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Archiver > DNA-R1B1C7 > 2007-08 > 1186801320


From:
Subject: Re: [DNA-R1B1C7] Network.exe
Date: Fri, 10 Aug 2007 23:02:00 EDT



In a message dated 8/10/2007 11:01:38 A.M. Central Standard Time,
writes:

John, I'm not sure I follow your reasoning and I haven't used this feature
of Network, but let me suggest what I think is a much easier and more
transparent approach. Just calculating a TMRCA without remaining
excruciatingly aware of the confidence intervals is sure to mislead.



Anne Turner's mutation calculator seems to yield about the same results as
the Network.exe and McGee utility.

You have only 1 or 0 mutations against the modal in your group of Ewings.

To get 1 mutation in the calculator, you use the following calculations:

1. Number of markers = 25
2. Mutation rate per marker = .002
3. Number of transmission events = 20

20 events x 30 years/gen = 600 Years TMRCA

The probability of 1 mutation is 38%; probability of 0 mutations, 38%.
probability of 2 mutations, 18%.


My question would be how do you go from Anne's .002 mutation rate in her
calculator to the mutation rate used by Trinity College in Network.exe?
(0.00069 per locus per 25 years (Zhivotovsky et al. 2004).

I like the Network.exe program because it combines phylogenic charts with
Time Calculations. I just don't have any idea what the most accurate
parameters would be.

It's pretty easy to figure out where Trinity got their 2131 years used in
their Network.exe TMRCA calculations. They started with this:

0.00069 per locus per 25 years (Zhivotovsky et al. 2004).

and converted it into 1 mutation per marker every xxxx years used by
Network.


.00069 times 17 (number of markers) = 0.01173

1 divided by .01173 = 85.25

85.25 times 25 years = 2131 years


If .00069 is not accurate or if there are better estimates being used
these figures could be changed in Network.exe.


John










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