----- Forwarded message from Chong
Ong
Date: Sat, 15 Sep 2012 22:25:33
-0400
From: Chong Ong
Reply-To: Chong
Ong
Subject: Homoplasy index questiom
To: morphmet@morphometrics.org
My name is Ren,
and I am an honours student at
the Australian National University. As part of my honours project, I am
looking at changes in leaf shape in the Australian
Pelargonium in a phylogenetic context. I have mapped a PCA on the
covariance matrix of my leaf Procrustes coordinates onto a phylogeny on
MorphoJ, and currently I am trying to look at extent of homoplasy
between taxa. I understand that the "Map onto phylogeny" function only
detects a presence of phylogenetic signal in shape data, while analysing
the extent of homoplasy within the group requires an additional
calculation of a homoplasy index instead. I have been trying to repeat
the methods that were
described in Klingenberg & Gidasewski (2010) to calculate this
homoplasy index, but I'm having a bit
of trouble figuring it out.
I understand that firstly I need to
measure the minimum amount of change i.e. the shortest tree possible
that connects my data points using Klingenberg's FindSteinerTree program. My
first
question is, what exactly are these data points that I need to put in?
Are they the values for PC1 and PC2 of each data point representing the
mean shape of each taxon?
My second question was regarding the
maximal amount of change. What do I have to do on MorphoJ to get the sum
of squared distances of each taxon from the overall mean shape in order to
calculate the star phylogeny?
I have only started using MorphoJ recently,
and any advice would be greatly appreciated! My email address is
u4463...@anu.edu.au
Cheers.
Ren
----- End forwarded message
-----
Hi
everyone,
