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From: "Earl Beaty" <>
Subject: Re: [DNA] SNP mutation rates
Date: Thu, 4 Aug 2005 09:05:48 -0600
References: <IGEOKAGLHNEKPCKPADIGOEIKKEAA.bbailey.lowedna@baileyconnection.com> <REME20050803190044@alum.mit.edu> <090b01c59884$6238c5c0$0200a8c0@c452380a> <REME20050803194536@alum.mit.edu>


On Wednesday, August 03, 2005 5:45 PM"John Chandler" said:
> The answer to this puzzle is the size of the Y chromosome: 60 million
> base pairs. If the mutation rate is 2 x 10^-8 per base pair per
> generation, that gives an expectation of about one new SNP for every
> man ever born.

And Gareth Henson said something similar.

John and Gareth,

Thanks for the response. The two of you are convincing that it is very
unlikely that any living man has the full set of SNPs of Y-Adam. I hadn't
considered that situation. But one of the reasons we don't see a very large
number of distinct haplogroups is because we have not tested all those
options. For this discussion wouldn't it be better to restrict the range of
SNPs to those which have been actually found? The 2005 chart has something
like 200-300 defined. With such a small number in consideration I would
expect that many, perhaps most, men would have none of the observed
mutations. This issue has obviously been well considered and understood. I
just find it counter-intuitive.

And Gareth added:

> The other point is about "founder effect". If an individual or small group
> becomes separated from an ancestral group, a mutation (SNP or STR) which
is
> rare in the original group can easily come to dominate the newly founded
> group. It is these founder events that create recognizable clusters of y

That raises another point where my intuition is in conflict with accepted
reality. Way back in time some guy was born with the M207 mutation, starting
haplogroup R, and making him different from all the thousands of other men
living at the time. Somehow his male-line descendants came to dominate
Europe, and all (almost) the others died out. It is easy to understand how
the M207 guy has more male-line descendants than his brothers. The problem
is the SIZE of the disparity. The result seems so overwhelmingly improbable.

I am hoping that one of you two or others will straighten me out. I should
note that you have already gone a fair way. The considerations at the top of
the page say that while there was only one man with the M207 mutation, many
(most) of the other men alive at the time had their own unique mutations. So
it wasn't a matter of how one particular man came to have so many male-line
descendants. Any of the other men could have produced the same result if
their descendants has been so lucky. That goes a long way toward making the
result plausible. The founder effect must have been an important mechanism.
It appears that for much of human existence we have been on the verge of
extinction. That makes wild fluctuations more likely.

After thinking about the above considerations I am still left with the
feeling that it couldn't have happened. This is important because in this
business we frequently need to convert "very unlikely" into "couldn't
happen". It helps to develop a feel for yow far the press that idea.

Thanks very much for the responses.

--Earl

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