[Taxacom] Fish phylogenetics paper

[Karl Magnacca]

On Wed, May 12, 2010 1:06 pm, Bob Mesibov wrote:
> Hi, Karl.
>
> So you didn't find the discussion on characters and homology
> interesting?

Not really; not so much because I don't think that people shouldn't
look for molecular synapomorphies (I do all the time), but because
of they seem to feel that subjective "thinking-out" of characters is
superior to optimization analysis.  While that may be true for some
things - for example, in a case where an exceptionally strong
morphological character conflicts with a weak molecular dataset -
it's not a *substitute* for analyzing aggregate data, which appears
to be what they advocate.  Somehow or other, there has to be a way
to resolve conflict among characters that isn't dependent on the
whims of the observer.

I admit that I sent off my first response a little too quickly.  But
after having read it a bit more, I don't find it any more
compelling.

> OK, so the characters (columns) are now defined. Now what? Well, in
> morphology structures don't evolve from nothing, and changes (even
> when drastic) have observable roots in pre-existing structures. In
> sequences, character state changes aren't like that. It's possible
> for any nucleotide to change into any other nucleotide. There are
> constraints, but we don't know what they are at any given position.
> Instead we have a zoo of models which give transition probabilities
> (that's mathematical transition, not transition/transversion
> transition), and fudge factors for autocorrelation along the
> sequence.

The exact same constraints exist for morphological constraints; the
difference is that the transition probability models are much too
complex to understand, let alone implement.  As a result, highly
subjective things like weighting are the only "modelling" available
to give a balanced picture of how things actually evolve.  IMO,
that's an advantage of molecular phylogenetics.

Karl

PS - sorry if I don't respond for the next couple of days, I'll be
off in the real world!
=====================
Karl Magnacca
Postdoctoral Researcher
University of Hawaii-Hilo