteria has changed, or an error was made. Regardless, I'd sure would appreciate someone from FTDNA investigating your situation and responding here, because something does not mesh...

                      Comment


                      • #26
                        Originally posted by wighty44 View Post
                        Either something in the matching criteria has changed, or an error was made. Regardless, I'd sure would appreciate someone from FTDNA investigating your situation and responding here, because something does not mesh...
                        I looked carefully at the work up on the FGS of both me and my match again. Not every mutation is mentioned. I suspect in determining haplogroups, as mentioned previously by Tomcat, or matches for that matter, not every mutation is as determinative as another. I know of at least one mutation that varies from mother to daughter. I also am aware of private mutations that are not considered in the haplogroup but may be in the matching. And there are other things out there like "shadow" mutations.
                        I suspect the answer that reconciles the information you received with my facts is that the difference in mutation is not significant from the point of view of matching and so ours is an exact match of those mutations considered in determining a match. This is just a guess on my part, a notion someone from FT DNA could of course disabuse me of and go on to explain the discrepancy. It is the only idea I have for reconciling the two communications, again, not having been privy to the email communication in full to gain context.

                        Comment


                        • #27
                          Originally posted by wighty44 View Post
                          I doubt it has anything to do with LA... Just when I think I'm beginning to understand something I find conflicting information.

                          On One hand, I have Darren's reply to my email questions about FGS matches (also posted here); and yet, I read that an FTDNA customer has a FGS match except for HVR2...

                          Either something in the matching criteria has changed, or an error was made. Regardless, I'd sure would appreciate someone from FTDNA investigating your situation and responding here, because something does not mesh...
                          In this thread, on 2/23 (#7) it seems that you got at least a partial answer from rucksack.

                          Comment


                          • #28
                            That explanation works for me

                            Originally posted by Enodoch View Post
                            In this thread, on 2/23 (#7) it seems that you got at least a partial answer from rucksack.
                            I went back and checked both Rucksack's comment and my results against those of my match and I do not have 309.1c and she did. But the FGS was considered a match.

                            Comment


                            • #29
                              Originally posted by Deirwha View Post
                              I went back and checked both Rucksack's comment and my results against those of my match and I do not have 309.1c and she did. But the FGS was considered a match.
                              You do seem to list 309.1C in your signature as one of your mutations.

                              I'm formerly T5, now T2, and know of one person who is just one private mutation away from me of being a perfect match. Still FTDNA shows me having no FGS matches.

                              John

                              Comment


                              • #30
                                Originally posted by Johnserrat View Post
                                You do seem to list 309.1C in your signature as one of your mutations.

                                I'm formerly T5, now T2, and know of one person who is just one private mutation away from me of being a perfect match. Still FTDNA shows me having no FGS matches.

                                John
                                I list 309.1C. I do not list 309.2C. She does. Sorry for the confusion but I typed 309.1C instead of 309.2C and did not catch it as I typed.

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