Exactly. That's why I wrote: "A problem is that then the statistical model is unclear/confusing."
But for nuisance variables in a multuple-regression type of model, I see no problem putting them on a star phylogeny if they are not phylogenetically distrubuted (e.g., assuming that a particular technique for measuring, say, home range size, does not tend to be applied in a clade-specific [biased] fashion). So far as I am aware, Nobody knows exactly jhow to do this, nor has tried to implement this, with PGLS or phylogenetic regression models! We mention this in Garland and Ives (2000). Cheers, Ted From: Alejandro Gonzalez [alejandro.gonza...@ebd.csic.es] Sent: Wednesday, April 17, 2013 9:38 AM To: Theodore Garland Jr Cc: Anne Kempel; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] trait correlations with PICs Can I risk a question here, maybe a result of ignorance... "With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among studies (e.g. Wolf et al., 1998; Perry and Garland, 2002; Rezende et al., 2004)." >From an evolutionary point of view, what does it mean when using different >sets of branch lengths for different traits? If we're testing co-evolution of >traits, I would tend to think - and I may very well be wrong - that the >interest would be in estimating a single rate describing this co-evolution and >by employing different branch lengths would we not loose the opportunity to >estimtate that rate? Cheers Alejandro On 17, Apr 2013, at 6:24 PM, Theodore Garland Jr wrote: For correlations per se, please check this paper: Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56:252-270. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate "pseudo-PICs" based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the "signal-traits" but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. Obviously, it is possible to do this. A problem is that then the statistical model is unclear/confusing. I could not find any reference doing this, and I wonder whether this is legal? We have discussed this here: Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035. Page 3032: "With IC, it is easier to employ different sets of branch lengths for different traits (e.g. Garland et al., 1992; Lovegrove, 2003; Rezende et al., 2004), which may be particularly useful when one trait does not actually show phylogenetic signal (e.g. Tieleman et al., 2003; Rheindt et al., 2004) and/or for traits that are only nuisance variables, such as details of measurement or calculation methods that differ among studies (e.g. Wolf et al., 1998; Perry and Garland, 2002; Rezende et al., 2004)." Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Skype: theodoregarland Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ Inquiry-based Middle School Lesson Plan: "Born to Run: Artificial Selection Lab" http://www.indiana.edu/~ensiweb/lessons/BornToRun.html ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Anne Kempel [kem...@ips.unibe.ch] Sent: Wednesday, April 17, 2013 5:37 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] trait correlations with PICs Dear all, I am dealing with plant traits of different plant species (28 plant species), and aim to correlate all traits with each other. I have a tree of my species, and some of those traits do have a phylogenetic signal, but most don't. Since I do not know, which trait depends on whom, I favour to do correlations instead of regressions - that's why I would like to use Phylogenetic independent contrasts (PIC) instead of PGLS. I have the impression that it does not make sense to calculate PICs for traits that do not have a signal. And here comes my question: is it allowed to calculate only PICs based on my tree for those traits having a signal, and to calculate "pseudo-PICs" based on a star phylogeny (independence between species) for those traits having no signal? This would allow me to correct the "signal-traits" but leave the other ones more or less as they are. The benefit: I then can correlate all traits with each other. I could not find any reference doing this, and I wonder whether this is legal? I am grateful for any comment and suggestion! Thanks a lot in advance and best wishes from Switzerland, Anne -- Dr. Anne Kempel Institute of Plant Sciences Altenbergrain 21 3013 Bern Switzerland _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ __________________________________ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: alejandro.gonza...@ebd.csic.es Web site (Under construction): Personal page: http://consevol.org/members/alejandro_combo.html Group page: http://consevol.org/people.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
