-------- Original Message --------
Subject: Re: Testing morphology for stasis
Date: Mon, 23 May 2011 10:15:41 -0400
From: Dean Adams <[email protected]>
To: [email protected]
Joe,
I agree that comparing the fit of distinct models of evolution to the
data and the phylogeny is one means to accomplish this. Evidence that
your data fit an OU model with a single optimum (over say, a BM model)
is consistent with the hypothesis of stasis, or at least stabilizing
selection to a single adaptive peak.
For multivariate data, comparing an OU vs. a BM model in R requires the
package OUCH. The package Geiger can also compare evolutionary models,
but does so only for single, univariate traits. If you provide it a data
matrix, Geiger will fit models for each column separately. However, for
shape, one requires a simultaneous assessment across all columns of this
multi-dimensional trait. Geiger cannot do this, but OUCH can.
You might also take the more 'paleontologically-driven' approach of
comparing changes in the distribution of morphological variation across
time steps, as suggested by Paolo and exemplified in his 2009 paper.
Recent methods for this are found in Woods et al. 2007 (cited in Paolo's
paper). For earlier discussions on this topic I also highly suggest you
take a look at Bookstein 1987.
Best,
Dean
--
Dr. Dean C. Adams
Associate Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
Ames, Iowa
50011
www.public.iastate.edu/~dcadams/
phone: 515-294-3834
On 5/23/2011 5:10 AM, morphmet wrote:
-------- Original Message --------
Subject: Re: Testing morphology for stasis
Date: Mon, 23 May 2011 03:33:19 -0400
From: Manabu Sakamoto<[email protected]>
To: [email protected]
Dear Joe,
I don't know if you are familiar with the statistics software R, but
there is a package for it called "geiger" that has functions to test for
possible models of character evolution across a given phylogeny,
including stasis, Brownian, Ornstein-Uhlenbeck, and trended. Perhaps you
could check it out?
kind regards,
Manabu
Manabu Sakamoto, PhD
Postdoctoral Research Associate
School of Earth Sciences
University of Bristol
Bristol, UK, BS8 1RJ
Tel: +44 (0) 117 954 5421
Fax: +44 (0)117 925 3385
Email: [email protected]
On 23 May 2011, at 06:56, morphmet wrote:
-------- Original Message --------
Subject: Testing morphology for stasis
Date: Fri, 20 May 2011 10:53:59 -0400
From: OWEN J.T.D.<[email protected]>
To: <[email protected]>
Dear morphmet,
I have a 3D dataset where I have been comparing morphology and phylogeny
at family level (suiforms). Specifically I have generated a phenogram
(based on procrustes distances) to compare and contrast with the family
phylogeny. The phenogram is lacking in some sub-species but has
representatives for the genus we are examining (the suids, the phylogeny
also uses Hippopotamus and Peccary as outgroups which we do not have).
I have genetically divergent but morphologically similar populations;
based on prior knowledge of species history, habitat and diet homoplasy
is deemed unlikely and as such I wish to test the dataset for stasis.
I was wondering if anyone knows of methods by which I could assess
stasis based on congruence between morphological and genetic
relationships, or point me in the direction of papers where this has
been done.
Thanks in advance
Joe
-----------------------------
Joseph Owen
PhD Research
Departments of Anthropology and Archaeology
University of Durham
