Richard Jensen rjensen at SAINTMARYS.EDU
Fri Jun 18 08:15:25 CDT 2004

John Grehan wrote:

> > From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
> > Behalf Of Richard Jensen
> >
> > 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.
> I think I see your perspective. I could restate my view to say that
> characters that are not limited to potential apomorphies through
> individual evaluation will result in analysis that represents overall
> similarity rather than necessarily phylogenetic relationship.

Only if a "phenetic" protocol, such as creating a matrix of Euclidean
distances among the taxa and using those distances for UPGMA cluster
analysis, is used.  Submitting the matrix of characters to a maximum
parsimony algorithm is not a phenetic analysis and does not yield a result
based on overall similarity.  It yields a result that is cladistic in the
sense that, whether you agree them or not, the outgroup determines what the
synapomorphies will be.  It may be bad cladistics (poorly chosen outgroup),
but it not based on overall similarity.

> > 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.
> Yes one can apply different alogorithms, but characters that are not
> limited to predicted apmorphies will not result in a cladistic phylogeny
> no matter that a cladistic algorithm is applied since one cannot
> construct patterns of nested synapomorphies from characters that are of
> themselves not apomorphies even though they may be presented as if they
> are.

I believe Pierre has already addressed this point of confusion.  In an
objective analysis, every character state (with the exceptions of those that
are invariant among the taxa, and those are unique to a single taxon) is a
potential synapomorphy (referring to them as "predicted apomorphies" implies
that you are weighting characters by some exteranl criterion) and the
algorithm will provide a pattern of cladistic relationships in the ingroup
based on the character states in the outgroup(s).  I think a problem here is
that you are deciding, a priori, which characters are to be included; that
introduces a bias that will clearly dictate the realtionships in the
output.  I don't see such a procedure is an objective approach.

> 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.
> Actually I don't have to accept anything(and neither do you of
> course)any more than I have to accept Darwinism simply because nearly
> everyone practices it. In this case I don't accept your assertion
> because I do not see it working in what I see as the real world of
> cladistics. Yes I might be wrong, and so may you.

Yes, you don't have to accept it.  You appear to have an eccentric view of
the "real world of cladistics" that is incommensurable with the way
cladistics is practiced by most systematists.  Neither of us has to accept
that fact that there is a unique solution to a particular mathematical
problem, either.  But we will be wrong if we reject that the existence of
such a solution.  Just because you don't accept that fact that relationships
based on overall similarity (i.e., phenetic relationships) are not produced
by cladistic algorithms, that doesn't mean it isn't so.  But it does suggest
that you don't understand the fundamental differences between the different
kinds of analyses.

> >
> > 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."
> I doubt anything fundamental is being overlooked - just a reflection of
> a different history of exposure to the subject.
>  snip...
> So one may take the total number of characters shared between humans and
> great apes and do a 'cladistic' analysis by rooting with some other
> taxon (actually a case where this was done recently using the orangutan
> as the outgroup because that assignment was beyond question) and make a
> cladogram out of it. But that cladogram does not represent a nested set
> of synapomorphies even though the characters may be treated as if they
> were. It seems to me it would be a case of garbage in, garbage out.

The cladogram does represent a hypothetical set of nested synapomorphies.
You may reject the hypotheses for any one or more of the individual
characters.  If the characters have been miscoded or represent clearly
misinterpreted states (i.e., are not reasonable homologies) then I agree,
garbage in, garbage out.  But, if you reject them, you must be able to
provide an objectively-based rationale for doing so.


> John Grehan

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

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