**GENEALOGY-DNA-L Archives**

From:"Alfred A. Aburto Jr." <>Subject:Re: [DNA] For the more mathematically-inclined on the list - questionon Mode / MLE and Walsh's paperDate:Sat, 14 Jan 2006 07:29:09 -0800References:<20060114000151.24499.qmail@web404.biz.mail.mud.yahoo.com>In-Reply-To:<20060114000151.24499.qmail@web404.biz.mail.mud.yahoo.com>> Gary Lee wrote:

>In Bruce Walsh's paper, Estimating the time to the MRCA, he presents various calculations for computing MRCA.

>

> In table 1, he shows for a n=50 marker test, a MLE (mode) of 5.1, 10.2 and 15.5 for a 1, 2 and 3 marker mismatch. I can replicate all of his calculations in this table for mean, SD, Median and confidence intervals, but am struggling with how he derives the MLE.

>

> Any ideas from the list?

>

> Thanks in advance.

> Gary Lee

> an-admitted non-Math-major in my undergraduate days

> mathematically

>

>

Ok, I found Walsh's paper :-)

The MLE is given by equation 5:

MLE = (1/(2*mu))*ln(n/k), where

n is the number of markers, for two individuals that match at k out of

n markers, and "mu" is the mutation rate. In the paper Walsh assumes a

mutation rate of mu = 1/500 ...

e.g.: for n=20,k=15, mu=1/500, MLE = 71.9205 generations ...

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I have my own question though (requires a new topic if anyone answers):

What bothers me, being new to this field, is that the MLE is based upon

markers while I think it should be based upon the number of repeats

within a marker! What have I missed? In this article is _marker_ being

confused with _repeat_? I suspect this is might be the case ...

Al

**This thread:**

- For the more mathematically-inclined on the list - question on Mode / MLE and Walsh's paper by Gary Lee <>
- Re: [DNA] For the more mathematically-inclined on the list - questionon Mode / MLE and Walsh's paper by "Alfred A. Aburto Jr." <>

- Re: [DNA] For the more mathematically-inclined on the list - questionon Mode / MLE and Walsh's paper by Doug McDonald <>

**Re: [DNA] For the more mathematically-inclined on the list - questionon Mode / MLE and Walsh's paper by "Alfred A. Aburto Jr." <>**