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Archiver > DNA-R1B1C7 > 2009-04 > 1239612926


From: "Sandy Paterson" <>
Subject: Re: [R-M222] Genetic Distance/Diversity
Date: Mon, 13 Apr 2009 09:55:26 +0100
References: <c2e.5003fcf0.3713caac@aol.com> <000001c9bc05$e8ecc820$bac65860$@com><49E2F292.4060408@aol.com>
In-Reply-To: <49E2F292.4060408@aol.com>


Hi John

>
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.
>

I think we're talking at cross purposes. Bookout and Doherty are separated
from each other by a gd of 15, yes. But Bookout is separated from the modal
by a gd of 7 and Doherty is separated from the modal by a gd of 10. What
I've calculated for each M222+ participant is simply the sum of the
differences between their allele values and the modal. I find 10
participants that are a gd of 11 or more away from the modal. The Magee
facility shows none.

>
There are different ways of calculating genetic distance.
>

I don't think so. Yes, you can make different assumptions regarding how a gd
came about and that may influence the conclusions you come to in your
modelling process. But a gd is a gd.


Sandy



-----Original Message-----
From:
[mailto:] On Behalf Of John Mclaughlin
Sent: 13 April 2009 09:07
To:
Subject: Re: [R-M222] Genetic Distance/Diversity

<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
R1b1c7 Research and Links:

http://clanmaclochlainn.com/R1b1c7/
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