DNA-R1B1C7-L Archives

Archiver > DNA-R1B1C7 > 2007-08 > 1186765549


From: "Paul Conroy" <>
Subject: Re: [DNA-R1B1C7] Network.exe
Date: Fri, 10 Aug 2007 13:05:49 -0400
References: <e0d2d2870708100900s77fef4b6vc838003e7d273b6d@mail.gmail.com>
In-Reply-To: <e0d2d2870708100900s77fef4b6vc838003e7d273b6d@mail.gmail.com>


David,

Great links - thanks.

I guess the kicker here is determining the Mutational Rate.

For Example:
If Person A and Person B are different by 1 GD from a modal, but Person A's
difference is on a slow mutating marker, while Person B's is on a fast
mutating marker, then probably Person B is more closely related to the modal
than Person A, right?

So are you coming up with the figure of .004 for your Ewing sample, by
counting what Ann Turner calls the "Transmission Events" and number of
mutational differences, then comparing them to the probabilities of
observing those - or am I getting this wrong?

Cheers,
Paul


On 8/10/07, David Ewing <> wrote:
>
> 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.
>
> I really like the results I get from the little TMRCA calculator based on
> Bruce Walsh's method and prepared by B.G. Galbraith, available for free
> download at www.clangalbraith.org/DNATesting/MRCA.htm. Rather than giving
> you a simple number, it gives you a set of probability distributions
> displayed in three different ways.
>
> Another cool little calculator is Ann Turner's Mutation Calculator that
> will
> calculate the probability of finding a specific number of mutations in a
> given number of generations. This can be downloaded for free through a
> link
> on www.genetealogy.com/resources/html/cat10.html. There are a number of
> other tools available through links on this page as well, but I think you
> are probably already familiar with most of them.
>
> As regards your calculations for a MRCA for Ewings and McLaughlins, know
> that if we use these calcuators on just the 12 men in our project known to
> be descendants of John Ewing of Carnashannagh b. c1648, (ranging between 6
> and 9 generations from him), and make the assumption of an average .002
> mutation rate per marker, we get results that don't square very well with
> what we know based on conventional genealogy.
>
> For example, two of these men are known 6th cousins twice removed (so one
> of
> them 9 generations from John of Carnashannagh and the other 7 generations)
> are at genetic distance 6/37 from one another; the calculation suggests
> that
> there is (round numbers) no chance of them having a MRCA w/in the last 100
> generations. On the other hand, we have two other men who are known 5th
> cousins once removed (one 6, the other 7 generations from John of
> Carnashannagh), who are at genetic distance zero (both matching the Ewing
> modal exactly), and the calculation more plausibly suggests that there is
> a
> 52.3% likelihood that the MRCA is 5 generations or less ago, and a
> 64.5%likelihood that the MRCA is 7 generations or less ago; however,
> the 95%
> confidence interval for MRCA is 0.2 to 24.9 generations.
>
> The last time I calculated the observed mutation rate in this kindred, it
> came out about .004, but we have added another couple of men since then
> and
> it may be slightly different than this. Most of the men in this kindred
> are
> at genetic distance 2 or 3 from one another. If we use the .004 mutation
> rate estimate and genetic distance 2/37, the calculation gives us a median
> MRCA at 9.3 generations and a 95% confidence interval of 2.1 to
> 25.1generations.
>
> Bottom line: be wary of TMRCA calculations.
>
> David Ewing
>
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