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
Post by t***@ucr.eduExactly 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)
http://www.biology.ucr.edu/people/faculty/Garland.html
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
Subject: Re: [R-sig-phylo] Help Interpreting Phylogenetic ANOVA
Results
Post by Liam J. RevellHi Dylan.
The way the phylogenetic ANOVA (sensu Garland et al. 1993; Syst.
Biol.)
Post by Liam J. Revellworks is by first computing a standard ANOVA, and then comparing
the
Post by Liam J. Revellobserved F to a distribution obtained by simulating on the tree
under a
Post by Liam J. Revellscenario of no effect of x on y. This "accounts for" the tree in
the
Post by Liam J. Revellsense that it attempts to account for the possibility that species
may
Post by Liam J. Revellhave similar y conditioned on x because x influences y; or because
they
Post by Liam J. Revellshare common history and are thus similar by virtue of this history
(and
Post by Liam J. Revellnot at all due to x)
It is not particularly surprising that your P-value was lower in
the
Post by Liam J. Revellphylogenetic ANOVA than in your regular ANOVA. In general, the
effect
Post by Liam J. Revellof 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
Post by Liam J. Revellphylogenetic 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/
blog: http://phytools.blogspot.com
Hi,
I am relatively new to phylogenetic methods. I'm hoping someone
can
Post by Liam J. Revellhelp me to understand my results.
I am working with a group of 21 species of fish. I want to know
how
Post by Liam J. Revelltheir 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
Post by Liam J. RevellAnalysis 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
Post by Liam J. Revell1. I am not sure I am interpreting what the phylogenetic p-value
means.
Post by Liam J. RevellAm I correct in saying that the phylogenetic p-value essentially
says
Post by Liam J. Revellthat, after "accounting for" phylogeny, the habitat has an effect
on body
Post by Liam J. Revellshape (PC1)?
2. I am confused as to why it goes from non-significant (in the
standard
Post by Liam J. RevellANOVA) to significant (phylogenetic p-value)? Does it mean that
the
Post by Liam J. Revellhabitat does not have an effect on body shape if you don't
consider
Post by Liam J. Revellphylogenetic relatedness?
I realize these might be very simple questions but I'd appreciate
it if
Post by Liam J. Revellsomeone can help. I'm not well versed in phylogenetics, so I feel
a bit
Post by Liam J. Revelllost.
Please feel free to respond directly to me at
Thank you!
-Daniel
----><((((º> -----><((((º> ----><((((º> ----><((((º>
----><((((º> ----
Post by Liam J. RevellDaniel P Welsh
University of Illinois at Urbana-Champaign
Champaign, IL, USA
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---- ><((((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