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  • mtDNA Haplogroups

    Is there a tree for the mtDNA Hgs using SNPs like the ISOGG Y-Tree? Also, what about a mtDNA Browser like the Y Chromosome Browser?

  • #2
    The mtDNA tree which is used by population geneticists and FTDNA is at http://www.phylotree.org/. FTDNA just started using Build 14 of this tree last week to assign haplogroups to its customers. The latest version is Build 15, which was issued at the end of September.

    I don't know of any browser for mtDNA, but here are a couple of links showing the ancestral values for each mtDNA location:

    rCRS - http://www.phylotree.org/resources/rCRS_annotated.htm
    RSRS - http://www.phylotree.org/resources/RSRS_annotated.htm

    RSRS is the new standard put forward earlier this year in a major paper. I believe that Geno 2.0 is using rCRS as its standard, since RSRS was published after the cutoff date to be included on the chip. Maybe someone else can speak to that.

    Comment


    • #3
      Originally posted by MMaddi View Post
      The mtDNA tree which is used by population geneticists and FTDNA is at http://www.phylotree.org/. FTDNA just started using Build 14 of this tree last week to assign haplogroups to its customers. The latest version is Build 15, which was issued at the end of September.

      I don't know of any browser for mtDNA, but here are a couple of links showing the ancestral values for each mtDNA location:

      rCRS - http://www.phylotree.org/resources/rCRS_annotated.htm
      RSRS - http://www.phylotree.org/resources/RSRS_annotated.htm

      RSRS is the new standard put forward earlier this year in a major paper. I believe that Geno 2.0 is using rCRS as its standard, since RSRS was published after the cutoff date to be included on the chip. Maybe someone else can speak to that.
      Thanks!

      So the numbers on the Geno raw data should correspond to those numbers on Build 15? Because my 239 is a G when it is seemingly either T or C and the ancestral is T.??

      Comment


      • #4
        Originally posted by JTR View Post
        Thanks!

        So the numbers on the Geno raw data should correspond to those numbers on Build 15? Because my 239 is a G when it is seemingly either T or C and the ancestral is T.??
        You're seeing the value(G) that would be obtained on the reverse strand when the forward strand is a C.
        A<->T
        G<->C
        So reverse strand ancestral is A, your reverse strand is G, which is derived.

        Thanks to Ann Turner for helping me figure this out; it was definitely confusing to me when I first looked at my raw data.

        Comment


        • #5
          Originally posted by MMaddi View Post
          ...
          RSRS is the new standard put forward earlier this year in a major paper. I believe that Geno 2.0 is using rCRS as its standard, since RSRS was published after the cutoff date to be included on the chip. Maybe someone else can speak to that.
          Even phylotree is rCRS. RSRS is not the new standard, yet. I expect Geno 2.0 will use rCRS as that is the standard employed by Geno 1.0. even though Geno 2.0 "ought" to use RSRS as it is, conceptually, a better fit with Project purposes. Perhaps Geno will do an RSRS run with the data for the sake of further insights into phylogeny.

          Don't want to discourage anyone from doing their own research on their own Geno data but do want to encourage users to also commit their Geno Y and mtDNA to an appropriate FTDNA haplogroup, geographical or lineage project where, through comparison to others, the data can be used to the best advantage of all!
          Last edited by tomcat; 20 December 2012, 10:01 AM.

          Comment


          • #6
            Geno 2.0 is still using rCRS for mtDNA data.

            Comment


            • #7
              [QUOTE=tomcat;353395]Even phylotree is rCRS. RSRS is not the new standard, yet. I expect Geno 2.0 will use rCRS as that is the standard employed by Geno 1.0. even though Geno 2.0 "ought" to use RSRS as it is, conceptually, a better fit with Project purposes. Perhaps Geno will do an RSRS run with the data for the sake of further insights into phylogeny.

              Don't want to discourage anyone from doing their own research on their own Geno data but do want to encourage users to also commit their Geno Y and mtDNA to an appropriate FTDNA haplogroup, geographical or lineage project where, through comparison to others, the data can be used to the best advantage of all![/QUOTE
              Hi all,

              The PhyloTree uses the RSRS. There is an rCRS version available for download.

              GenoChip or Geno 2.0 uses the RSRS, based on PhyloTree Build 14.

              Having developed a version of the mthap utility that would translate GenoChip data files, Jim Lick now reports that GenoChip data files have recently changed format so that the mthap now longer works for them.

              FTDNA personal pages default to the RSRS, updated to PhyloTree Build 14. One click and you can see the rCRS version.

              FTDNA project pages are still only in rCRS format.

              The GenoChip and FTDNA will upgrade to PhyloTree Build 15 eventually. (I would say "soon." but I've been down that road.)

              Then the PhyloTree will release Build 16, perhaps before the previous paragraph.

              Bill Hurst

              Comment


              • #8
                [QUOTE=Bill Hurst;353401]
                Originally posted by tomcat View Post
                Even phylotree is rCRS. RSRS is not the new standard, yet. I expect Geno 2.0 will use rCRS as that is the standard employed by Geno 1.0. even though Geno 2.0 "ought" to use RSRS as it is, conceptually, a better fit with Project purposes. Perhaps Geno will do an RSRS run with the data for the sake of further insights into phylogeny.

                Don't want to discourage anyone from doing their own research on their own Geno data but do want to encourage users to also commit their Geno Y and mtDNA to an appropriate FTDNA haplogroup, geographical or lineage project where, through comparison to others, the data can be used to the best advantage of all![/QUOTE
                Hi all,

                The PhyloTree uses the RSRS. There is an rCRS version available for download.

                GenoChip or Geno 2.0 uses the RSRS, based on PhyloTree Build 14.

                Having developed a version of the mthap utility that would translate GenoChip data files, Jim Lick now reports that GenoChip data files have recently changed format so that the mthap now longer works for them.

                FTDNA personal pages default to the RSRS, updated to PhyloTree Build 14. One click and you can see the rCRS version.

                FTDNA project pages are still only in rCRS format.

                The GenoChip and FTDNA will upgrade to PhyloTree Build 15 eventually. (I would say "soon." but I've been down that road.)

                Then the PhyloTree will release Build 16, perhaps before the previous paragraph.

                Bill Hurst
                geno and FTDNA will not upgrade mtdna to v15 unless they can upgrade the y-dna at the same time. Y-dna is stuck at date of november 2011.

                It would be illogical and time wasting to leave one left behind while advancing the other for geno sake.

                I envisage an upgrade by June 2013, so v16 would be used and v15 by-passed. More then 1 upgrade per year seems improbable.

                Comment


                • #9
                  [QUOTE=Bartot;353410]
                  Originally posted by Bill Hurst View Post

                  geno and FTDNA will not upgrade mtdna to v15 unless they can upgrade the y-dna at the same time. Y-dna is stuck at date of november 2011.

                  It would be illogical and time wasting to leave one left behind while advancing the other for geno sake.

                  I envisage an upgrade by June 2013, so v16 would be used and v15 by-passed. More then 1 upgrade per year seems improbable.
                  Hi Bartot and all,

                  I don't see a necessary connection between mtDNA apples and Y-DNA oranges. Elliott Greenspan at the Conference last month said the Geno would use Build 14 and then progress to Build 15; he didn't tie it to Y-DNA.

                  Bill Hurst

                  Comment


                  • #10
                    Originally posted by ScooterCat View Post
                    You're seeing the value(G) that would be obtained on the reverse strand when the forward strand is a C.
                    A<->T
                    G<->C
                    So reverse strand ancestral is A, your reverse strand is G, which is derived.

                    Thanks to Ann Turner for helping me figure this out; it was definitely confusing to me when I first looked at my raw data.
                    Thanks! This is dishearting for newbies who want to enter into their own research regarding their data - what good is the data if I have to be familiar with different versions without knowing which one it is to begin with and without asking someone hoping for an answer on some 3rd party forum. Then to boot I have to do iterations with the data to figure out what is derived and not derived. Why couldn't they just put in the data whether it is derived or not?

                    Then on top of this FTDNA can't even downlaod the data properly - they mislabeled at least 15 markers as positive when in fact they were negative - and I have not even checked all of them - still have about 200 left to check - and that's if they actually got that right.

                    I have been getting answers, thanks to you guys, but it's like traveling down a freaking maze made by some sick twisted jokester.
                    Last edited by JTR; 20 December 2012, 01:59 PM.

                    Comment


                    • #11
                      Originally posted by tomcat View Post
                      Don't want to discourage anyone from doing their own research on their own Geno data but do want to encourage users to also commit their Geno Y and mtDNA to an appropriate FTDNA haplogroup, geographical or lineage project where, through comparison to others, the data can be used to the best advantage of all!
                      But FTDNA can't get that right either - what help is it if they are labeling your markers wrong?

                      Comment


                      • #12
                        [QUOTE=Bill Hurst;353411]
                        Originally posted by Bartot View Post
                        Hi Bartot and all,

                        I don't see a necessary connection between mtDNA apples and Y-DNA oranges. Elliott Greenspan at the Conference last month said the Geno would use Build 14 and then progress to Build 15; he didn't tie it to Y-DNA.

                        Bill Hurst
                        I cannot see geno not updating anf FTDNA updating, the data sent to one another will eventually be useless to a degree.
                        They both need to update together

                        Comment


                        • #13
                          Can you skip a node in your Hg by not having any derived mutations at the node but have ones above and below it?

                          Comment


                          • #14
                            Originally posted by JTR View Post
                            Can you skip a node in your Hg by not having any derived mutations at the node but have ones above and below it?
                            Hi JTR and all,

                            If you have the defining mutation(s) for a subclade (or node), then not for the next lower one, but do have it or them for the next lower one, you have probably had a back mutation at the subclade or node in question. I had a case in October where a project member had the defining mutation for K1a and K1a3a, but not for K1a3, so FTDNA labeled him just a K1a. After I wrote them, they changed him to K1a3a. Then the major update happened last week that should have put him into the even deeper K1a3a3, since he had the defining mutation for that. But the FTDNA program now has him just in K1a3a, which means he is past the back mutation but still not quite right. They are working to get that fixed.

                            Back mutations happen and sometimes FTDNA's program will account for it; sometimes not. If it doesn't, you have to write them and present your case. In the above case, the project member knew where he belonged all along. In other cases, they would have no idea. That's why everyone should join their haplogroup project and hope the project administrator understands how the system works or how it needs tweaking.

                            We had an even worse case in the past, with several members missing two out of the three defining mutations for K2a. At the time, FTDNA's program could only handle one back mutation, not two. So they sat at "K2" until last week's update. The program now knows to put them into K2a9. Nice when something actually works!

                            Remember that every missing mutation does not imply a back mutation. Sometimes the phylogenetic tree needs to be revised, with separate branches for those with and without the mutation(s). The Ashkenazi K2a2a has moved down to K2a2a1 because sequences were found that didn't have one of it's defining mutations. In this case, the PhyloTree was revised and the revision was formally adopted last week by FTDNA.

                            I'm sure - well, no I'm not - there is a course somewhere in Applied MtDNA Phylogeny, but some of us are learning it the hard way.

                            Bill Hurst

                            Comment


                            • #15
                              Originally posted by Bill Hurst View Post
                              Hi JTR and all,

                              If you have the defining mutation(s) for a subclade (or node), then not for the next lower one, but do have it or them for the next lower one, you have probably had a back mutation at the subclade or node in question. I had a case in October where a project member had the defining mutation for K1a and K1a3a, but not for K1a3, so FTDNA labeled him just a K1a. After I wrote them, they changed him to K1a3a. Then the major update happened last week that should have put him into the even deeper K1a3a3, since he had the defining mutation for that. But the FTDNA program now has him just in K1a3a, which means he is past the back mutation but still not quite right. They are working to get that fixed.

                              Back mutations happen and sometimes FTDNA's program will account for it; sometimes not. If it doesn't, you have to write them and present your case. In the above case, the project member knew where he belonged all along. In other cases, they would have no idea. That's why everyone should join their haplogroup project and hope the project administrator understands how the system works or how it needs tweaking.

                              We had an even worse case in the past, with several members missing two out of the three defining mutations for K2a. At the time, FTDNA's program could only handle one back mutation, not two. So they sat at "K2" until last week's update. The program now knows to put them into K2a9. Nice when something actually works!

                              Remember that every missing mutation does not imply a back mutation. Sometimes the phylogenetic tree needs to be revised, with separate branches for those with and without the mutation(s). The Ashkenazi K2a2a has moved down to K2a2a1 because sequences were found that didn't have one of it's defining mutations. In this case, the PhyloTree was revised and the revision was formally adopted last week by FTDNA.

                              I'm sure - well, no I'm not - there is a course somewhere in Applied MtDNA Phylogeny, but some of us are learning it the hard way.

                              Bill Hurst
                              Thanks Bill! Assuming I am reading the data correctly then I guess I missed 3 nodes (two of them in a row). Here is what it looks like - the Line #'s are from the Geno data file where the marker is located. The red are what I read to mean positive/derived. Am I correct in reading this? Is it possible to have that many back mutations and what does this do to the time factor for your HG? My Hg is H6a1b3a - Thanks Again!

                              G2706A, T7028C > T239C, T16362C, A16482G > G3915A, G93801A > A4727G > G10589A > T204C, C16193T, A16219G > T10463C, T13768C

                              H
                              G2706A Line 6646 A
                              T7028C Line 4166 C

                              H6
                              T239C Line 2931 G
                              T16362C Line 8514 C
                              A16482G Line 3819 C

                              H6a
                              G3915A Line 3262 A
                              G93801A Line 7788 A

                              H6a1
                              A4727G Line 232 G

                              H6a1b
                              G10589A Line 1141 T

                              H6a1b3
                              T204C Line 2873 G
                              C16193T Line 6553 A

                              A16219G Line 6555 G

                              H6a1b3a
                              T10463C Line 1103 G
                              T13768C Line 1999 C

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