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Archiver > GENEALOGY-DNA > 2005-08 > 1123292615


From: (John Chandler)
Subject: Re: SMGF [was Re: [DNA] FTDNA Genetic Distance Calculations...]
Date: Fri, 5 Aug 2005 21:43:35 -0400 (EDT)
References: <IGEOKAGLHNEKPCKPADIGOEIKKEAA.bbailey.lowedna@baileyconnection.com><REME20050803190044@alum.mit.edu><6.0.0.22.0.20050805102153.06137ba8@wells.org><REME20050805150049@alum.mit.edu> <6.0.0.22.0.20050805123622.052bd670@wells.org>
In-Reply-To: <6.0.0.22.0.20050805123622.052bd670@wells.org> (message fromOrinWells on Fri, 05 Aug 2005 12:45:36 -0700)


Orin wrote:
> In this particular case, to confirm the mutations, this individual was
> tested using a variety of tests.

That's rather vague. Exactly what sorts of tests did you do? Buccal,
for starters, of course. Blood? Semen? Only the latter would give
you conclusive proof that it wasn't a somatic mutation.

> I disagree. You can not rule this out unless you were to run a large test
> utilizing three generations. What we are seeing in the father-son testing
> is simply a confirmation of what we are seeing in the general
> population.

A pedigree study inevitably covers more than three generations. The
point I was making, but didn't state explicitly, is this: a father-son
study will be sensitive to all three types of mutations that you are
proposing, (1) "permanent" mutations, (2) "transient" mutations, and
(3) reversions of the latter. Obviously, types 2 and 3 must occur with
equal frequency in equilibrium. A pedigree study will not see any
transient mutations except those occurring in the testees themselves
and will not see any reversions at all. Therefore, the general
agreement between pedigree studies and father-son studies demonstrates
that types 2 and 3 cannot be at all common.

> The question then is how many of the mutations seen in the
> father-son testing might have actually been transient and at the same ratio
> as in the general population. I would agree it is probably a very small
> number, but it is also probably finite.

The issue is whether the number is big enough to change the statistics
in an observable way. If not, then "finite" is effectively the same
as "zero".

> There are some interesting implications here. If this transient behavior
> also applies to DNA on other chromosomes, and there is no reason why it
> wouldn't, it is quite possible various identifiable traits appear and
> disappear from generation to generation.

As Ken pointed out, there is a known mechanism that does this and has
been observed, namely, recombinant duplication. In this process, a
sequence of DNA is copied over to replace the homologous sequence on
the other chromosome of the pair (or, in the case of Y DNA, on the
other side of a palindrome). Obviously, this cannot occur for
single-copy Y markers. Also, it doesn't occur immediately, but only
occasionally. Otherwise, it's similar to what you propose.

John Chandler

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