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Haplogroup change after Big Y results!

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  • Haplogroup change after Big Y results!

    I did Big-Y hoping to find new subclades in F as it is less known and researched. But today, when I login, I saw my BigY results and I am shocked !!

    I was a confirmed F-M89 haplogroup before the Big-Y with the following test results:
    M170-, M201-, M304-, M69-, M89+, M9-

    But, after Big-Y, I am now a confirmed A-P108 (A1 haplogroup) and had the following result:
    L141+, M168+, M213+, M294+, M299+, M42+, M89+, M94+, P108+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P305+, P316+, P9.1+, P97+, PK1+, SRY10831.1+, M170-, M201-, M304-, M31-, M69-, M9-, P114-

    Just for curiosity sake, I took these values and tried to find the haplogroup from the tree using MorleyDNA Y-SNP Subclade Predictor and it gave me with G2a3b.

    So, what's going on? Had anyone faced these unexpected haplogroup change after Big-Y?

  • #2
    I am sending a note to someone higher up.
    Originally posted by felix View Post
    I did Big-Y hoping to find new subclades in F as it is less known and researched. But today, when I login, I saw my BigY results and I am shocked !!

    I was a confirmed F-M89 haplogroup before the Big-Y with the following test results:
    M170-, M201-, M304-, M69-, M89+, M9-...

    Comment


    • #3
      Originally posted by felix View Post
      So, what's going on? Had anyone faced these unexpected haplogroup change after Big-Y?
      Yes, and I suspect that this is going to be quite common--until FTDNA fully implements a new haplotree with a new haplogroup classification algorithm.

      The problem is that the older, simpler classification algorithm presumes that every SNP is unique, when in reality--as Big Y will show--most SNPs have occurred more than once in human history, to someone somewhere sometime.

      Here are two examples from my own project:

      Kit 247882 is M170+ M438+ and hence ought to be I2, but is instead now classified as A-P108.

      Kit 109223 is M170+ M438+ P37.2+ M423+ and hence ought to be I2a2, but is instead listed as A-P108.

      Note that this has happened before with Geno 2.0 and individual SNP test results. For example:

      Kits 282865 and N116138 actually belong to haplogroup N, but they tested L226+ in Geno 2.0 and so were listed as R-L226 for a while. Rather than fix the problem, FTDNA simply (temporarily) suppressed the L226+ result so that they would continue to be listed as haplogroup N.

      Comment


      • #4
        Originally posted by lgmayka View Post
        Yes, and I suspect that this is going to be quite common--until FTDNA fully implements a new haplotree with a new haplogroup classification algorithm.

        The problem is that the older, simpler classification algorithm presumes that every SNP is unique, when in reality--as Big Y will show--most SNPs have occurred more than once in human history, to someone somewhere sometime.

        Here are two examples from my own project:

        Kit 247882 is M170+ M438+ and hence ought to be I2, but is instead now classified as A-P108.

        Kit 109223 is M170+ M438+ P37.2+ M423+ and hence ought to be I2a2, but is instead listed as A-P108.

        Note that this has happened before with Geno 2.0 and individual SNP test results. For example:

        Kits 282865 and N116138 actually belong to haplogroup N, but they tested L226+ in Geno 2.0 and so were listed as R-L226 for a while. Rather than fix the problem, FTDNA simply (temporarily) suppressed the L226+ result so that they would continue to be listed as haplogroup N.
        Please tell me this: on which FTDNA page are you seeing A-P108+? I have not yet seen a Big Y terminal SNP associated with any Big Y results in projects that I administer or co-administer.

        Stephen

        Comment


        • #5
          Originally posted by lgmayka View Post
          Yes, and I suspect that this is going to be quite common--until FTDNA fully implements a new haplotree with a new haplogroup classification algorithm.

          The problem is that the older, simpler classification algorithm presumes that every SNP is unique, when in reality--as Big Y will show--most SNPs have occurred more than once in human history, to someone somewhere sometime.

          Here are two examples from my own project:

          Kit 247882 is M170+ M438+ and hence ought to be I2, but is instead now classified as A-P108.

          Kit 109223 is M170+ M438+ P37.2+ M423+ and hence ought to be I2a2, but is instead listed as A-P108.

          Note that this has happened before with Geno 2.0 and individual SNP test results. For example:

          Kits 282865 and N116138 actually belong to haplogroup N, but they tested L226+ in Geno 2.0 and so were listed as R-L226 for a while. Rather than fix the problem, FTDNA simply (temporarily) suppressed the L226+ result so that they would continue to be listed as haplogroup N.
          Thanks lgmayka. Now I am identified as F-M89 With negative for F1 (P91, P104), F2 (M427, M428), F3 (L279, L281, L284, L285, L286, M282, P96) and even the new F4 (M481).

          Does that mean I am a confirmed F* ? ... Waiting for a new subclade of F yet to be discovered sometime in future?

          Comment


          • #6
            Another quick question:

            While I was changed to F-M89, after some analysis, I noticed that I am completely negative for CT.

            CT is the parent of CF which is the parent of F.

            I think the tree needs a change. How can I be totally negative for CT which is the parent of CF,F and positive for F ?

            Take a look at this:

            Attached Files
            Last edited by felix; 10th March 2014, 02:55 AM.

            Comment


            • #7
              FYI, I used http://ytree.morleydna.com/ , the latest experimental tree for analysis.

              Comment


              • #8
                I now feel it is morleydna experimental ytree which could be wrong that adds all these other negative markers. ISOGG and FTDNA only includes M168/PF1416, M294, P9.1 for CT for which I am positive for all.

                Comment


                • #9
                  A further update based on what I found:

                  I read the following from ISOGG Haplogroup H

                  On 24 Feb 2014 Haplogroup H was redefined slightly from its traditional definition. The new Haplogroup H is defined by the SNPs L901/M2939 and M3035/Z4329 and this newly discovered node is one step higher in the tree than is the M69 node, the previous node defining H. The old Haplogroup H-M69 becomes Haplogroup H1-M69 in the new scheme. The former Haplogroup F3-P96 is also under the new H, as is a newly discovered subgroup defined by Z5857 that will be named H3. This renaming will simplify the nomenclature for the early branches within Haplogroup F, and it will unify the major haplogroups of south Asia into the same overall haplogroup. It is important to emphasize that the former Haplogroup F3 has not been found to be a subgroup of the previous Haplogroup H-M69, nor has the new subgroup defined by Z5857, which would have been reported earlier as F*. There are a few other minor F haplogroups (e.g., F1, F2, F4) that have not been tested with respect to L901, so it is not known if their position in the tree will change. Listed 25 February 2014.
                  Based on the latest tree from ISOGG, I believe I am not F-M89 but H3a2a (H-Z5865)

                  -F: M89+ (and a host of other positive markers)
                  ---GHIJK: PF2622+
                  -----HIJK: PF3494+ (but F929 is negative)
                  -------H: L901+
                  ---------H3: Z5857+
                  -----------H3a2: Z5863+
                  -------------H3a2a: Z5865+

                  I wish, FTDNA can update with the latest ytree.

                  Comment


                  • #10
                    Originally posted by felix View Post
                    I wish, FTDNA can update with the latest ytree.
                    We all do.

                    And word is that it's coming so, as they say, watch this space.

                    Comment


                    • #11
                      Originally posted by felix View Post
                      A further update based on what I found:

                      I read the following from ISOGG Haplogroup H



                      Based on the latest tree from ISOGG, I believe I am not F-M89 but H3a2a (H-Z5865)

                      -F: M89+ (and a host of other positive markers)
                      ---GHIJK: PF2622+
                      -----HIJK: PF3494+ (but F929 is negative)
                      -------H: L901+
                      ---------H3: Z5857+
                      -----------H3a2: Z5863+
                      -------------H3a2a: Z5865+

                      I wish, FTDNA can update with the latest ytree.
                      These SNP positives or discoveries are only as useful as the tree they have, which itself relies upon others taking the test.

                      PS: A prime example is your negative for F929. This should results in diligent revision to the tree, and comparison with other HIJK males.
                      Last edited by rdbox26hs; 10th March 2014, 09:59 AM.

                      Comment


                      • #12
                        According to http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html and http://ybrowse.isogg.org, F929 and PF3494 are the same mutation.

                        Comment


                        • #13
                          Originally posted by Jessant View Post
                          According to http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html and http://ybrowse.isogg.org, F929 and PF3494 are the same mutation.
                          Thanks for noting it. You are right. I double checked and noticed that when I typed F929 in BigY table it was actually showing me PF929 which is negative. Hence, I am positive for PF3494/F929. Silly mistake from me.

                          Comment


                          • #14
                            Originally posted by felix View Post
                            I now feel it is morleydna experimental ytree which could be wrong that adds all these other negative markers. ISOGG and FTDNA only includes M168/PF1416, M294, P9.1 for CT for which I am positive for all.
                            A reply from Chris Morley. I also sent my BigY raw data to him.

                            Hello Felix,

                            I appreciate you pointing this out. I had actually suspected there might be issues with the "novel" SNPs at the CT level. For evidence of my prior suspicions, refer to pages 8 and 48 of http://ytree.morleydna.com/oldtrees/...ny20130907.pdf (and also the legend on page 4 for the meaning of the "F" symbol). My online classifier uses an older version of the tree, predating these suspicions. (Most of the feedback I receive relates to the the experimental tree rather than the online classifier, so I'm spending my time refining my phylogenetic algorithm. Once the algorithm and data structure have stabilised then I might go back and update the online classifier.)

                            Let me explain how the SNPs PF1269, PF258, CTS125, etc. came to be placed at the CT level in my experimental trees. These trees are based on Geno 2.0 data (and supplemented with data from non-Geno FTDNA kits). There is scarce Geno 2.0 data for people not descending from CT. The sole public haplogroup B example can be found here: http://www.familytreedna.com/public/...x?section=ysnp (kit N114481). There are some haplogroup A examples here: http://www.familytreedna.com/public/...x?section=ysnp .

                            None of these non-CT samples are reported positive (on the FTDNA project pages) for SNPs such as PF1269, PF258, etc. This means that FTDNA's Geno-import algorithm (which has some known issues and some other suspected ancestral/derived state reversals) found them to be positive. I do not have access to any haplogroup A or B raw Geno files, so I do not know the Genochip non-CT states for the markers in question. For what it's worth, I did manually check PF1269 and PF258, and found that their raw-data Geno states for kits below CT (A and T, respectively), were the *ancestral* states according to Thomas Krahn's dataset (ybrowse.isogg.org). Maybe FTDNA's Geno-import algorithm has the states for these SNPs backwards. Or maybe Thomas Krahn's dataset does. I don't know.

                            For the time being, for lack of conclusive evidence to the contrary, my Geno-based trees will continue to place SNPs such as PF1269, etc. at the CT level.

                            I have also generated experimental trees using data from other sources. I already have a BigY-based tree, and am currently fine-tuning it to compensate for BigY's varying coverage and other source-specific quirks. To this end, I am looking for diverse BigY data to further refine my BigY-based tree. I am in particular looking for some haplogroup A and B representation, so that we can better examine the issue you describe above. I would also be interested in your halplogroup F data, and invite you to send the .zip archive containing your BED and VCF files to me at [email protected].

                            In closing, the experimental tree you reference is implied by Geno 2.0 data. No single source/testing method is perfect, and the resulting tree will likely be discrepancies when compared with data from other sources. I am constructing separate trees for each source. The fusion of these trees (which I am hoping to automate; I have an algorithm designed but not implemented or tested) will show us which aspects of the phylogeny are in agreement and which require further investigation.

                            If this reply is satisfactory then feel free to re-post it in the FTDNA forum thread you reference.

                            Kind regards,

                            Chris Morley

                            Comment


                            • #15
                              Haplogroup Change from I to J

                              Received my Big Y results today and the test incorrectly had me as M284- when I should be M284+ and FTNDA moved me from I2a2a1a1* to J1a2b2 L147.1.

                              Not certain how they will fix this and I'm rather upset with how this has turned out. I can't even access my Walk the Y results anymore for comparison as the page says it's still being tested.

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