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  • EA correlation for Haplotypes?

    So, I have had the full Haploview with EA and tested positive for R1b,now I am negative for the entire R1b "the works". Can someone help me to differentiate? Haploview determines Haplotype and the "works" determines subclade? Or...is it possible that they have no way scientifically to classify me and that I fit best with R1b?

    Cheers,

    Rosario

  • #2
    Rosario,

    I believe that the Haploview establishes your basic haplogroup, which is R1b1c. "The Works" tests for all known SNPs downstream of R1b1c. Since you're negative for all those, you're R1b1c*, until someone discovers a SNP (defining a new subclade) for which you're positive.

    Mike

    Comment


    • #3
      Zaru:

      I think vince (vizachero) was saying that most Italians R1b do not fit into one of the currently known SNP, which are instead based on northern (UK etc.) data.

      As an example, is your DYS393=12? This is for instance associated with some Mediterranean R1b, rather than nordic.

      cacio

      Comment


      • #4
        Originally posted by cacio
        Zaru:

        I think vince (vizachero) was saying that most Italians R1b do not fit into one of the currently known SNP, which are instead based on northern (UK etc.) data.

        As an example, is your DYS393=12? This is for instance associated with some Mediterranean R1b, rather than nordic.

        cacio
        Thank you Cacio-

        This is the conundrum. I am wondering if it is possible that since my DYS393=12, and some other modals match well with J2, if I (we) may be a hybrid mediterranean strand, of R1b1 and J2. I realise that according to science, the paternal lines are concentrated to a single line, but are we not all offspring of another haplogroup?

        I was interested in Vince's theory, and I am I believe, a GD of 1 off from Cinnioghlu's Turkish man on Ysearch.

        One other question- Sicily was a part of Africa at one point-is it not conceivable that man made it to the island in a migration?

        Cheers,

        Zaru

        9epze/Ysearch

        Comment


        • #5
          Zaru:

          very interesting. So you seem to be a more eastern/mediterranean type of R1b, rather than the standard northern type. Obviously, lineages don't mix, so any similarities with other haplogroups are purely coincidental. Out of 12 markers, similarities are not uncommon, but at higher number of markers, one is always closer to one's own haplogroup members rather than to outside ones.

          I don't think Sicily was ever connected to Africa at least in the past 100,000 years. But it's true that during the last glacial maximum, Sicily was connected to Italy and went much further into the Mediterranean than it does now. In any case, humans could have easily moved to and from N Africa. However, while this must have happened, my reading is that there's not much evidence that such movements had a large impact. R1b and J2 are not particularly frequent in N Africa, and most of the Sicilian J2 and E3b's and the like seem to fit in the general Mediterranean pattern, that is, a movement from the M East through Anatolia and along the N coast, rather than directly from Africa.

          cacio

          Comment


          • #6
            Cacio:

            I just ran a statistical comparison between myself and all others within the Sicily Project. I took specific loci in which I differed from those within my Haplogroup (R1b1) and compared them to all of the others within the project to determine frequencies wihin the other haplogroups.

            The haplogroups listed within the Sicily Project include:
            E3b1
            G
            I1a
            I1b
            I1c
            J1
            J2
            K2
            Q
            R1a
            R1b
            R1b1c6,9,10
            R1b1b

            Where no stats are provided for a specific HG, it is assumed that there are no matches OR participants did not have any loci tested. These modal values are that of my own and the comparisons are of course against my values.

            DYS 393= 12:

            R1b1= 10/43
            K2...= 1/4
            J2....= 26/32
            J1....= 6/6
            I1a..= 1/2
            E3b1= 1/27

            This appears to be demonstrative of haplogroup J, and is a seemingly rare occurrence outside of J.

            DYS456= 17:

            R1b1= 1/20
            J2....= 1/13
            E3b1= 2/8

            This has an extremely low frequency anywhere, but the percentage nods toward E3b1.

            DYS449= 32

            R1b1= 1/22
            R1b1b= 1/1
            R1a...= 1/2
            E3b1= 4/11

            This value only occurs in one other HG outside of of the R's, with the highest frequency percentage going to that HG of E3b1. Extremely rare.

            DYS385a= 12

            R1b1= 5/43
            G.....= 1/16
            I1b..= 3/5
            J1....= 3/6
            J2....= 7/18
            K2...= 1/4

            Another DYS indicative of HG J, another rare value.

            DYS437= 14

            R1b1= 4/22
            R1b1c9= 1/1
            R1a...= 2/2
            Q......= 1/1
            K2.....= 1/1
            J2.....= 7/18
            J1.....= 5/5
            I1c....= 2/3
            E3b1..= 11/11

            As you can see, this value occurs 100% in the E3b1's tested, and about 57% in the J's, that have a high representation relatively speaking. A modest to low frequency amongst R.

            Dys464c= 17 is only a value that R1b1 reflects as it only occurs twice outside of R1b1, once in J2 and once in E3b1. A pattern is beginning to evolve here.

            DYS607= 14

            R1b1= 5/20
            Q....= 1/1
            J2...= 9/14
            J1...= 2/4
            I1c..= 2/3
            I1b..= 2/2
            G....= 2/6

            Another nod to J in terms of percentages, however it is interesting to note that HG I has one less match in a very low sample pool in comparison to that of R1b1.

            My reasons for doing this is that although they have me in HG R1b1, there are several tell tale loci whose modals are demonstrative of J/E3b1. Although it is perceived by the scientific community as purely coincidental, I cannot help to believe that since the recurrence seem to be only with those specific HG's that there must be some type of relationship.

            On YSearch beyond twelve markers I am not even close to anyone in the database and those who are somewhat close within 12-16 markers are all over the map. I don't know if this breakdown proves anything other than me trying to figure this whole ideology out.

            Cheers.

            Comment


            • #7
              Rosario,

              The basic point to make is that you have a SNP test from EA that proves you're R1b, as you state in your first posting in this thread. I was assuming that you had a positive result for M269, which would make you R1b1c. Is my assumption correct?

              A SNP test is definitive. You can vary on your results for various STR markers and be out on the edge of a haplogroup, but a SNP test, without question, tells you your haplogroup. You are descended from one paternal line and that paternal line, going back thousands of years, is R1b of some sort.

              Take a look at the ISOGG haplogroup tree (http://isogg.org/tree/ISOGG_YDNATreeTrunk07.html), which provides a good overview of which haplogroups descended from earlier haplogroups. You can see that both J and R1b descend from F. I and J are more direct descendants of F, while R1b is, metaphorically speaking, a great-grandson of F, through K and P. If you were actually to be a J, you would have to test positive for one of these SNPs - 12f2.1, M304, S6, S34, S35 - which no K or P has.

              Another point for you to consider is to take a look at your haplogroup tab on your FTDNA personal account page. This page compares your STR results to those of everybody in the FTDNA database who has had a SNP test. Looking at that, I note that at the level of 12 markers there is only match, with a mismatch at 4 markers, which is not an R1b of some sort. That is O. A mismatch of 4 at 12 markers indicates there is really not much of a match - "mutations happen." All your matches at 12 markers, of either 1, 2 or 3 mismatches, are an R1b of some sort. These are dozens of matches, but not 1 J shows up there as a close match. The basic principle is look at your entire haplotype, not one or two or three marker values.

              If you want to use the method of comparing individual markers for members of the Sicily Project, try looking at DYS392. This is 13 for 86% of R1b's and 14 for another 11% - a total of 97% of R1b's have one of these two values. All the other major European haplogroups have either 11 or 12. In fact, 12 is found at its highest level in these haplogroups only in I and only at the level of 25%. (You can see all this at a page on Leo Little's website - http://freepages.genealogy.rootsweb....logy/yfreq.htm - which gives the frequency by major haplogroup of values in ysearch for each of the 67 markers that FTDNA includes in its basic testing. There are values on this page for thousands of haplotypes.) So it would seem that DYS392 is perhaps the key marker that would distinguish R1b from the other major European haplogroups; even R1a has 0% for DYS392=13 or 14.

              Looking at the DYS392 of those in the Sicily Project, you have DYS392=13, making it very clear that your SNP test result should not be doubted. Three of the 4 K2's have DYS392=13 and 42 of the R1b's of some sort have that too. Five of the various flavors of R1b (including me) have 14. Our only Q has 15 and the fourth K2 has 16. Note that K is the grandfather haplogroup of R1b and Q is a brother haplogroup of R1b, both descending from P. One of the R1b's does have a DYS392=12, a rare value for R1b's. It seems to me that this comparison of the DYS392 values among project members is pretty conclusive and says that you're an R1b.

              Again, the basic principle is look at your entire haplotype, not one or two or three marker values. When you do that it's clear that you're not a J. Plus, as I started off in this posting, you have a SNP test, so that tells you all you need to know. Perhaps some of your specific marker values that are unusual may tell you what variety of R1b you are, but no marker value you have changes your SNP test result.

              Mike

              Comment


              • #8
                Originally posted by cacio
                Zaru:

                I think vince (vizachero) was saying that most Italians R1b do not fit into one of the currently known SNP, which are instead based on northern (UK etc.) data.

                As an example, is your DYS393=12? This is for instance associated with some Mediterranean R1b, rather than nordic.

                cacio
                Actually that is not correct. Most Italian R1b1c who have tested the full range of subclade markers have tested either S28+ (R1b1c10) or S21+ (R1b1c9*). As far as I can tell, with the relatively few numbers, an Italian is more likely than someone from the UK to test S28+, reflecting the ancient La Tene Celtic heritage (Insubres, Lingones, Senones, Boii etc.) of that country. According to the Myres et al. (2007) study, 9% of Italian R1b was S21+.

                DKF.

                Comment


                • #9
                  Mike-
                  Excellent reponse with much value and lucidity. I do not question my haplogroup, but rather, its' relationship with the other "mediterranean" haplogroups. I am seeking to figure out if the relationship that I see is a calculated one or strictly coincidental. Your analogies compel me to see a certain relationship-but what about the schism of R1b's from the North as opposed to the south?

                  What specifically prompted the shifts into alter haplogroups anyway? Migration?- which would make natural adaptability certain, or was it something else?

                  Any idea if any study has occurred with regard to the Isle of Man?

                  Thanks agin for the insight.

                  Cheers,

                  Rosario

                  Comment


                  • #10
                    Zaru:

                    as Maddi pointed out, any similarity must be coincidental. It's easy to find similarities on single markers, but then one can find dissimilarities in other markers - so only looking at the whole thing can one make meaningful comparisons.

                    I don't think there's anything else here. If we were talking about a gene that confer some advantage, then it could be possible that the same haplotype appear in different lineages. For instance, skin color seems to have evolved independently in European and East Asians, because both populations were subject to a clear selective pressure. But there's nothing like that in the Y chromosome, and these DYS are anyway in the junk part of the chromosome.

                    cacio

                    Comment


                    • #11
                      Originally posted by Zaru
                      Mike-
                      Excellent reponse with much value and lucidity. I do not question my haplogroup, but rather, its' relationship with the other "mediterranean" haplogroups. I am seeking to figure out if the relationship that I see is a calculated one or strictly coincidental. Your analogies compel me to see a certain relationship-but what about the schism of R1b's from the North as opposed to the south?

                      What specifically prompted the shifts into alter haplogroups anyway? Migration?- which would make natural adaptability certain, or was it something else?

                      Any idea if any study has occurred with regard to the Isle of Man?

                      Thanks agin for the insight.

                      Cheers,

                      Rosario
                      I meant to state clearly, and forgot, that haplogroups are defined by SNPs, which occur very rarely and in a single man. He then passes it down to all his paternal line descendants. So a specific haplogroup, if it still exists today, will many times be found at its highest levels in the area or nearby where the man with the original mutation lived. Of course, with human migrations over thousands of years (the scale of how often SNPs occur), haplogroups have moved into nearby or even far areas. In the case of R1b, it originated somewhere in western Asia or eastern Europe (maybe the area of Ukraine or Russia near the Black Sea), although there's debate about that, while J pretty clearly originated in the Middle East, probably in the area of the Fertile Crescent or perhaps eastern Turkey. So R1b and J probably didn't meet up until both arrived in Europe.

                      The mutations on specific STR markers occur, in most cases, over the course of hundreds of years. They are not reliable indicators of your haplogroup, although in combination as a haplotype of 12 or more markers, FTDNA or anyone with some knowledge can accurately predict your haplogroup. So, it's interesting that DYS392 being above 12 seems to be found only in those haplogroups descended from K, for instance Q and R1b (but not R1a), as I noted above. I wonder if the O (descended from K), whom you mismatch on 4 of 12 markers, has DYS392=13 like you.

                      Why is all this the case? No one knows for sure, other than to say that mutations on specific STR markers are random. But why do the mutations stay in a certain range, either for all haplogroups or for specific haplogroups? Maybe some day we'll find some specific chemical mechanism or physical principle that explains this. Until then, all we can say is that "mutations happen" and rely on SNP tests to be sure about haplogroups.

                      You ask about the split between northern and southern European R1b. If you believe the standard explanation from the Genographic Project and population genetics in general (which I don't), R1b1c was in Europe well before the worst part of the Ice age came (they claim the cave painters of southern France of 30,000 years ago were R1b), then retreated south about 20,000 years ago to northern Spain to escape the spreading glaciers in northern Europe. And supposedly all or almost all the R1b1c's in Europe came from there after spreading back across Europe when the glaciers finally left 10,000 years ago.

                      Well, R1b came from the east and R1b1c9 is mainly found in northern Europe (especially the Netherlands, northern Germany and Denmark) and R1b1c10 is mainly found in central and eastern Europe and there seems to be a form of R1b1c in Turkey that has DYS393=12 and DYS461=11, seemingly not found in anywhere but parts of Italy and eastern Europe. Is it possible that these forms of R1b1c, being closer to the origin of R1b to the east, may predate all of the R1b1c*'s we assume to be the ancestors (from the Ice Age Spanish refuge) of all the R1b1c's in Europe today? Time will tell and maybe answer your basic question.
                      Last edited by MMaddi; 12 October 2007, 02:03 PM.

                      Comment


                      • #12
                        Originally posted by DKF
                        According to the Myres et al. (2007) study, 9% of Italian R1b was S21+.DKF.
                        Do you have a link on that Myres paper?

                        Thanks,
                        Joe

                        Comment


                        • #13
                          Here's the link to the Myres paper - http://www.cmj.hr/2007/48/4/17696299.pdf. This study refers to S21 as M405.

                          Comment


                          • #14
                            Originally posted by MMaddi
                            Here's the link to the Myres paper - http://www.cmj.hr/2007/48/4/17696299.pdf. This study refers to S21 as M405.
                            Thanks Mike. EA received my sample on 9/18 so I am patiently waiting for the results. With 492=13 it looks like I may be S21+.

                            Joe.

                            Comment


                            • #15
                              NW Irish?

                              It's an odd thought- as I have not tested +M222, however the Modal Haplotypes for the first 12 markers are strikingly similar to mine, including dys 393=12,and are far more numerous than in any other anthro-genetic group that I have seen. I had not realised that 393=12 was that prevalent there-they have results not included in the FTDNA database in an external link from the homepage. Very interesting.

                              Comment

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