[Mesquitelist] phylogenetically corrected PCA

[Marcin Czarnoleski]

Hi,
I would be grateful for an advice how to solve my problem with 
phyllogenetic analysis pased on PCA (possibly with Mesquite). I use data 
on some traits of several species. I would like to use PCA to calculate 
PC scores from these traits, and use these scores to correlate with 
other characters of the species. But I would like to correct my analysis 
on a phylogentic signal. So basically, I should calculate 
phylogenetically corrected PC scores and then correlate them with 
contrasts of other species characters. But I have a question, should I 
first run PCA on raw data, and then calculate contrasts of the PC scores 
obtained from this PCA, and finally use these contrasts in correlattions 
with contrasts of other characters of species. Or alternativelly, I 
should run PCA on contrasts of species traits, and then use scores of 
these PCs to correlate them with contrasts of other charactes of 
species? If the second approach is recommended then I see two problems. 
First, to run PCA on contrasts it is adviced to use correlation matrix 
from contrasts (but correlations are forced through 0 and positivised). 
If I calculate such matrix and use it as an input file for PCA in an 
ordinary statistical software, I am unable to calculate PC scores 
because the information about species (cases) is missing (correlation 
matrix provides PCA only with correlation coefficients). So withought 
the scores I cannot proceed further and test correlations between 
phylogenetically corrected PC scores and contrasts of other traist. 
Second, even if I was able to obtain phylogenetically corrected PC 
scores, how should I analyse their correlation with contrasts of other 
traits. I understand that a normal correlation on contrasts requires 
prior positivisation and forcing through 0, but I am not sure what 
should be done in terms of this requirement in the case of scores vs 
contrasts correlation. I should be grateful for any opinion on my 
problem and I would be also grateful for the information whether 
Mesquite can help solve my problem.
Marcin Czarnoleski