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Archiver > GENEALOGY-DNA > 2008-01 > 1199310522


From: "Tim Janzen" <>
Subject: Re: [DNA] Chances for Finding Clade-separating SNP
Date: Wed, 2 Jan 2008 13:48:42 -0800
In-Reply-To: <000001c84d2e$45f15f60$0100a8c0@john>


Dear John, Ken, Ron, Richard, Ann, and others,
See also my response to Ann's post. Richard, let's say that we
throw out all SNPs from among the 132 SNPs I listed that are from the
Yq11.21 region. Per my post on December 31 on 17 of the 132 SNPs were
located between positions 12000000 and 15000000 on the Y chromosome. That
would still leave us with 115 SNPs that look promising for helping to divide
R1b1c into smaller subclades and possibly some of them will also divide
R1b1c9 into smaller subclades.
Ron, I hope that all of James Watson's 757 novel SNPs will prove to
be true SNPs and not sequencing errors. In any case he seems to have 989
previously reported SNPs that are thus unlikely to be sequencing errors.
That is a lot of SNPs. I sorted these 989 previously reported SNPs by
location on the Y chromosome. The breakdown for these by location is as
follows:
2.72-3 million: 6
3-4 million: 158
4-5 million: 30
5-6 million: 85
6-7 million: 31
7-8 million: 2
8-9 million: 2
9-10 million: 0
10-11 million: 59
11-12 million: 41
12-13 million: 14
13-14 million: 10
14-15 million: 2
15-16 million: 1
16-17 million: 2
17-18 million: 1
18-19 million: 0
19-20 million: 10
20-21 million: 3
21-22 million: 1
22-23 million: 2
23-24 million: 0
24-25 million: 0
25-26 million: 0
26-27 million: 0
27-28 million: 15
28-57.39 million: 0 (not sequenced since it is
heterochromatin)
57.37-57.45 million: 513

If we were for purposes of discussion to simply ignore Watson's
novel SNPs and if we assume that the MRCA for Watson and the HUGO R1b1c male
lived 15,000 years ago this translates into a SNP rate per generation of
about 1 SNP per generation (989 divided by [15,000 + 15,000 divided by 30]),
which is consistent with the rate that Charles Kerchner has previously
suggested. I hope that the 1 SNP per generation rate will prove to be a
true average as we get more Y SNP data. What puzzles me is why Watson has
so many SNPs relative to the HUGO Reference Sequence (1746 in total), but
there are only 132 SNPs between the HUGO Reference Sequence and the
Ventor/Watson MRCA. Does anyone know how many of Ventor's 7662 Y SNPs have
previously been reported and how many of them were novel?
John, I also agree with your idea of testing a panel of 100 of very
slow mutating STRs. SNPs and STRs should be used in combination.
Ken, I agree with the summary you posted this morning. We would
expect that if the time periods you suggested when the MRCAs lived is
correct that in general about 2/11 of the 132 SNPs would on the short
branch between the MRCA for all three and the Ventor/Watson MRCA, while 9/11

would be on the branch line from MRCA for the three to contemporary HUGO.
I fully agree that the WOY project is very worthy of support and it
will be efforts like this that move things forward in locating deep
subclades SNPs and hopefully also family SNPs. As I tried to emphasize in
my December 31 post, however, the location where the WOY sections are done
will likely have significant bearing on how many SNPs are discovered per
50,000 bp section. It would seem prudent to avoid the palindromes and other
sections of the Y chromosome that are either difficult to sequence or prone
to RecLOH events. The palindromes generally seem to have few SNPs relative
to other portions of the Y chromosome, apparently because they are prone to
RecLOH events. Some regions of the Y chromosome seem to be relative SNP
"deserts" and other areas seem to be more promising for locating SNPs. In
any case, we need a lot more data from multiple complete sequences of Y
chromosomes (or at least from lengthy blocks of the Y) before we get a much
better understanding of where to find the most SNPs on the Y chromosome.
Sincerely,
Tim Janzen

-----Original Message-----
From:
[mailto:] On Behalf Of Alister John Marsh
Sent: Wednesday, January 02, 2008 2:57 AM
To:
Subject: Re: [DNA] Chances for Finding Clade-separating SNP

Tim,

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?

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.

John.


-----Original Message-----
From:
[mailto:] On Behalf Of Ron Scott
Sent: Wednesday, January 02, 2008 7:41 AM
To:
Subject: Re: [DNA] Chances for Finding Clade-separating SNP

That's 1-2 SNPs per 50k bp run:
http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2007-12/1199088762.
Watson's full-sequence yielded 1,746 SNPs, 757 novel. In other words,
57,772,955 / 50,000 = 1155, or, ~1.5 novel SNPs per 50k.

Ron Scott

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