Phylogenetic PCA has many unusual properties, and does not remove the effects of phylogeny. Yes, it is the case that the variance of the scores on the first phylogenetic principal component can be higher than the second PC. We recently had a paper in the Hystrix morphometrics volumes about the properties of pPCA and what it does and does not do.
Polly, P. D., A. M. Lawing, A.-C. Fabre, and A. Goswami. 2013. Phylogenetic principal components analysis and geometric morphometrics. Hystrix, 24: 1-9 Paper is available open access from the publisher or from here: http://mypage.iu.edu/~pdpolly/Publications.html P. David Polly Geological Sciences Adjunct, Anthropology and Biology Indiana University 1001 E. 10th Street Bloomington, IN 47405-1405 pdpo...@indiana.edu +1 (812) 855-7994 http://mypage.iu.edu/~pdpolly/ > On 27 Mar 2015, at 7:49 AM, Alex Marshall <alpmar...@googlemail.com> wrote: > > Hello everyone, > I'm a MSci student new to morphometrics and this group. I'm studying > morphological integration in squamate crania and one of the things I'd like > to do is an Evolutionary PCA of all my species, accounting for phylogeny and > allometry. > > I think I do this correctly but in the PCA results the PCs are not ranked by > proportion of variance e.g. PC5 has greater % variance that PCs 3 & 4. Is > this normal? > > To conduct the evolutionary PCA I created independant contrasts of all my > shape data, regressed centroid size on shape and conducted PCA on the > residuals. After this I applied the resultant PC scores to another PCA of my > original data. > > Would anyone kindly confirm if this is the right way to do it? > > Many thanks, > > Alex Marshall > MSci Student > University College London > alexander.marshall...@ucl.ac.uk > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
