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RE: Unified Cladistics

> From: owner-dinosaur@usc.edu [mailto:owner-dinosaur@usc.edu]On Behalf Of
> Betty Cunningham
> I assumed fixing the parts of a cladogram that change with every user
> (the character data) by making a global data set of the characters that
> describes each species would give us reproduceable results no matter who
> tests the shape of the tree (cladistics).  I thought that was the
> point.
> But now somebody says in plain words that this sort of 'formulation and
> testing' is not one of the goals of cladistic?
> I mean, really what's the point?  Now I'm confused.

Okay, I'll try to unconfuse you (I hope).

In the grandest of terms, the goal of phylogenetic systematics is the
estimation (to the best of our abilities) the branching order of the Tree of

However, this is about the same as saying "astronomy is the study of the
universe": while true, it doesn't address the practicalities of the field.
In practice, astronomy proceeds from each little tidbit learned from each
particular observational experiment.

In phylogenetic systematics, we want to uncover the Tree of Life, but we
have to work at it piece by piece and bit by bit.  Sometimes the experiment
in question covers Very Big relationships (the phylogeny within all
eukaryotes, for instance); at other times, it can be more specific (i.e.,
the relationships between species of woodpeckers).

To address a specific aspect of your question, though:
> a global data set of the characters that
> describes each species would give us reproduceable results no matter who
> tests the shape of the tree

A given data set run using EXACTLY the same taxon/character matrix and
EXACTLY the same ordering, outgroup, etc. parameters will produce EXACTLY
the same result.

In the past reviewers of papers have tended not to run said matricies while
editing a manuscript, and after the papers get published people find out
that they cannot duplicate the results published.  This is at least in part
due to typos in the matrix tables in the manuscripts.  (I strongly recommend
that anyone reviewing manuscripts put the matrix into a MacClade or PAUP or
Hennig file and run the test yourself under the conditions specified to make
sure the results in the Results section really are the results of the test!
I've managed to find a couple of typos in different papers in the past this

However, as I stated in the previous posting, describing _Archaeopteryx_ in
the context of amniotes in general is different from describing
_Archaeopteryx_ in the context of other primitive eumaniraptorans.  Features
which would be non-informative in the first study (i.e., the process on the
posterior surface of the proximal portion of the ischium) become much more
important in the second.  In technical terms, it would be an autapomorphy in
the first study, and potential synapomorphy in the second.

To think about it another way: in a study trying to find out if
tyrannosaurids are closer to  echinoderms than to nematodes, the
arctometatarsus and the maxillary fenestra are useless characters; in trying
to find out if tyrannosaurids are closer to ornithomimids than to
spinosaurids, they are very important characters.

Note that BOTH types of study are important!!  We *need* the big scale
studies to establish general patterns, and the small scale studies to
determine the specifics.  Because of computational limits, you can't put the
data of all specimens of all organisms at all growth stages into a computer
and generate results.  That doesn't mean that the results we get with more
limited studies aren't useful.

(By the same token, we can still generate useful morphometric information
about, for example, human populations without having to go out with sets of
calipers and measuring every single human that has ever lived!).

For people who still wonder something about how phylogenetic systematics
operates, you can always check out:
http://www.ucmp.berkeley.edu/clad/clad4.html or similar sites elsewhere.

                Thomas R. Holtz, Jr.
                Vertebrate Paleontologist
Department of Geology           Director, Earth, Life & Time Program
University of Maryland          College Park Scholars
                College Park, MD  20742
Phone:  301-405-4084    Email:  tholtz@geol.umd.edu
Fax (Geol):  301-314-9661       Fax (CPS-ELT): 301-314-7843