[R-sig-phylo] Help Interpreting Phylogenetic ANOVA Results

dwelsh at life.illinois.edu dwelsh at life.illinois.edu
Wed Mar 16 21:38:54 CET 2011


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:  tgarland at 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.revell at umb.edu>
>     Subject: Re: [R-sig-phylo] Help Interpreting Phylogenetic ANOVA
>     Results
>     To: dwelsh at life.illinois.edu
>     Cc: r-sig-phylo at 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.revell at umb.edu
>     >blog: http://phytools.blogspot.com
>     >
>     >On 3/13/2011 9:28 PM, dwelsh at 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
>     dwelsh at 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 at r-project.org
>     >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>     >
>     >_______________________________________________
>     >R-sig-phylo mailing list
>     >R-sig-phylo at 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



More information about the R-sig-phylo mailing list