GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2010-03 > 1269224053


From: Bonnie Schrack <>
Subject: Re: [DNA] Equivalent Mutations ,relationship between clades and phylogentic tree of Y Chromosome
Date: Sun, 21 Mar 2010 22:14:13 -0400
References: <800388.48060.qm@web26201.mail.ukl.yahoo.com>
In-Reply-To: <800388.48060.qm@web26201.mail.ukl.yahoo.com>


Hi Kamel,

I didn't see whether anyone has answered this on the list. I'll try in
any case.

> By reference to Ytree.ftdna draft version maintained by Thomas,
> equivalent mutations are mutations which are dispalyed in the same line
> (example M410,L152,L212)
> This means that all people who have one of these mutations have also
> the other ones
> but I wonder if is that 100% sure ?

No, it's really just a hypothesis, when it comes to these new SNPs.

>
> 1-For example, are we sure that all people who are M410+ are also
> L152+ and L212+ ?

No, since only a few have been tested for them. That's why it's a draft
tree.

> Is it interesting to test some perons who are J2a* with deletion in
> DYS447 for L152 and L212 ?

Sure. But one of them, kit 96954, has already been tested for L212 (he
was positive).

It would be more interesting, I think, for J2a* from *other* clusters to
be tested for L212. That would be very valuable.

No one has been tested for L152 yet. I think there is some technical
reason. . . let me see. Oh yes. . . Thomas wrote to us about it, 11/24/09:

> We have some issues with L152 because it is on a highly repetitive
> region on the Y chromosome and apparently the occurrence of L152 is
> coupled with (at least) rs9786888 and rs2704708 by ways of a recLOH event.
He showed how BLAST results would find many copies of the same sequence
at different places in the Y.
> There are multiple matches within a small region of the Y chromosome.
> So we should consider L152 rather as a structural variant of a
> repetitive region rather than a SNP.

I don't know, but it sounds as though L152 may not be a very usable SNP.

> if we find people who are M410+ are L152- or are L212- it will
> change dramatically the J2a phylogenetic tree

Yes, it could.

>
> 2-the same question for L26, L27, L228
> if we find people wo are who are L26+ and L228-, it will change the
> J2a4 phylogenetic tree

Yes, though we have tested a number of J2a4* for L228, from several
clusters, there are definitely more who should be tested for L228, for
the reason you state.

>
> 3- the same question for L24, L207.1 (J2a4h)

Your co-administrators would know more about that. . .

>
> 4-the same question for M92, M260 (J2a4b1)

Isn't M260 already included in the Deep Clade test?

> Another question, who is ready or interested to pay for such tests
> which are very usefull to update the phylogenetic tree ?

I wish members of J2 would be motivated to come forward! I could use a
lot of help to promote this, since apparently they won't do it if not
prodded. . . . Generally there has been little interest in paying for
other people's tests in J2, I'm sorry to say. In J1, we have some more
motivated, passionate people. The reality is that at least a few
well-off people are needed, who can afford to sponsor multiple tests.
But it could also be done by amassing a lot of small contributions. I
will be very grateful for anything you can do to build up our General
Fund. There are any number of tests that ought to be ordered, for
example, for some people who have never tested more than 12 markers, and
have had no SNP tests at all. These could be hiding a variety of new
discoveries.


> Is it up to the testing companies like FTDNA, or to academic
> researchers or to us, the clients of testing companies ?

It used to be that FTDNA would take on more of this, but with the huge
number of new SNPs, it seems they are not willing to do many free tests
any more, even for valuable new SNPs. So we have to do it. . . academic
researchers don't seem to be aware of what's happening. If we wrote to
some who are interested in the populations we've seen these SNPs
occurring, some of them might get interested.

Bonnie


This thread: