Ted makes an important distinction, but I think that in both situations
you can use GLS since the variance-covariance matrix among all nodes
(internal and terminal) of the phylogeny can be computed. The formulae
are in Martins & Hansen (1997, Am Nat) and used internally in some
functions in ape.
tgarl...@ucr.edu wrote on 28/10/2009 14:43:
Do you only have phenontypic data at the tips of the phylogeny, or were the lineages also
phenotyped "along the way" e.g., at the time of some of the bifurcations? If the former,
then it seems like a straightforward phylogenetic analysis (unless I am missing
something). If the latter, then it is more complicated.
I guess that Ivo's problem falls in the former. In that case there is
indeed no problem in using phylogeny-based comparative methods, even
though the tips of the tree are not contemporaneous. Standard functions
in ape can be used.
Emmanuel
Cheers,
Ted
Theodore Garland, Jr., Ph.D.
Professor
Department of Biology
University of California
Riverside, CA 92521
Phone: (951) 827-3524 = Ted's office (with answering machine)
Phone: (951) 827-5724 = Ted's lab
Phone: (951) 827-5903 = Dept. office
Home Phone: (951) 328-0820
FAX: (951) 827-4286 = Dept. office
Email: tgarl...@ucr.edu
http://biology.ucr.edu/people/faculty/Garland.html
List of all publications with PDF files:
http://biology.ucr.edu/people/faculty/Garland/GarlandPublications.html
Garland, T., Jr., and M. R. Rose, eds. 2009. Experimental evolution: concepts, methods,
and applications of selection experiments. University of California Press, Berkeley,
California.
http://www.ucpress.edu/books/pages/10604.php
Associate Director
Network for Experimental Research on Evolution
http://nere.bio.uci.edu/
(A University of California Multicampus Research Project)
---- Original message ----
Date: Wed, 28 Oct 2009 11:42:25 +0000
From: r-sig-phylo-boun...@r-project.org (on behalf of Ivo Mimoso
<ivon...@gmail.com>)
Subject: [R-sig-phylo] Repeated measures on Phylogenies
To: r-sig-phylo@r-project.org
Dear all,
I'm trying to get the association between two variables (one is allele
frequency and the other is a phenotype) that evolved experimentally under a
given phylogeny. In the terminal nodes of the tree the different populations
were analyzed at different time points (generations).
I'm afraid that although "standard" phylogenetic comparative methods can
correct for experimental correlation they may fail in comparing different
time trends for the different populations.
I see this as a repeated measures experiment where the populations are
related through a phylogeny, in the sense of Guo et al. 2007 MBE paper.
Does anyone know if there is an implementation of this in the "R world", or
if this approach makes sense to you at all?
cheers,
Ivo M. Chelo, PhD.
Evolutionary Genetics
IGC Instituto Gulbenkian de Ci�ncia
Lisbon, Portugal
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Emmanuel Paradis
IRD, Montpellier, France
ph: +33 (0)4 67 16 64 47
fax: +33 (0)4 67 16 64 40
http://ape.mpl.ird.fr/
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