Re: [MORPHMET] testing for convergence in 3D shape space

2016-01-27 Thread Tristan Stayton 
Hello Christy,

My R package *convevol* may do exactly what you want it to do - this
package can perform two different types of tests for convergence, both of
which utilize phylogenies and can employ full data sets (of Procrustes
coordinates or any other kind of continuous data).  The two tests are
described here:

Stayton, C.T.  2015.  The definition, recognition, and interpretation of
convergent evolution, and two new measures for quantifying and assessing
the significance of convergence.  Evolution 69:2140-2153.

This is my first package, so if you encounter any trouble or maybe want to
make any changes to customize the tests to your data or questions, please
don't hesitate to contact me!

Cheers,

Tristan

On Wed, Jan 27, 2016 at 12:40 AM, Christy Hipsley <
chips...@museum.vic.gov.au> wrote:

> Dear All,
>
> I'm working with a 3D GM data set and am looking for a specific test of
> convergence that also accounts for phylogeny. After some searching it's
> still not clear to me what is appropriate - so far I only see programs that
> use reduced PC axes as continuous characters, but nothing that uses the
> full Procrustes coordinates. I've applied a phylogenetic ANOVA in Geomorph
> to at least show that after accounting for phylogeny, morphological shape
> is significantly different among ecological groups (in this clade several
> unrelated lineages occur in the same ecological niche).
>
> Does anyone know of a method for testing for convergence across a
> phylogeny using the full shape data or is it always using PC scores? What
> about using scores from a CVA instead, since they are specifically
> addressing the question of differences among the a priori ecological groups
> (and PCA does not)? Could those be mapped onto a phylogeny and modelled in
> terms of BM vs OU, to test if that morphological change is adaptive?
>
> Any advice on these analyses would be appreciated. I'm aware of the
> package Surface but I'm not convinced that is right for my system.
>
> My shape data has a significant phylogenetic signal and I suspect that one
> ecological group in particular is highly convergent.
>
>
> Thanks for any help!
>
> Christy
>
> School of BioSciences
> University of Melbourne
> Parkville VIC 3010, Australia
> Email: chips...@unimelb.edu.au
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
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>



-- 
C. Tristan Stayton
Associate Professor of Biology
Bucknell University
Lewisburg, PA  17837

Office:  570-577-3272

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[MORPHMET] testing for convergence in 3D shape space

2016-01-27 Thread Christy Hipsley 
Dear All,

I'm working with a 3D GM data set and am looking for a specific test of 
convergence that also accounts for phylogeny. After some searching it's still 
not clear to me what is appropriate - so far I only see programs that use 
reduced PC axes as continuous characters, but nothing that uses the full 
Procrustes coordinates. I've applied a phylogenetic ANOVA in Geomorph to at 
least show that after accounting for phylogeny, morphological shape is 
significantly different among ecological groups (in this clade several 
unrelated lineages occur in the same ecological niche). 

Does anyone know of a method for testing for convergence across a phylogeny 
using the full shape data or is it always using PC scores? What about using 
scores from a CVA instead, since they are specifically addressing the question 
of differences among the a priori ecological groups (and PCA does not)? Could 
those be mapped onto a phylogeny and modelled in terms of BM vs OU, to test if 
that morphological change is adaptive?

Any advice on these analyses would be appreciated. I'm aware of the package 
Surface but I'm not convinced that is right for my system.

My shape data has a significant phylogenetic signal and I suspect that one 
ecological group in particular is highly convergent.


Thanks for any help!

Christy

School of BioSciences  
University of Melbourne 
Parkville VIC 3010, Australia
Email: chips...@unimelb.edu.au

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Re: [MORPHMET] testing for convergence in 3D shape space

2016-01-27 Thread Paolo Piras 
Hi!
maybe these are inherent


*Piras P.,* Sansalone G., Teresi L., Kotsakis T., Colangelo P. & Loy A.
(2012) - Testing convergent and parallel adaptations of talpids humerus
mechanical performance by means of Geometric Morphometrics and Finite
Element Analysis. *Journal of Morphology*, 273: 696-711.
*Piras P.,* Sansalone G., Teresi L., Moscato M., Profico A., Eng R., Cox T.
C., Loy A., Colangelo P. & Kotsakis T. (2015) - Digging adaptation in
insectivorous subterranean eutherians. The enigma of *Mesoscalops
montanensis* unveiled by geometric morphometrics and finite element
analysis. *Journal of Morphology*, 276: 1157–1171.

ciao
paolo

2016-01-27 6:40 GMT+01:00 Christy Hipsley :

> Dear All,
>
> I'm working with a 3D GM data set and am looking for a specific test of
> convergence that also accounts for phylogeny. After some searching it's
> still not clear to me what is appropriate - so far I only see programs that
> use reduced PC axes as continuous characters, but nothing that uses the
> full Procrustes coordinates. I've applied a phylogenetic ANOVA in Geomorph
> to at least show that after accounting for phylogeny, morphological shape
> is significantly different among ecological groups (in this clade several
> unrelated lineages occur in the same ecological niche).
>
> Does anyone know of a method for testing for convergence across a
> phylogeny using the full shape data or is it always using PC scores? What
> about using scores from a CVA instead, since they are specifically
> addressing the question of differences among the a priori ecological groups
> (and PCA does not)? Could those be mapped onto a phylogeny and modelled in
> terms of BM vs OU, to test if that morphological change is adaptive?
>
> Any advice on these analyses would be appreciated. I'm aware of the
> package Surface but I'm not convinced that is right for my system.
>
> My shape data has a significant phylogenetic signal and I suspect that one
> ecological group in particular is highly convergent.
>
>
> Thanks for any help!
>
> Christy
>
> School of BioSciences
> University of Melbourne
> Parkville VIC 3010, Australia
> Email: chips...@unimelb.edu.au
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>

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