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Archiver > GENEALOGY-DNA > 2006-04 > 1146345838


From: "Ken Nordtvedt" <>
Subject: Re: [DNA] Re: R1b SNP page updated
Date: Sat, 29 Apr 2006 15:23:58 -0600
References: <E1FZwnh-000K2d-MM@mk-webmail-1.b2b.uk.tiscali.com>


Did you mean to leave the impression that all known SNPs are "associated"
with STRs? I guess that could be the effective situation if all searches
for SNPs up until now have been done near STRs, but I did not know that was
the case, although searches near STRs could be common.

Ken
----- Original Message -----
From: <>
To: <>
Sent: Saturday, April 29, 2006 3:16 PM
Subject: Re: [DNA] Re: R1b SNP page updated


> 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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