Christy,
Yes, the ‘slopes’ component of the output contains the regression parameters
for each species. These can then be used as input for ancestral state
estimation and other down-stream analyses that you have planned.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/<http://www.public.iastate.edu/~dcadams/>
phone: 515-294-3834
From: Christy Hipsley [mailto:chips...@museum.vic.gov.au]
Sent: Tuesday, September 6, 2016 2:00 AM
To: MORPHMET <morphmet@morphometrics.org>
Cc: damien.esque...@anu.edu.au
Subject: [MORPHMET] Re: allometry and phylogeny
To follow up on Damien's question and Dean's response, which values from the
advanced.procD.lm results would one use for reconstructing species ontogenetic
slopes? There are several outputs relating to slope from that test, like
"slopes", "slope.lengths", "slopes.dist", "slopes.angles".
I understand these each describe different parameters of the slope vector like
length and orientation - basically magnitude and direction of shape change per
unit size. So should one reconstruct ancestral states of each of these each
separately to compare with tip taxa?
Thanks for any advice,
Christy
On Friday, July 1, 2016 at 12:31:37 AM UTC+10, dcadams wrote:
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/<http://www.public.iastate.edu/~dcadams/>
phone: 515-294-3834
From: Damien Esquerre Gheur [mailto:damien....@anu.edu.au<javascript:>]
Sent: Thursday, June 30, 2016 6:50 AM
To: morp...@morphometrics.org<javascript:>
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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