GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2006-09 > 1157119362


From: Doug McDonald <>
Subject: Re: [GENEALOGY-DNA] can we do better for genetic distance?
Date: Fri, 01 Sep 2006 09:04:09 -0500
References: <090120060117.29363.44F78A250002F243000072B322058891169C9C0EA0AC@comcast.net><REME20060831221846@alum.mit.edu>
In-Reply-To: <REME20060831221846@alum.mit.edu>


John Chandler wrote:
> Sam wrote:
>> May I suggest
>>
>> Most_Likely_Estimate = 1/(2*Mutation_Rate))*LN(Number_of_Markers/(Number_of_Markers-Number_of_Mutations)) = 31 generations given 25 matches out of 32 markers and a mutation rate of 4 per 1000 events
>
> You seem to have spelled everything out except "LN" -- did you perhaps
> mean "ln" instead? If so, then that formula is indeed a good
> approximation for the MLE, but only if all the marker differences are
> one step each. A two-step difference shifts the MLE more than a one-
> step difference, but less than two one-step differences (provided you
> recognize that multi-step mutations do occur).
>
>

I've been thinking about two-step mutations and recLOH events.

It seems to me that a simple way of taking them
into account in TMRCA calculation is to consider them
as "different markers" with a negligible (pending knowing
their actual rate of course) mutation rate.

Thus, if you are convinced there was a two-step mutation
in a 37 marker test, and it was the only one, you in fact
use 38 markers, and assume 37/38 matches. You use the same
TOTAL mutation rate for the 38 markers as for the 37,
so the average rate you put into a calculator program
is 37/38 the original 37 marker value. (Of course,
if you think you know the two-step rate you can add that in.)

John, what do you think of this? The obvious problem is that
the rate of two-step mutations is in some unknown way
already included in the average rates we use.

Doug McDonald

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