Molecular taxonomy: on way out?

[John Grehan]

I received the following comments from one individual who felt for
whatever reason that they were not for the list, but I felt that a
couple of response may help clarify to others my point of view.

> My point is there is, methodologically, no problem with including
> plesiomorphic characters ( meaning character states that are
> plesiomorphic for your ingroup but derived for your outgroup) because
> by definition these states CANNOT support relationships in modern
> analyses. 

This is the crux of the matter in that my point about using algorithms
to 'decide' which characters are derived becomes an artifact of the
algorithm making assumptions about the character states in the outgroup
being primitive. The result for molecular genetics is that characters
that are really primitive may be treated as being derived and there
seems to be no independent test of the choice because the sequences
cannot be shown to be primitive or derived in the first place sequence
by sequence (at least that is my understanding and I am interested to be
shown to be wrong).

Only in phenetic analyses can a plesiomorphy 'support' a
> group - but modern molecular phylogenetics are not phenetic.

They are if they treat plesiomorphies as synapomorphies as an artifact
of the analysis.

> Plesiomorphic characters never support groups, only apomorphic states
> do. 

Agreed - which is why analyses need to be limited to characters that one
can make a case for being derived in the first place. You can do that
with morphology (anyone using unordered characters in morphology is, in
my opinion, saying that they don't understand the character
distribution).

> Plesiomorphies are IGNORED by the algorithms...

Not if they are treated as apomorpies.

John Grehan