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 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
