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From: "Sandy Paterson" <>
Subject: [DNA] Asymptotic Distributions for General Mutation Models- NAUGHTYCHILDREN
Date: Thu, 9 Jun 2011 09:22:41 +0100


[The actual number of mutation events between me and this person could be 6,

7, 8, 9, 11, 13, or 15 or more, before you start getting into speculations
on whether there have been parallel or back mutations on other of the 111
markers.]

The clarity of the above observation makes me think that your real
difficulty lies with the mathematics of genetic genealogy rather than with
simulation. There is in fact very little mathematics in simulation. It is
merely an attempt to mimic the mutation process as understood by molecular
biologists. But conceptually, it's really very simple.

And provided you have done a sufficient number of simulations, you don't
need a mathematical formula to estimate TMRCA's. You just search through
your files and count the number of times the TMRCA was

1
2
3
.
.
.
and so on.

>From that you can construct a table showing the cumulative frequency
distribution for the TMRCA's.

Of course defining 'sufficient' is not easy, but you can avoid doubt by
doing many more simulations than you think are necessary.

The example you gave of the 111-marker match at a GD of 9 is interesting,
and could be quite illuminating. Can you post the GD's at 12,25,37 and 67
markers? Or perhaps point me to where I can have a look at the two
haplotypes?


Sandy



-----Original Message-----
From:
[mailto:] On Behalf Of Alister John Marsh
Sent: 09 June 2011 01:53
To:
Subject: Re: [DNA] Asymptotic Distributions for General Mutation Models-
NAUGHTY CHILDREN

I still have difficulty with the mathematics of mutations.

NAUGHTY CHILDREN:

I think of mutations as NAUGHTY CHILDREN. They never seem to do what the
formulas assume they do.



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