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Archiver > DNA-R1B1C7 > 2009-04 > 1239606191


From: "Sandy Paterson" <>
Subject: Re: [R-M222] Genetic Distance/Diversity
Date: Mon, 13 Apr 2009 08:03:11 +0100
References: <c2e.5003fcf0.3713caac@aol.com>
In-Reply-To: <c2e.5003fcf0.3713caac@aol.com>


Hi John

>
This is a huge file though, something like 20 meg. It takes quite a while
to download and display in a browser. It works better if you save it to
your hard disk and run it from there..
>

It took about 15 seconds. I have quite a fast computer (quad-core with 4
megs of ram).

A quick glance at the output worries me. The highest gd shown is 10
(Doherty,Conroy,Brennan,Ewing,McLelland), yet my software finds no fewer
than 10 haplotypes with a gd of 11 or more from the modal :

NameGD

Bonner11
Brennan13
Burgess14
Conroy15
Doherty12
Dunn11
McCord21
McCord11
McHughen12
Spier12

Frankly, I can't see how the McCord with a gd of 21 could possibly be M222+.
Conroy (gd 15) has been SNP tested so he's definitely M222+, but his gd is
shown as 10 in the Magee Utility output. So it seems that the Magee software
makes all gd's greater than 10 equal to 10. If so, that's not very helpful.

Sandy



-----Original Message-----
From:
[mailto:] On Behalf Of
Sent: 12 April 2009 23:52
To:
Subject: Re: [R-M222] Genetic Distance/Diversity

In a message dated 4/12/2009 5:49:41 A.M. Central Daylight Time,
writes:

I've checked McCord manually and the figure of 21 seems right. Is it easy
for you to run it through the McGee utility again?

I can work on that again. It takes some work to get the spreadsheet data
in McGee format and I usually eliminate all but 37 marker tests.

I posted the last version online if you want to look at it.

_http://clanmaclochlainn.com/R1b1c7/gd.htm_
(http://clanmaclochlainn.com/R1b1c7/gd.htm)

This is a huge file though, something like 20 meg. It takes quite a while
to download and display in a browser. It works better if you save it to
your hard disk and run it from there..

You can run large datasets through the McGee utlitity but it takes a long
time and times out constantly.

It seems logical that an older population would show greater genetic
diversity than a younger offshoot population. That seems to be the theory
behind John McEwan's statement about diversity. It also seems logical that
one
could apply that to the M222 populations in Ireland and Scotland. I've
wondered if this could gives us a clue as to whether M222 originated in
Ireland
or Scotland. Of course we find M222 in other areas too - England,
Germany, even some Scandinavian countries, but those two are the main
concentrations. Mostly people seem to measure this by genetic distance
against a
group modal. But when I do this I don't see a huge difference in
populations.
It's also difficult to categorize many of the surnames in the M222
project. Is Cowan Irish or Scottish? Many of these names could be either
one.

It would be quite a chore to work through the 500 samples in the M222
project and attempt to classify them as Scottish, Irish, English or
whatever.
Some are pretty obvious. Doherty is probably mostly if not all Irish.
Ewing, Dunbar and probably McCord are Scottish. I think most of our M222
McLaughlins are probably Irish but some could be Scottish.

How exactly do we measure the kind of diversity John McEwan talked about
between populations? Gd's against a group modal or some other method?


John











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