-------- Original Message --------
Subject: Re: approach to compare similarity of morphological integration
and phylogenetic distance in MorphoJ
Date: Sun, 22 Aug 2010 21:52:20 +0100
From: Chris Klingenberg <[email protected]>
Reply-To: [email protected]
Organization: University of Manchester
To: morphmet <[email protected]>
Dear Daniela
So far, I am not aware that anyone has looked into the evolution of
integration patterns very seriously. There is not a lot of theory on how
covariance structures evolve on a phylogeny, and what's out there is not
overly helpful. That is the primary reason why there is nothing in
MorphoJ on this (the other reason is that I haven't yet gotten around to
work on some ideas I've been sitting on for some time).
The existing theory is about the evolution of phenotypic means. In the
context of geometric morphometrics, that is the evolution of average
shapes and average centroid sizes. For more information on this, see the
following recent paper:
Klingenberg, C. P., and N. A. Gidaszewski. 2010. Testing and quantifying
phylogenetic signals and homoplasy in morphometric data. Syst. Biol.
59:245–261.
The evolution of integration is a different kettle of fish. Along the
lines that you mention, I could see that you could look for a
phylogenetic signal by computing a measure of dissimilarity between the
covariance matrices (e.g. one minus the matrix correlation, as in Debat
et al. 2006) or a different measure of similarity such as those of
Mitteroecker and Bookstein (2009) or Dryden et al. (2009), and then
relating a matrix of dissimilarities of integration among species to a
matrix of phylogenetic distances (separation on the tree). The different
measures of covariance matrix dissimilarity focus on different aspects
of the covariance matrices (e.g. they may or may not respond to changes
in overall scale), and therefore different measures are likely to
produce different results. No systematic comparison of the different
measures exists, so that it is difficult to say what those differences
from a biological point of view. Moreover, note that this approach
throws away a lot of information when collapsing the relationships
between covariance matrices into a single index for each comparison and
that the comparison between the integration dissimilarity matrix and the
phylogenetic distance matrix is subject to the critiques of the Mantel
test made by Fred Bookstein on Morphmet some time ago and the more
recent ones by Harmon and Glor (2010).
Debat, V., C. C. Milton, S. Rutherford, C. P. Klingenberg, and A. A.
Hoffmann. 2006. Hsp90 and the quantitative variation of wing shape in
Drosophila melanogaster. Evolution 60:2529–2538.
Dryden, I. L., A. Koloydenko, and D. Zhou. 2009. Non-Euclidean
statistics for covariance matrices, with applications to diffusion
tensor imaging. Ann. Appl. Stat. 3:1102–1123.
Harmon, L. J., and R. E. Glor. 2010. Poor statistical performance of the
Mantel test in phylogenetic comparative analyses. Evolution 64:2173–2178.
Mitteroecker, P., and F. L. Bookstein. 2009. The ontogenetic trajectory
of the phenotypic covariance matrix, with examples from craniofacial
shape in rats and humans. Evolution 63:727–737.
With MorphoJ, you can compute the matrix correlation, but then you have
to compute the dissimilarity matrix etc. in other software.
You mention that you use the symmetric and asymmetry components from the
analysis of object symmetry. This is biologically very informative, but
add complications because the two components inhabit mutually orthogonal
subspaces in shape tangent space. That causes trouble if you want to
compare the patterns of integration between the symmetry and asymmetry
components. For the matrix correlation, MorphoJ automatically makes the
adjustments outlined in Klingenberg et al. (2002). For other distance
measures of covariance matrices (Mitteroecker & Bookstein, Dryden et
al.), similar adjustment should be considered in that context.
Klingenberg, C. P., M. Barluenga, and A. Meyer. 2002. Shape analysis of
symmetric structures: quantifying variation among individuals and
asymmetry. Evolution 56:1909–1920.
I hope this helps.
Best wishes,
Chris
On 8/22/2010 3:55 PM, morphmet wrote:
-------- Original Message --------
Subject: approach to compare similarity of morphological integration and
phylogenetic distance in MorphoJ
Date: Thu, 12 Aug 2010 12:20:52 -0400
From: Daniela Sanfelice <[email protected]>
To: [email protected]
Hi!
We are investigating morphological integration in pinniped skulls using
3D data and mostly MorphoJ. Presently we would like to do a comparison
of similarity of integration and phylogenetic distance. Is it possible
to do in MorphoJ?
I mean, we know that using "Map onto Phylogeny" it is possible to
reconstruct the history of change in the traits of interest or to
account for the effects of phylogeny in a study about processes of
evolution. But what about integration and phylogenetical signal?
Besides multi-Rv analysis and stuff, we also calculated the covariance
matrix for the symmetric and assymetric components of each species.
After that we calculated the correlation matrix between pairs of species
(for both, symmetric and asymmetric component). We also have the nexus
files with the phylogenies...
Many thanks in advance for your kind collaboration.
Cheers, Daniela Sanfelice.
--
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Christian Peter Klingenberg
Faculty of Life Sciences
The University of Manchester
Michael Smith Building
Oxford Road
Manchester M13 9PT
United Kingdom
Telephone: +44 161 275 3899
Fax: +44 161 275 5082
E-mail: [email protected]
Web: http://www.flywings.org.uk
Skype: chris_klingenberg
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