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Archiver > GENEALOGY-DNA > 2006-03 > 1141589647


From: "Alfred A. Aburto Jr." <>
Subject: Re: [DNA] Is the CMH J1?
Date: Sun, 05 Mar 2006 12:16:56 -0800
References: <440B0F51.80100@comcast.net>
In-Reply-To: <440B0F51.80100@comcast.net>


> Bonnie Schrack wrote:

> Sorry I hadn't seen Al's posting yet, when I wrote earlier.
>
>> ________CMH J1 J2
>> DYS393 = 12 12 12
>> DYS390 = 23 23 23
>> DYS19 = 14 14 14
>> DYS391 = 10 10 10
>> DYS385a = 13 -- --
>> DYS385b = 15 -- --
>> DYS426 = 11 -- --
>> DYS388 = 16 16 15
>> DYS439 = 12 11 11
>> DYS389I = 13 13 13
>> DYS392 = 11 11 11
>> DYS389II = 30 30 29 (these are not right because I should have done
>> 389II-389I)
>> (couldn't fix 389II right now because my computer crashed, CPU fan
>> went belly-up)
>> (will fix tomorrow)
>
>
> Nice job, Al! You've found the modal J1 and J2 haplotypes all right,
> the same ones that show up in my data, which is not all SNP-tested of
> course. DYS426 is of course 11 in all of J. I haven't had a chance
> (yet) to calculate DYS385 as a connected single marker, but DYS385a
> has a modal of 13 in J1, J2a1*, and J2a1k. The modal for DYS385b is
> 18 in J1, 15 in J2a1* (which could actually change if I enter more
> data), and 16 in J2a1k. But people should not dream of using that
> marker to distinguish clades, since it's highly variable.
>

My computer, offline now, with all my data for the above, will take
longer to fix, but when I get it fixed, I'll send you the locus
distributions for J1 and J2. I did J too. I'll send that too. The
results are interesting to me. DYS388 for example surprised me because
it has such a large spread over alleles. I think that indicates it might
be a fast mutator. Others have very little spread, indicating slow
mutators. DYS385a looks very steady, but DYS385b shows more spread. Same
with DYS389I and DYS389I.

>Bonnie wrote:
>You're stating in another way what I said: the 12-marker CMH, we're
told, is 12, while the J1 modal is 11. J1 also normally has slightly
higher >DYS388 values than J2, with a modal value of 16, as seen in the
CMH. Anyway, the point is that the CMH haplotypes are close to the J1
>modal, and this can also be seen at many other markers, when you look
at 25- and 37-marker haplotypes which have the CMH in their first 12
>markers. The correlations in the markers beyond those first 12, make
it clear that they belong to J1 and not to J2.

Humm, interesting. I just, during this discussion, learned of the 12
marker set for the CMH. I didn't know you already knew of it Bonnie.
I think it would be best to ignore the 12 marker set until something
more official is published. At least ignore it for any type of further
research work.

> Now on to the next:
>
>> I did't realize DYS413 was a UEP, a SNP! So then there appears to be a
>> challenge here that the CMH is specific to J1?
>>
> Not really. DYS413 can certainly be considered a UEP, but that
> doesn't make it a SNP -- Dienekes is saying that the deletion at
> DYS413 is another kind of Unique Event Polymorphism, although it's not
> a Single Nucleotide Polymorphism -- this is correct.
>

Well, Malaspina's paper is indicating "yes, indeed CMH is part of
J2a1", but still from what I can tell their case looks weak, not a
strong argument at all. But they are making a strong statement. I mean
they were saying these seemingly J2 Italian Cohanim had the DYS413<18
constraint. However, that said, it doesn't seem right to ignore
published technical material (Malaspina's paper) over that which has not
been published or peer group reviewed (FTDNA). I wouldn't take FTDNA's
12 marker set as scientific evidence until it appears in the open peer
group reviewed literature. They are _not_ following standard scientific
practice and methods.

>> Yes, the 6 Y-STR CMH is found in both J1 and J2. Also, if one uses
>> FTDNA's (unpublished!) 12 Y-STR CMH then it appears that J1 is indicated
>> instead of J2. However, as Sasson said, apparently it is not known if
>> the real Cohanim, and therefore the source of the CMH, are J1 or J2. I
>> think it is certain that SNP testing has been done on Cohanim, but no
>> one is talking. It appears to be a very sensitive issue, so I can
>> understand the secrecy or perhaps hesitancy to publish such knowledge...
>>
>> A 12 or more Y-STR CMH would clarify things greatly. However, FTDNA's 12
>> Y-STR CMH must be treated as unsubstantiated until it is published in a
>> peer group reviewed open literature scientific journal. The whole issue
>> surrounding the CMH remains, well, fuzzy ...
>
>

> Well, for now, anyway, I choose to accept FTDNA's 12-marker CMH as
> basically accurate; I think they have access to information on real
> Cohanim families, even if they don't feel that they're yet in a
> position to publish the substantiating evidence. It could well be
> that this is a preference of people or communities who are directly
> involved? Anyway, I don't think the issue is really so fuzzy or
> unclear as it's being seen in this discussion.
>

But be aware that things might change on you, because FTDNA is saying
things and doing things outside of normal scientific preview and even
outside an open forum (like here).

> David wrote:
>
>> YAP identifies the DE branch of the tree. It doesn't apply to J.
>
>
> It was just one of the SNPs they tested for, in those early days, to
> place their samples in a haplogroup.
>
>>
>> There was a recent study which reported finding the CMH pattern in
>> BOTH J1
>> and J2. It was mentioned on the list about six or eight weeks ago, if my
>> internal timekeeper is working this morning. This outcome would seem to
>> require reinterpretation of the Cohanim data, or even a search for
>> additional data that might help draw finer CMH distinctions than we have
>> right now.
>
>
> David, any number of studies can easily show that a 6-marker CMH
> haplotype can be found all over the place. The point is that the
> 6-marker CMH is not very meaningful, precisely for that reason. The
> fact that it's found in J2 as well as J1, doesn't require
> reinterpretation of the Cohanim data (unless I mistake your meaning),
> it just means that we need more markers to have a meaningful CMH. And
> now, we do, albeit unofficially. Hey, how "official"are any of John
> McEwan's STR clusters? The fact that they are unpublished doesn't
> detract an iota from their usefulness. We can all think of more
> examples of useful modal haplotypes discovered by genetic
> genealogists, which have not been published. Why should this be held
> to so much more exacting a standard?
>

I'd say that by FTDNA's methods, it is very unofficial. John McEwan's
STR clusters are done in a much more open environment I'll bet, not just
announced as FTDNA did ...

Al


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