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Archiver > GENEALOGY-DNA > 2005-10 > 1130693383


From: <>
Subject: Re: [DNA] R1b Among Native American Men
Date: Sun, 30 Oct 2005 17:29:43 -0000
References: <a9.7ed8f63a.30964dba@aol.com>


Ann

P25 is DYS194-469. The whole DYS194 locus, as originally extracted and
cloned, is about 1515 bases long, and P25 is at position 469. The specific
primers listed in YCC for P25 start at position 391 so the C to A mutation
is at position 79 of the PCR amplified section.
DYS194 also contains SNPs P7, P18, P20, P21 and P33. P7 is close to P25 and
has the same primers, P18 and P20 are at the start of DYS194 and have
different forward primers but the same reverse primers as P25. P21 and P33
are right at the end of DYS194 and share the same primers.
We now know there are 3 copies of DYS194 (in the same triplicated sections
as DYF399S1), so there are three copies of all the above SNP loci, with a
mutation at one of the copies in the relevant haplogroups. So the problems
experienced in testing P25 potentially apply to all these SNPs. One is a
testing protocol issue - the ancestral value outnumbers the derived value
two-to-one even in positive samples, so the result is not called from the
base detected more frequently, but the proportion of the less frequent base.
The other is that recombination can delete/overwrite the derived value and
so negative does not always mean ancestral. Papers analysing these problems
have only appeared recently so results using P25 may be quite inaccurate in
older papers.

Gareth


----- Original Message -----
From: <>
To: <>
Sent: Sunday, October 30, 2005 4:24 PM
Subject: Re: [DNA] R1b Among Native American Men


> Oppenheimer refers to haplogroup R as Ruslan (like Sykes giving names to
> mtDNA haplogroups). With that little bit of insider knowledge, I found the
> reference on page 329 (another keyword to narrow the search would be
Baikal), but
> things don't hang together too well. The SNP tree on page 329 shows
M173-M207,
> which would just be haplogroup R. But the text says that this is found in
30% of
> Europeans and 12% of Native Americans, seemingly too low for the former
and
> too high for the latter, based on other studies. Oppenheimer said it was
> "higher than could be explained by recent European admixture."
>
> The footnote refers to haplotype 37 in Hammer's 2001 "Hierarchical
patterns
> of global human Y-chromosome diversity"
> http://www.ftdna.com/pdf/Hammer_MBE_2001.pdf. This predates the 2002 YCC
tree, but the percentages are as given in
> Oppenheimer. However, the SNP for this haplotype is given as DYS194-469
(the
> 469 is written as a subscript).
>
> Using Google Scholar, there were some references that implied DYS194-469
was
> a synonym for P25, which would indeed be R1b. But going back to the YCC,
P25
> is shown as a mutation in position 79 of a 327bp amplicon inside DYS194,
and
> there are no listings for anything at position 469.
>
> http://ycc.biosci.arizona.edu/nomenclature_system/data.html
>
> So my trail ends with a puzzlement, but I agree that 12% seems too high
for
> Native Americans. The nomenclature changes make it hard to pin down,
though.
>
> Ann Turner



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