Re: [MORPHMET] allometry and phylogeny

[Joe Felsenstein]

Damienet al. --


>
Thanks a lot for the answer Joe!
> However, I think you need to have species average for using methods like
> independent contrasts and PGLS right? How would you do it for a trajectory
> or series of specimens per species?
>

I not quite sure about the trajectory issue.  However for samples from each
species, when one does not have precise population means, one has to ask
how phylogenetic comparative methods cope with that.   The relevant papers
are by Ives, Midford and Garland (Evolution, 2007) and of course best of
all my own 2008 paper in American Naturalist.  Alas, it is not just a
matter of getting contrasts and then treating those as independent.  I have
options in my PHYLIP program Contrast that can do this case.

"Trajectory", I'm less sure.

Joe

Joe Felsenstein j...@gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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Re: [MORPHMET] allometry and phylogeny

[Damien Esquerre]

Thanks a lot for the answer Joe!
However, I think you need to have species average for using methods like
independent contrasts and PGLS right? How would you do it for a trajectory
or series of specimens per species?

On Thu, Jun 30, 2016 at 11:18 PM, Joe Felsenstein 
wrote:

>
> Damien Esquerre Gheur  wrote:
>
>> Dear morphometricians,
>>
>>
>> I have a pretty big dataset of specimens for most species of pythons
>> encompassing most of the size range for every species. I have been
>> projecting the allometric trajectories and doing pairwise slope comparisons
>> and things like that in Geomorph. However, it seems very obvious that the
>> is a very strong phylogenetic signal in the data, as species within the
>> same clade tend to have parallel trajectories.
>>
> ...
>
>> Would there be a way, for example, to extract a value for the slope and
>> do an ancestral state reconstruction on that? Also, is there a way to
>> incorporate phylogeny in slope comparison models?
>>
>
> I don't know which package of morphometric programs you should use for
> that, but in phylogenetic comparative methods, you can use your tree of N
> species and obtain  N-1  phylogenetic contrasts from your data.  Those can
> then be treated as independent data points, each of which has your full set
> of coordinates.
>
> You could obtain a Generalized Procrustes superposition of your forms,
> without resizing the specimens, then feed the resulting coordinates for
> each species into one of the phylogenetic comparative methods packages.
>
> Joe
> 
> Joe Felsenstein j...@gs.washington.edu
>  Department of Genome Sciences and Department of Biology,
>  University of Washington, Box 355065, Seattle, WA 98195-5065 USA
>
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[MORPHMET] RE: allometry and phylogeny

[Adams, Dean [EEOBS]]

Damien,

Yes, one can take the regression parameters for each species and use these as 
‘tips’ data to obtain ancestral estimates of the regression slope. In this 
case, the species’ data is the multivariate set of slope coefficients for each 
multivariate regression. Thus, the ancestral state of the allometry is also a 
multivariate set of parameters.

Since you are using geomorph the slopes for each species’ allometry trajectory 
may be found in the output list from advanced.procD.lm.

Best,

Dean


Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
   Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

From: Damien Esquerre Gheur [mailto:damien.esque...@anu.edu.au]
Sent: Thursday, June 30, 2016 6:50 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] allometry and phylogeny


Dear morphometricians,



I have a pretty big dataset of specimens for most species of pythons 
encompassing most of the size range for every species. I have been projecting 
the allometric trajectories and doing pairwise slope comparisons and things 
like that in Geomorph. However, it seems very obvious that the is a very strong 
phylogenetic signal in the data, as species within the same clade tend to have 
parallel trajectories.

I have been trying to find a way to analyse this data in a phylogenetic 
framework, and so far I know there is no straightforward solution. I know in 
Adams and Nistri 2010 the trajectories where coded ad isometric and allometric 
and then reconstructed the ancestral states but the case it not so binary with 
my data.

Would there be a way, for example, to extract a value for the slope and do an 
ancestral state reconstruction on that? Also, is there a way to incorporate 
phylogeny in slope comparison models?

Any help would be greatly appreciated


Damien Esquerré
PhD Student, Keogh Lab
Division of Evolution, Ecology and Genetics, Research School of Biology
The Australian National University
44 Daley Road, ACTON ACT 2601, Australia

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Re: [MORPHMET] allometry and phylogeny

[Joe Felsenstein]

Damien Esquerre Gheur  wrote:

> Dear morphometricians,
>
>
> I have a pretty big dataset of specimens for most species of pythons
> encompassing most of the size range for every species. I have been
> projecting the allometric trajectories and doing pairwise slope comparisons
> and things like that in Geomorph. However, it seems very obvious that the
> is a very strong phylogenetic signal in the data, as species within the
> same clade tend to have parallel trajectories.
>
...

> Would there be a way, for example, to extract a value for the slope and do
> an ancestral state reconstruction on that? Also, is there a way to
> incorporate phylogeny in slope comparison models?
>

I don't know which package of morphometric programs you should use for
that, but in phylogenetic comparative methods, you can use your tree of N
species and obtain  N-1  phylogenetic contrasts from your data.  Those can
then be treated as independent data points, each of which has your full set
of coordinates.

You could obtain a Generalized Procrustes superposition of your forms,
without resizing the specimens, then feed the resulting coordinates for
each species into one of the phylogenetic comparative methods packages.

Joe

Joe Felsenstein j...@gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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[MORPHMET] allometry and phylogeny

[Damien Esquerre Gheur]

Dear morphometricians,


I have a pretty big dataset of specimens for most species of pythons 
encompassing most of the size range for every species. I have been projecting 
the allometric trajectories and doing pairwise slope comparisons and things 
like that in Geomorph. However, it seems very obvious that the is a very strong 
phylogenetic signal in the data, as species within the same clade tend to have 
parallel trajectories.

I have been trying to find a way to analyse this data in a phylogenetic 
framework, and so far I know there is no straightforward solution. I know in 
Adams and Nistri 2010 the trajectories where coded ad isometric and allometric 
and then reconstructed the ancestral states but the case it not so binary with 
my data.

Would there be a way, for example, to extract a value for the slope and do an 
ancestral state reconstruction on that? Also, is there a way to incorporate 
phylogeny in slope comparison models?

Any help would be greatly appreciated


Damien Esquerré
PhD Student, Keogh Lab
Division of Evolution, Ecology and Genetics, Research School of Biology
The Australian National University
44 Daley Road, ACTON ACT 2601, Australia

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