[phylocom-user] problem calculating phylogenetic signal

Susan Letcher susan.letcher at ots.ac.cr
Fri Oct 29 10:53:52 PDT 2010


I think I figured it out. for some reason, AOT doesn't work unless there are
=> 3 columns of traits in the traits file. I just added two more columns of
randomly generated "trait data," and the calculations work! It might be
worth putting a note in the manual that trait files must contain at least
three columns of data. 

 

Thanks for your help!

 

From: David Ackerly [mailto:dackerly at berkeley.edu] 
Sent: Monday, October 25, 2010 1:20 PM
To: Susan Letcher
Subject: Re: [phylocom-user] problem calculating phylogenetic signal

 

Hi Susan,

 

Just as a check, have you run the test files distributed with the program?
The VarContr = 0 and the contrasts of 0 suggest that somehow the program is
entering all the data as identical values - I don't think I've seen this
happen. Can you send your tree and trait files for a quick look?


David Ackerly

dackerly at berkeley.edu

 

On Oct 25, 2010, at 10:56 AM, Susan Letcher wrote:





 

Hi all,

 

I am having trouble with the aot module. I'm trying to determine whether
there is phylogenetic signal in a set of functional traits. For each trait
(e.g., wood density), I have a phylo file containing the species for which I
have data, and a trait file with the data. I am using

 

phylocom aotf -f myphylo.txt -t wdtrait.txt >results.txt

 

(I have tried it with and without the -x 1 switch, and it doesn't make a
difference.)

 

The trait file header is set up correctly, as far as I can tell:

 

type <tab>       3 <return>

name    <tab> WD <return>

[data]

 

In the output, I get values that look reasonable in the first table ("Trait
conservatism by node"). In the second table, though, I get zeros for every
contrast value, and the output for "Phylogenetic signal" looks like this:

 


Trait<tab>

NTaxa<tab>

VarContr<tab>

VarCn.rankLow<tab>

VarCn.rankHi<ret>


traitA<tab>

254<tab>

0<tab>

1000<tab>

1000<ret>

 

As far as I understand from reading the manual and examining the results of
studies that have used aot, it should be possible to calculate independent
contrasts and phylogenetic signal in a univariate context to ask whether a
single trait is conserved across the entire phylogeny. Am I wrong, or is
soemthing wrong with the way I'm conducting the analysis?

 

I have checked the tree for zero-length branches, so I don't think the
problem arises from that. Any input would be welcome.

 

Thanks in advance,

 

Susan G. Letcher

Resident Professor

Organization for Tropical Studies
Apartado Postal 676-2050
San Pedro de Montes de Oca, Costa Rica 
tel. 506-2524-0607 ext. 1542 
fax 506-2524-0608

 

 

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