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Archiver > DNA-R1B1C7 > 2009-04 > 1239610002


From: John Mclaughlin <>
Subject: Re: [R-M222] Genetic Distance/Diversity
Date: Mon, 13 Apr 2009 03:06:42 -0500
References: <c2e.5003fcf0.3713caac@aol.com><000001c9bc05$e8ecc820$bac65860$@com>
In-Reply-To: <000001c9bc05$e8ecc820$bac65860$@com>


<Frankly, I can't see how the McCord with a gd of 21 could possibly be
M222+.

I don't think he is either. I'm not sure he got included in the M222
section but I'll take him out (39163). However I do not see 39163 in
the McGee utility chart.

< So it seems that the Magee software
makes all gd's greater than 10 equal to 10. If so, that's not very helpful.

I don't think that's correct because there are plenty of GDs in the
chart higher than 10 when compared not to the modal but against each
other. Just to pick one example a Bookout and a Doherty are a GD of 15.

There are different ways of calculating genetic distance. The McGee
utility defaults to the Infinite Allele Mutation Model. FTDNA and
Ysearch use the Hybrid Mutation Model. It would probably agree with
your figures if the FTNDA method was used. But I'd definitely have to
re-run the DNA to find out.

Here's a discussion from the McGee utility.

Genetic Distance

If this table is enabled then a table of genetic distances between every
pair of haplotypes is created. The diagonal elements of the table
indicate the number of allele data existing for that haplotype. The
calculations can be of two types:

1. Hybrid Mutation Model

The target of this model is to match that used by Ysearch and
FTDNA. It uses the stepwise mutation model for all alleles except DYS464
and YCA which use the infinite allele model. The stepwise model says
that each mutation is allowed to change the allele value by exactly one,
so a difference of two means that two mutations occurred and a
difference of three means that three mutations occurred. The infinite
allele model says that the entire difference between allele values, no
matter how large, is the result of one mutation.


2. Infinite Allele Mutation Model

The infinite allele model says that the entire difference between
allele values, no matter how large, is the result of one mutation.


I have no idea which method is better or why the McGee utility used the
Infinite Allele Mutation model as the default.



John

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