GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2004-03 > 1079037205


From: "Richard Cottrell" <>
Subject: Re:[DNA] Logic of the Phylogenetic Software?
Date: Thu, 11 Mar 2004 14:33:25 -0600


To all:

This is what I used the chart for and my thinking could be wrong but I went ahead and gave it a try.

Let me give a little background.

I have 15 participants I am grouping that have the surname Cottrell. And within these groups I found a genetic distance step down between the groups that was interesting.

Group 1 Group 2
10/12 distance with Group 5 11/12 distance with Group 6
9/12 distance with Group 2 and 6 9/12 distance with Group 1, 3, and 5
8/12 distance with Group 3 5/12 distance with Group 4
5/12 distance with Group 4

Group 3 Group 4
10/12 distance with Group 5 6/12 distance with Group 5 and 6
9/12 distance with Group 2 5/12 distance with Group 1 and 2
8/12 distance with Group 1 and 6 4/12 distance with Group 3
4/12 distance with Group 4

Group 5 Group 6 (This is me)
10/12 distance with Group 1, 3 and 6 11/12 distance with Group 2
9/12 distance with Group 2 10/12 distance with Group 5
6/12 distance with Group 4 9/12 distance with Group 1
8/12 distance with Group 3
6/12 distance with Group 4

Group 6 (me) is the reason I tried the Phylogenetic Chart because I found it interesting that I stepped down a genetic distance with each group as an independent. And the step down was in numerical order until I got to group 4.

Also group 4 had a genetic distance step down that was in numerical sequence. Except it was combined on the first two step downs and independent on the last one.

I also found it interesting that Group 1, 3, and 6 had a 10/12 distance with Group 5 which was a participant from England. And the surname spelling was Cotterell.

My figures are this:

Markers
393,390,19,391,385a,385b,426,388,439,389-1,392,389-2

(Note in the actual program I changed 389-1 to 389a and 389-2 to 389b, the program had trouble with 389-1 it came out as 3891??)

G1 (*Group 1)
13,23,14,10,11,14,12,12,14,13,13,29 (*Values)
4 (* amount of participants having the numbers or the frequency)

G2
13,24,14,11,12,14,12,12,13,13,13,29
4

G3
13,24,15,11,11,14,12,12,12,13,13,29
4

G4
13,24,14,10,13,15,12,12,11,12,13,28
1

G5
13,24,14,10,11,14,12,12,12,13,13,29
1

G6
13,24,14,10,12,14,12,12,13,13,13,29
1

Now that is the way I can enter them doing it through the program or I can also enter it like that using Notepad and assigning the extension .ych to the file.

Upon doing that I ran a calculation for a Reduced Median Chart and I have uploaded the chart at: http://www.cottrellweb.com/dna/Cot12.jpg

Then I ran a calculation for a Median Joining Chart and I have uploaded that chart at: http://www.cottrellweb.com/dna/Cot12a.jpg

On the Reduced Median Chart I have 5 median vectors and on the Median Joining Chart I have 2 median vectors. The charts are different in structure.

The Reduced Median Chart seemed to show the genetic distance step down for each group to each group.

However the Median Joining Chart did not have the same effect.

Does anyone know why there is a difference between Reduced Median and Median Joining??

Is there a reason for going from 5 median vectors to 2 median vectors??

Or am I making any sense at all for anyone to answer the questions??

Richard






This thread: