----- Forwarded message from Joe Felsenstein <[email protected]> -----
Date: Wed, 4 Dec 2013 10:03:10 -0500
From: Joe Felsenstein <[email protected]>
Reply-To: Joe Felsenstein <[email protected]>
Subject: Re: Discussion on GM and phylogeny
To: [email protected]
In reply to Shobnom Ferdous, who asked:
>> Why we cant incorporate a morphological
>> phylogeny or Geometric morphometrics analysis,
>> Molecular phylogeny all together to get a
>> phylogeny for a particular group, rather we use
>> a molecular phylogeny and overlay that with GM
>> work? I have read the related papers but some
>> discussion is much appreciated.
Aki Watanabe said:
> Geometric morphometrics can be incorporated
> as characters in a phylogenetic analysis (see
> Goloboff and Catalano papers in the journal
> Cladistics for parsimony analysis of aligned GM
> data), but I don't think it has been implemented
> in maximum likelihood or Bayesian analysis
> before perhaps because choosing probabilistic
> and prior distribution models for evolution of
> landmark data is a tricky issue.
>
> That said, I personally prefer NOT to use GM
> data as phylogenetic data because of few
> reasons: (1) phylogenetic characters need to be
> independent of each other, but landmarks that
> are close together will likely not be
> independent; (2) it is suspicious that
> individual landmarks appropriate evolutionary
> units, especially whether "geometrically or
> functionally" homologous landmarks are
> "evolutionarily" homologous; and (3) if x, y,
> (and z) coordinates of each landmark are taken
> as separate characters, then the result will be
> dependent on the orientation of the specimens
> after alignment (Goloboff and Catalano's method
> treats each landmark as character so this
> problem doesn't apply to their method).
A few comments: People have been using landmark
coordinates (appropriately superposed) in
phylogenetic comparative methods since at least
2002. Those methods are based on Brownian
Motion models of correlated quantitative characters,
using likelihood inference. Bayesian inference
is possible for that too. Of course, the
characters covary -- in fact, inferring those
covariances is the whole point in that case.
For GM coordinates or in fact for any quantitative
traits, it is not appropriate to use them for
inferring phylogenies unless you have some way
of dealing with the covariances. Assuming that
they are i.i.d. is bad statistical practice, as
Watanabe sees.
This applies to Goloboff and Catalano's method
if that method is considered to be making a
statistical inference. But if G&C intend some
other philosophical framework then all that
need be noted is that their method might be
philosophically mandated ... but that does not
settle what are its statistical properties.
Joe
----
Joe Felsenstein [email protected]
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
----- End forwarded message -----
