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CMH Question: I was but am I still?

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  • #16
    I have exhausted the topic and this is the last post I intend. I agree that modes describe populations not individuals. However FTDNA has "individualized" the situation by informing individuals if they belong to the CMH cluster or by "dropping" individuals from that designation as in the case of HapJ1. I am not criticizing FTDNA for doing this nor am I stating that FTDNA was wrong for going to 12 markers. My point is simply that it is difficult to evaluate the shift to 12 markers without published data.
    Last edited by josh w.; 1 February 2007, 12:05 PM.

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    • #17
      I find myself agreeing with Josh. We're at the point of reducing modal haplotypes to meaninglessness.

      Perhaps I should seek the opinion of Dr. Nebel. With the pioneering work he's done on modal haplotypes, I assume he'd agree that they are more than mere averages .

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      • #18
        marker

        Originally posted by josh w.
        I have no problem with developing a modal haplotype, but why call it the Cohen Modal haplotype if it is not designed to see if one falls on the Cohen genetic line. I understand that FTDNA went to 12 markers in order to reduce the number of J2s who would qualify as CMHs. This is what I meant by reducing the number of false positives. The issue is that by resolving one problem they probably exacerbated another problem namely that of false negatives. That is, getting higher resolution in one direction may well produce lower resolution in the other direction. I agree that very few will base their religious identity on genetic data, although this kind of information might be helpful for those who suspect that their family was once Jewish or who suspect Cohen ancestry. Nevertheless it might be disconcerting for a family with a Cohen genealogical history to be informed that they are no longer CMHs in the shift to a 12 marker definition.

        (I hope my numerical example was clear. By going from 6 to 12 makers the number of Cohen families with CMHs will be reduced. This is what happens when one raises thresholds. Current data suggests that around 50% of Cohens share the 6 marker CMH. Generally when there is an increase in the number of markers in a haplotype the number of matches will be reduced. This is what most people discover when they upgrade from 12 to 37 markers. This is how I came up with the guess of 33% Cohens having the CMH on a 12 marker test).

        I doubt they would let that happen. I wouldnt be surprized that FTDNA increased the number of markers after realizing that it didnt have a material impact on the number of Jewish Cohens that tested positive on the 6 marker test. Apparently, they discovered that Cohens tend to have a dys 439 value of 12 rather than the more common 11 among non Jewish J1 and J2s. So they made it a part of their test. However, Im still waiting for someone to determine if J2 Samaritans, Bene Israelites and Ash and Seph. Cohens and Jews share a recent common ancestor/ modal haplotype. From what I have read, I think J1 is absent among Samaritans and the Bene Israelites.

        regards,

        bob

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        • #19
          My last last. Bob, I wish I could be sure there was little impact. My guess is that FTDNA was mainly concerned with making the CMH an essentially J1 pattern rather than maximizing the number of Cohens in the cluster. By going to 12 markers there will be a reduction in Cohens (People named Cohen or with a Cohen family history) within the CMH cluster, but without data the extent of this reduction is unknown. One of my questions is whether they introduced a finagler's constant by arbitralily broadening the definition of the CMH cluster in order to deal with the reduction problem. Another question is whether the decision rules can be replicated or cross validated with a new sample.
          Last edited by josh w.; 1 February 2007, 06:56 PM.

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          • #20
            Samaritans, Cohens, CMH and M267 (J1)

            Bob, this from Peidong Shen's study.

            There are indeed J1 (M267) Samaritans, viz...

            The Cohen family represents an interesting subgroup of the Samaritans. It can be traced to a single individual some 250 years ago [Cazes and BonneĀ“-Tamir, 1984]. Consistent with a previous report [BonneĀ“-Tamir et al.
            2003], the Samaritan Cohens did not carry the Cohen modal haplotype (data not shown), which is defined by the repeat numbers 14, 16, 23, 10, 11, and 12 at the Ychromosome microsatellite loci DYS19, DYS388, DYS 390, DYS391, DYS392, and DYS393, respectively [Thomas et al., 1998]. This six-microsatellite haplotype, together with its one-mutation neighbors, form a cluster that is found at frequencies of 69.4 and 61.4% in Ashkenazi and Sephardic Cohanim, while its frequency in the general Jewish population is about 14% [Thomas et al., 1998; Nebel et al., 2001]. The Cohen modal
            cluster is invariably associated with haplogroup J, which probably originated some 15,000 years ago in the northern part of the Fertile Crescent [Hammer et al., 2000; Quintana-Murci et al., 2001], whence it began its expansion throughout the Middle East 7,500 years ago [Nebel et al., 2001; Quintana-Murci et al., 2001]. To our surprise, all non-Cohen Samaritan Y-chromosomes
            belonged to the Cohen modal cluster. The single exception was an M67 lineage from the Danfi family. It was two microsatellite mutation steps removed from the Cohen modal haplotype. Based on the classification by
            Nebel et al. [2001], the Samaritan M172 lineages carried the so-called Muslim Kurd modal haplotype (14-15-23-10-11-12). The Samaritan M267 lineages differed from the classical Cohen modal haplotype at DYS391, carrying
            11 rather than 10 repeats. Based on the close relationship of the Samaritan haplogroup J six-microsatellite haplotypes with the Cohen modal haplotype, we speculate that the Samaritan M304 Y-chromosome lineages present a subgroup of the original Jewish Cohanim priesthood that did not go into exile when the Assyrians conquered the northern kingdom of Israel in 721 BC, but married Assyrian and female exiles relocated from other conquered lands, which was a typical Assyrian policy to obliterate national identities.

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            • #21
              Originally posted by HapJ1
              Perhaps I should seek the opinion of Dr. Nebel. With the pioneering work he's done on modal haplotypes, I assume he'd agree that they are more than mere averages .
              If he has any background in mathematics, I don't think he'd have much choice but to concede that a mode is merely a type of mathematical average. A mode, by its very definition, is a statistical measure of central tendency.

              Don't get me wrong, modal haplotypes can be very useful tools in the analysis of populations. And I concede that care must be taken to ensure that the mode actually represents the population it purports to represent, which I think is the point Josh is most focused on.

              The main point I am trying to convey is that matching the modal haplotype of a population is not a test for "membership" in that population. Most members any the population will not match the modal haplotype exactly.

              I fear that people have tendency to form an emotional attachment to modal haplotypes without fully understanding the limits of their use. I suspect that FTDNA has encouraged this mindset through their behavior. It would probably be better for everyone involved if they simply stopped awarding "buttons" for matching modal haplotypes of any sort.

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              • #22
                J1 Samaritans

                Alan: Thanks for the references.

                regards,

                bob

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                • #23
                  Vineviz, I agree.

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                  • #24
                    Another CMH question

                    Hi All,

                    I'm new to the Forum and I've enjoyed reading the posts on this topic. I'm wondering if any of you know the answer to this question. Can anyone tell me the significance of a J1 12 marker sequence that matches the CMH except for DYS385b = 21? Thanks,

                    Vinnie

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                    • #25
                      Vinnie, being off by just a single marker still puts one in the CMH cluster as far as FTDNA is concerned. This would especially be the case for J1s.

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                      • #26
                        Josh, thanks much for your reply. But I'm wondering what the significance is of that particular STR value; I can't find anything published that specifically addresses it. Also, from the discussion in this thread and the published studies I've looked at, it seems that matching the 12 marker sequence and being J1 is synonymous, whereas one can have just the 6 marker CMH and be either a J1 or J2. Additionally, one can be a J1 and not have the CMH, so what markers actually distinguish J1's from J2's?
                        Last edited by vinnie; 17 February 2007, 03:37 PM.

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                        • #27
                          One can be J1 and not be in the CMH cluster as is illustrated by the first post on this thread.. This is why I have been stressing the need for published data on the 12 marker set. What percent of J1s are within the cluster? What percent of J2s are within the cluster? What percent of non-Jewish Semites are within the cluster? What percent of Cohens are within the cluster? Etc.

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                          • #28
                            By non-Jewish Semites, are you referring to people who may have had a Jewish ancestor sometime in the past, but who were not raised Jewish, or someone of Arabic origin, or both?

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                            • #29
                              Mainly someone of "Arabic" origin. I used the quotation marks because there are many Muslim and Christian Near Eastern peoples who speak Arabic but do not have origins in Arabia. For example this would include some Palestinians and Lebanese. I should note that the term Semitic really denotes a language rather than a genetic group. I am using the term to refer to peoples who spoke Semitic languages even before the spread of Islam.
                              Last edited by josh w.; 19 February 2007, 11:41 AM.

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                              • #30
                                Further clarification--There appear to be two groups of Arab haplotypes. One group overlaps with Jewish haplotypes while the other appears to be unique to Arabs. I would expect that there would be some CMHs in the first group although CMH data for the second group would be of interest. A complicating factor is that some Jews converted to Islam in seventh century Palestine and beyond.

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