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From:
Subject: Re: [DNA] Re: R1b SNP page updated
Date: Sat, 29 Apr 2006 22:16:25 +0100


Joe

gene conversion is one form of recLOH and it can happen in P25 because P25
is actually a 3 copy locus, only one copy of which has a SNP. So the SNP is
occasionally reversed when one of the unmutated copies overwrites the
mutated one. IMO if this was a newly discovered variation it would not be
acceptable as a haplogroup branch defining SNP. (Yes - we have just
published a new version of the tree and P25 is still there but despite the
many changes we have had to be quite conservative in places).

S21 is different, it is a single copy locus and I do not believe it has been
observed to revert. All SNPs can revert in principle but without a backup
copy elsewhere the chances of this happening are very very small. I think
John meant that P25 could revert equally in men who are S21+ and S21-, not
that S21 would revert as well.
I assume S26 is similarly stable as it is associated with a single copy STR.
SNPs associated with multicopy STRs will be subject to gene conversion -
e.g. the G to C SNP underlying the DYS464X test sometimes appears in two
copies or all four copies rather than the usual three out of four.

Gareth


----- Original Message -----
From: "Joe Fox" <>
To: <>
Sent: Saturday, April 29, 2006 9:52 PM
Subject: [DNA] Re: R1b SNP page updated


> John
>
> Is gene conversion the same thing as a rec(LOH) event? If it can cause P25
> and S21 to revert, can it also cause S26 to revert? I take it that M269
> does not undergo gene conversion?
>
> Joe Fox
> Lafayette, CA
> ----- Original Message -----
> From: "John McEwan" <>
> To: <>
> Sent: Saturday, April 29, 2006 3:47 AM
> Subject: R1b SNP page updated
>
>
> > Dear List
> >
> > The R1b SNP page has been updated. There are 9 new changes.
> >
> > See www.geocities.com/mcewanjc/s21.htm
> > www.geocities.com/mcewanjc/r1bsnp.htm
> >
> >
> >
> > M269+ P25-
> > **************
> > Finally a little bit on M269+ P25- individuals. Today I was rereading
> > the paper on P25 reversions (Adams 2006, The case of the unreliable SNP.
> > Recurrent back-mutation of Y-chromosomal marker P25 through gene
> > conversion. Forensic Science International 159:14-20) and noted some
> > facts that I had previously overlooked. They tested 1000 males from the
> > Iberian peninsula and found 10 M173(xSRY1532b) P25- individuals (1%) and
> > 22 out of 421 in the British sample (5.2%). Of these 31/32 were M269+
> > and one was also SRY2627+ (in the paper given as M167+).
> >
> > My R1b SNP list in has 2 P25- out of 92 P25 tests that are otherwise
> > consistent with being R1b (2.2%) and this estimate is in a mid range
> > estimate of the above 2 populations. The combined results show that
> > there has been at least TWO reversions one in SRY2627+, and one in S21+.
> > What is not clear is what number, if any, have been within
> > R1b1c(xSRY2627,S21). The Adams paper Y STR network diagram based on 19
> > STRs provides only equivocal evidence of multiple founding events and
> > the variability observed of the reversions was similar to R1b as a
> > whole.
> >
> > I say this, because I suspect the significantly higher level in the
> > "Great Britain" sample may be because of the percentage of S21 positives
> > in this population.
> >
> > It has been estimated that gene conversion events occur much more
> > frequently than SNPs, but perhaps at a 10X lower rate than STR
> > mutations. If so the number of reversion events may be modest and some
> > lineages could be of reasonable size. The new EA SNPs may be able to
> > resolve this issue and identify at least some of the founding events.
> >
> > The r1b SNP list also has a result Denney RS4EF, which has not yet been
> > tested for S21. Such a test would confirm at least a third reversion
> > event if it was S21-. I would certainly recommend that any individual
> > who is M269+ P25- to also tests for at least S21, S28 and SRY2627. The
> > outcome could be quite a reasonable diagnostic family SNP(s) especially
> > when also paired with STR markers.
> >
> > As usual if you note any errors or omissions please contact me and also
> > if you have new data.
> >
> > Cheers
> >
> > John McEwan


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