Dear Daniel, OK, then I think your results make sense. You have, in fact, designed a comparative study in which the power to detect a statistical effect of Habitat (i.e., a group difference) will be higher if analyzed phylogenetically than if analyzed in the conventional fashion assuming a stat phylogeny. This point has been made in various places, including:
Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265-292. Vanhooydonck, B., and R. Van Damme. 1999. Evolutionary relationships between body shape and habitat use in lacertid lizards. Evolutionary Ecology Research 1:785-805. Garland, T., Jr. 2001. Phylogenetic comparison and artificial selection: two approaches in evolutionary physiology. Pages 107-132 in R. C. Roach, P. D. Wagner, and P. H. Hackett, eds. Hypoxia: From Genes to the Bedside. Advances in Experimental Biology and Medicine, volume 502. Kluwer Academic/Plenum Publishers, New York. In addition, you have made the within-species (and hence between habitat) branch lengths arbitrarily very short relative to the among-species branches in the rest f your tree. Hence, if you do have a Habitat effect, it would be very unlikely to have occurred via Brownian motion character evolution. So, you phylogenetic P values becomes (much) lower than your non-phylogenetic P value. As a reality check, I would run your analyses on a star phylogeny (a giant hard polytomy) and see if you get P values that are the same (actually, just very close to unless you do a lot of simulations) as for a nonphylogenetic analysis. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu Main Departmental page: http://www.biology.ucr.edu/people/faculty/Garland.html List of all Publications: http://www.biology.ucr.edu/people/faculty/Garland/GarlandPublications.html Garland and Rose, 2009 http://www.ucpress.edu/books/pages/10604.php ---- Original message ---- Date: Wed, 16 Mar 2011 15:38:54 -0500 From: dwe...@life.illinois.edu Subject: Re: [R-sig-phylo] Help Interpreting Phylogenetic ANOVA Results To: tgarl...@ucr.edu Cc: r-sig-phylo@r-project.org >Hi Liam and Ted, > My apologies for not writing sooner. I've been sick. > First off, let me thank you both for helping to clarify what the >phylogenetic ANOVA is and what it means. > I thought I would explain a little more than I did in my initial post >since Ted seemed curious to know more. > I am using geometric morphometrics to analyze body shape in a family of >freshwater fish (topminnows). I ran a PCA to "condense" the >morphometric analyses into PC scores. I'm using the PC scores in the >phylogenetic ANOVA. Because I would like to know how phylogeny >"effects" habitat-specific differences in body shape, I run the >phylogenetic ANOVAs with the tips being a species-habitat combination. >Essentially, it looks like this: > > |---- Species A Habitat 1 > | > |------| > | | >---| |---- Species A Habitat 2 > | > | > | > | |---- Species B Habitat 1 > | | > |-----| > | > |---- Species B Habitat 2 > > The tree for these species was made in Mesquite and based off of a tree >from a recent molecular phylogeny that came out (Whitehead 2010 >Evolution paper). The tree for the phylogenetic ANOVA includes branch >lengths, obviously. Because I don't know if there is any genetic >distance between the same species from the two different habitats, I set >the branch lengths to a really small value (0.00001) in R. > All of the 21 species used to run the phylogenetic ANOVA have >populations in both habitats, so in that sense it's "balanced". Where >the species fall on the tree is pretty scattered, throughout the tree >(the tree contains about 20 more species that I did not include in this >analysis, so I don't know if that matters). Just visually glancing at >it, there are two main clades in the tree and 14 come from one clade and >7 come from the other clade, so, if anything, I would think they'd be >more "clumped" than overdispersed. However, I could be wrong. > I would be happy to share the real tree and my data with anyone who is >interested. > > > > > >-Daniel > > > >> Exactly as Liam wrote, except that it is usually uncommon to find real >> data that are "overdispersed phylogenetically," so normally one finds that >> the P values when done phylogenetically are larger (less significant) than >> when done via conventional, non-phylogenetic ANOVA. I'd be curious what >> your data are and how they appear to be scattered across the tips of your >> phylogeny. Are they really overdispersed? >> >> Cheers, >> Ted >> >> Theodore Garland, Jr. >> Professor >> Department of Biology >> University of California, Riverside >> Riverside, CA 92521 >> Office Phone: (951) 827-3524 >> Wet Lab Phone: (951) 827-5724 >> Dry Lab Phone: (951) 827-4026 >> Home Phone: (951) 328-0820 >> Facsimile: (951) 827-4286 = Dept. office (not confidential) >> Email: tgarl...@ucr.edu >> >> Main Departmental page: >> http://www.biology.ucr.edu/people/faculty/Garland.html >> >> List of all Publications: >> http://www.biology.ucr.edu/people/faculty/Garland/GarlandPublications.html >> >> Garland and Rose, 2009 >> http://www.ucpress.edu/books/pages/10604.php >> >> >> ---- Original message ---- >> >> Date: Mon, 14 Mar 2011 16:22:58 -0400 >> From: "Liam J. Revell" <liam.rev...@umb.edu> >> Subject: Re: [R-sig-phylo] Help Interpreting Phylogenetic ANOVA >> Results >> To: dwe...@life.illinois.edu >> Cc: r-sig-phylo@r-project.org >> >> >Hi Dylan. >> > >> >The way the phylogenetic ANOVA (sensu Garland et al. 1993; Syst. >> Biol.) >> >works is by first computing a standard ANOVA, and then comparing >> the >> >observed F to a distribution obtained by simulating on the tree >> under a >> >scenario of no effect of x on y. This "accounts for" the tree in >> the >> >sense that it attempts to account for the possibility that species >> may >> >have similar y conditioned on x because x influences y; or because >> they >> >share common history and are thus similar by virtue of this history >> (and >> >not at all due to x) >> > >> >It is not particularly surprising that your P-value was lower in >> the >> >phylogenetic ANOVA than in your regular ANOVA. In general, the >> effect >> >of the phylogenetic ANOVA on P depends on the distribution of the >> >factor, x. If x is clumped on the tree, than the P-value of a >> >phylogenetic ANOVA will tend to be higher than a regular ANOVA. By >> >contrast, if x is overdispersed phylogenetically, the P-value of >> the >> >phylogenetic ANOVA will tend to be lower than the regular ANOVA. >> > >> >I hope this is of some help. >> > >> >- Liam >> > >> >-- >> >Liam J. Revell >> >University of Massachusetts Boston >> >web: http://faculty.umb.edu/liam.revell/ >> >email: liam.rev...@umb.edu >> >blog: http://phytools.blogspot.com >> > >> >On 3/13/2011 9:28 PM, dwe...@life.illinois.edu wrote: >> >> Hi, >> >> I am relatively new to phylogenetic methods. I'm hoping someone >> can >> >> help me to understand my results. >> >> I am working with a group of 21 species of fish. I want to know >> how >> >> their habitat may influence body shape and whether phylogenetic >> >> relatedness may influence body shape as well. I performed a >> >> phylogenetic ANOVA using the GEIGER package in R. My "metric" of >> body >> >> shape is a PC score. Here's the output: >> >> >> >> Standard ANOVA: >> >> Analysis of Variance Table >> >> >> >> Response: td$data >> >> Df Sum Sq Mean Sq F value Pr(>F) >> >> group 1 4.01 4.0134 0.4595 0.5017 >> >> Residuals 40 349.35 8.7337 >> >> >> >> >> >> Phylogenetic p-value: 0.000999001 >> >> >> >> I'm a bit uncertain as to how to properly interpret the result. I >> think >> >> my confusion is two fold: >> >> >> >> 1. I am not sure I am interpreting what the phylogenetic p-value >> means. >> >> Am I correct in saying that the phylogenetic p-value essentially >> says >> >> that, after "accounting for" phylogeny, the habitat has an effect >> on body >> >> shape (PC1)? >> >> >> >> 2. I am confused as to why it goes from non-significant (in the >> standard >> >> ANOVA) to significant (phylogenetic p-value)? Does it mean that >> the >> >> habitat does not have an effect on body shape if you don't >> consider >> >> phylogenetic relatedness? >> >> >> >> I realize these might be very simple questions but I'd appreciate >> it if >> >> someone can help. I'm not well versed in phylogenetics, so I feel >> a bit >> >> lost. >> >> Please feel free to respond directly to me at >> dwe...@life.illinois.edu. >> >> Thank you! >> >> >> >> >> >> >> >> >> >> -Daniel >> >> >> >> >> >> ----><((((º> -----><((((º> ----><((((º> ----><((((º> >> ----><((((º> ---- >> >> >> >> Daniel P Welsh >> >> University of Illinois at Urbana-Champaign >> >> Champaign, IL, USA >> >> >> >> _______________________________________________ >> >> R-sig-phylo mailing list >> >> R-sig-phylo@r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > >> >_______________________________________________ >> >R-sig-phylo mailing list >> >R-sig-phylo@r-project.org >> >https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > > >---- ><((((º> ----- ><((((º> ---- ><((((º> ---- ><((((º> ---- ><((((º> ---- > >Daniel P Welsh >PhD Student >Teaching Assistant >Department of Animal Biology >University of Illinois at Urbana-Champaign >202 Shelford Vivarium >606 E. Healey Street >Champaign, IL 61821 >lab phone: (217) 333-5323 > _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo