Depends on what you want. Do you want to cluster based on how different mean shapes are (Procrustes distances) or do you want to cluster based on the ease with which one can discriminate between different shapes (generalized distances)?
In both cases you have to decide whether or not to use distance or squared distance. One might wish to use squared distance if you were willing to assume a simple Brownian motion model of evolution and you wanted to cluster squared distances as an index proportional to evolutionary time. That idea may make sense for Procrustes distances but I think it seems less reasonable for generalized distances. A general observation: just because a method "takes into account" some information does necessarily mean that the method uses that information in an appropriate way. ----------------------- F. James Rohlf, Distinguished Professor State University of New York, Stony Brook, NY 11794-5245 www: http://life.bio.sunysb.edu/ee/rohlf > -----Original Message----- > From: morphmet [mailto:[EMAIL PROTECTED] > Sent: Sunday, May 01, 2005 7:20 PM > To: morphmet > Subject: UPGMA in morphometrics > > > Hi all, > > in literature, several people have been using Procrustes > distances as the data for a cluster-analysis, more > specifically UPGMA. When doing so, the Procrustes distances > between the consensus configurations of each OTU are used to > calculate a tree based on shape similarities between the > consensusses. However, when using Procrustes distances, one > is ignoring possible differences in the amount of > within-group variation (or is assuming it is the same for all > the OTU's), not? The Procrustes distance between the means of > three groups can be the identical, but because of overlapping > variations within two of them, the shape distance will in > many cases be much lower. > > So my question is, whether it is not wiser to use the Squared > Mahalanobis distances of a canonical variate analysis (based > on weight matrix), as a measure of shape distance between > group means for a UPGMA, as this does take into account the > amount of within-group variation (and as I understood even > standardises it). Does this make sense or is there some > mathematical-statistical pitfall behind it? > > cheers > > Dominique Adriaens > > > > > > Prof. Dr. Dominique Adriaens > > Ghent University > > Evolutionary Morphology of Vertebrates & Zoology Museum > > K.L. Ledeganckstraat 35, B-9000 Gent > > BELGIUM > > tel: +32 9 264.52.19, fax: +32 9 264.53.44 > > E-mail: [EMAIL PROTECTED] > > URL: http://www.fun-morph.ugent.be/ > > http://www.zoologymuseum.ugent.be/ > > > > > > -- > Replies will be sent to the list. > For more information visit http://www.morphometrics.org > -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
