Characters.

[Richard Jensen]

John Grehan wrote:

Jensen wrote:

> > I assume (and you will correct me if I'm wrong) that your comment
> about
> > certain practices not conforming refers to analyses of molecular data.
> If
> > someone compiles a matrix of putative molecular homologies, and
> applies a
> > maximum parsimony algorithm, then that is not, no matter what some
> cladist
> > might tell you, a phenetic analysis.  It simply does not conform to
> what
> > phenetics is.

Grehan replied:

>
>
> It does if the characters represent overall similarity - that the
> homologies used to select the characters for analysis are not limited to
> apomorphies.
>

This reply is proof that you are choosing to ignore a fundamental fact of
taxonomic analysis: characters do not represent overall similarity.  Overall
similarity is a function of the way the characters are analyzed and has
nothing to do with the methods by which characters are defined or coded.  As
several of us have repeatedly emphasized, the same data matrix my be used to
construct either phenetic (i.e., overall similarity) or cladistic (i.e.,
patterns of nested synapomorphies) relationships.  This is something you
just have to accept (sort of like gravity) - you can't ignore it or explain
it away by special pleading or ignorance.

I will admit that I may be overlooking something very fundamental.  So,
please explain to me how a character (or a set of characters) can "represent
overall similarity."

Dick



--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen