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Archiver > GENEALOGY-DNA > 2008-01 > 1199271448


From: "Alister John Marsh" <>
Subject: Re: [DNA] Chances for Finding Clade-separating SNP
Date: Wed, 2 Jan 2008 23:57:28 +1300
References: <016501c84ce6$e0110520$6400a8c0@Ken1><200801020701.m02711tV004595@mail.rootsweb.com>
In-Reply-To: <200801020701.m02711tV004595@mail.rootsweb.com>


Tim,

I understand at least a small part of the HUGO reference sequence is from a
male who was not R1b1c. I have heard I haplogroup mentioned, which would be
a branch off the line to R1b perhaps more than 40,000 years ago. I don't
know if this includes parts of Y-DNA, or how small small is, or if the whole
thing is just a myth.

But if you are counting SNP differences between the HUGO and the HUGO/
Watson/ Ventor ancestor, and the Watson/ Ventor ancestor, the position may
be complicated if HUGO is not just one person.

In your earlier posting, you indicated some parts of Y-DNA have higher
numbers of SNP differences in the Watson/ Ventor line compared to HUGO.
Perhaps that is the part of HUGO which was not R1b1c?

In your earlier post, you indicated that roughly half of the SNPs where the
Watson/ Ventor ancestor differed from HUGO, were in about 10% of the Y-DNA.
If this 10% was the non R1b1c part of HUGO, it might impact on your
estimates.

You estimates are interesting, and do show that perhaps the situation is not
as promising as we might have hoped. If a significant part (say 10%) of
HUGO Y-DNA was not R1b1c, then it might be a tad worse than it could have
been.

If useful SNPs were not at one per generation, but perhaps one per 10
generations, it could explain why we have a shortage of useful SNPs
discovered to date. That has always puzzled me.

The WOY project will be enlightening, one way or another. I still believe
it is the most promising way forward.

What we may find from WOY, is some useful mutation activity on any very slow
mutating shorter STRs in the WOY regions. These may compensate, if the SNP
count is lower than expected. If useful SNPs only occur on Y once ever 10
generations or so, some of the very slow STRs might need to be considered as
defacto subclade clade definers.

I have previously said it would be interesting to have a test company market
a test for say 100 very slow mutating STRs. If 67 STRs cost say $270 to
test, then 100 very slow STRs might cost $400, or less if newer technology
kept costs down. It would be surprising if 100 very slow STRs did not add
some useful insights into branching of the Y tree.

On the bright side, in the 2 test runs of WOY, I believe there were about 2
SNPs discovered per person. If that were a realistic indication, it would
still be a valuable hit rate. Many will test if those were realistic odds.

John.



-----Original Message-----
From:
[mailto:] On Behalf Of Tim Janzen
Sent: Wednesday, January 02, 2008 8:01 PM
To:
Subject: Re: [DNA] Chances for Finding Clade-separating SNP

Dear Ken,
I see your point now. I now see that I misstated the situation in
my earlier messages. I should have stated that those 132 SNPs must have
occurred at some point in the line between the contemporary HUGO male and
the Watson/Ventor/HUGO MRCA or between the Watson/Ventor MRCA and the
Watson/Ventor/HUGO MRCA. Thus, this situation isn't as promising as I had
originally suggested. Many of the 132 SNPs could be SNPS that occurred in
the line between the contemporary HUGO male and the Watson/Ventor/HUGO MRCA.
It is also quite possible that a number of these 132 SNPs are sequencing
errors in the HUGO Reference Sequence. The Wikipedia article that Vince
referred to at http://en.wikipedia.org/wiki/Shotgun_sequencing says that
most of the HUGO sequence was sequenced at 12X or greater coverage, so
hopefully there are relatively few sequencing errors in the HUGO Y
chromosome sequence.
Let's assume for a minute that there were no sequencing errors in
the HUGO Y chromosome sequence. I don't know when the original
Watson/Ventor/HUGO R1b1c MRCA male lived, but let's assume for the sake of
discussion that he lived ca 15,000 years ago. We also don't know exactly
when the Watson/Ventor R1b1c9 MRCA lived, but he likely lived less than 9000
years ago. The article on R1b at Wikipedia says that the R1b1c9 haplogroup
originated about 9000 years ago
(http://en.wikipedia.org/wiki/Haplogroup_R1b_%28Y-DNA%29). There appear to
be a lot of differences between Watson's and Ventor's Y chromosomes so it
would seem probable that they don't share a MRCA who lived within the past
several thousand years. Let's assume that the Watson/Ventor MRCA lived 5000
years ago. This would give us a total of 25,000 years (15,000 + 10,000) in
which these 132 SNPs could have occurred. If we assume 30 years per
generation then this would suggest that there were about 833 generations
during which these 132 SNPs could have occurred. This would calculate out
to about 1 Y SNP per 6.3 generations.
This whole situation doesn't bode particularly well for finding
family Y SNPs with any significant frequency if 1 SNP per 6.3 generations
ends up being the true frequency. I had been hoping that we would end up
finding Y SNPs occurring about one every generation as suggested by Charles
Kerchner's discussion at the bottom of this web page:
http://www.kerchner.com/dnamutationrates.htm.
In the best case scenario the Watson/Ventor/HUGO R1b1c MRCA male
lived ca 10,000 years ago and the Watson/Ventor MRCA lived ca 8000 years
ago. This would reduce the number of generations in which the 132 SNPs
occurred to 400 (10,000 + 2000 divided by 30) and the rate of SNPs occurring
would improve to about 1 SNP per 3 generations.
This whole situation also suggests that a lot of the reputed SNPs in
Ventor's and Watson's Y chromosome sequences are actually sequencing errors
and not true SNPs or we would see far more than 132 SNPs present between the
contemporary HUGO male and the Watson/Ventor/HUGO MRCA or between the
Watson/Ventor MRCA and the Watson/Ventor/HUGO MRCA. Watson's SNP file on
Ron Scott's web site shows 1746 SNPs and Ventor's SNP file shows 8634 SNPs.
Many of Ventor's SNPs in particular should be considered suspect.
In any case, all 132 of the SNPs I mentioned should be carefully
evaluated to see where they fall on the Y chromosome SNP tree below R1b1c
(M269+). It seems probable that some (most?) of them will help divide R1b1c
into smaller subclades and possibly some of them will also divide R1b1c9
into smaller subclades. We need more publicly available complete (or at
least largely complete) R1b1c Y chromosome sequences that we can use for
reference so that we can study these 132 SNPs more carefully. Hopefully,
technology will move forward in the near future so that complete or nearly
complete Y chromosome sequencing can be done economically.
Sincerely,
Tim

-----Original Message-----
From:
[mailto:] On Behalf Of Ken Nordtvedt
Sent: Tuesday, January 01, 2008 6:26 PM
To:
Subject: Re: [DNA] Chances for Finding Clade-separating SNP

Tim,

My question or doubt is about how you could assume they (the 132 SNP
mutations) are between the Watson/Ventor MRCA and the Watson/Ventor/HUGO
MRCA?

I take it the evidence is that there are 132 sites where Watson and Ventor
show different state than HUGO, but Watson and Ventor are the same. If that

is the evidence, why are you throwing out the possibility that the SNP
mutations occured on the branch line from Watson/Ventor/HUGO MRCA and the
contemporary HUGO ?

Ken



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