Characters.

[John Grehan]

Richard Jensen wrote:

It may be bad cladistics (poorly chosen
> outgroup),
> but it not based on overall similarity.

I will disagree on that. If the characters were all cladistic (all
proposed apomorphies) it seems to me that a parsimony analysis would
result in an overall similarity of the most parsimonious set of
synapomorphies. Since the synapomorphies are themselves apomorphies at
the outset then I can see the result being cladistic (tracking
phylogenetic sequence of differentiation). If the characters are
phenetic (giving overall similarity due to the failure to properly
identify and restrict characters to apomorphies) the result will be
phenetic - a measure of overall similarity that does not have any
necessary relationship to phylogeny. At least that's how I see the
situation.

> > > 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.

Ok, but I argue that it makes a difference at the outset if the original
data matrix was not restricted to apomorphies that are evaluated
character by character.

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) 

I would agree with that, but my contention is that in the human
phylogeny question there are characters that are treated as cladistic in
the analysis by imposition of an outgroup while they may in actual fact
not be apomorphic at all (i.e. they are misdiagnosed as apomorphies). It
is this misdiagnosis that I suspect is the case in molecular studies.

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.

In one sense there is nothing purely 'objective' in science outside
pre-dtermined parameters should one accept those parameters in the first
place. Recipes are objective once their criteria are set, setting those
criteria are not objective in the sense that they are the result of
one's judgment of the evidence and what constitutes relevant evidence in
the first place.

> 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.  

This is interesting in that eccentric is being defined as what is not
practiced by most practitioners. I guess I would then have to agree that
I am eccentric. So was Darwin in his time. So was Croizat etc. Thanks
for the compliment!

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.  

Unless it is not a fact in the first place.

But it does
> suggest
> that you don't understand the fundamental differences between the
> different
> kinds of analyses.

It only suggests that we have a different understanding.

> >
> > 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.

Only if the characters are apomorphies in the first place. By assuming,
for example, that orangutans were the outgroup, characters were
polarized such that they were treated as apomorphies whereas in actual
fact they might not be.

But, if you reject them, you must be able to
> provide an objectively-based rationale for doing so.

Sure, or at least provide a testable argument (i.e. identify what
constitutes the evidence for making that decision that others can refer
to and make their determination.

John Grehan


John R. Grehan
Director of Science and Collections
Buffalo Museum of Science
1020 Humboldt Parkway
Buffalo, NY 14211-1193
email: jgrehan at sciencebuff.org
Phone: (716) 896-5200 ext 372
 
http://www.sciencebuff.org/biogeography/Panbiogeography/Panbiogeography-
Gate.htm
http://www.sciencebuff.org/primates/Human%20origins/Humanorigins.htm
http://www.sciencebuff.org/HepialidaeGate.htm