Re: Martin 2004 critique (somewhat lengthy)

[David Marjanovic <david.marjanovic@gmx.at>]

> <You are using "cladistics" as the overarching expression for both 
> cladistics
> and phenetics. This is incorrect.>
>
>  Cladistics has nothing to do with phylogeny, and it seems that the 
> continuing
> issue of confusion that it does have something to do with phylogeny 
> implicitly
> may be why so many are adverse to using it as a tool. Cladistics, like 
> hand
> clading, is simply a tool used to find a topology, either via parsimony,
> likelihood, or other algorithms.

Parsimony and likelihood methods -- together: cladistics -- don't make any 
sense except in phylogenetics. Neighbor-joining, UPGMA, WPGMA and so on, on 
the other hand, are not cladistics -- they are phenetics. It follows that 
cladistics is the tool to find a phylogeny.

> As I noted before, application of the saem
> software can be used to create a data matrix of just about anything and 
> find
> best-fit matches. This results in a graphical output of closest-match 
> versus
> farthest-match in the same data set based on the input.

Yes, and all this is phenetics = the representation of similarity in a tree 
shape, without an attempt to tell plesiomorphies and apomorphies apart.

> Phylogenetic inferrence comes from the separate hypothesis that the input 
> be taxa
> versus characters and that the shared characters represent acquisitions in 
> evolution.

For this phenetic methods must not be used*. Instead cladistic methods must 
be used -- and can be used only here.

* OK, _if_ homoplasy is sufficiently rare, then phenetics and cladistics 
give the same tree...

> At this point,
> it becomes easy to interpret the method of cladistics (branching 
> arrangements
> from common reference poits of shared versus unshared data, in other 
> words, as
> in reference to the term's etymology) as separate from phylogeny or 
> phenetics.

If it's just "shared versus unshared data", it is phenetics. If an attempt 
is made to distinguish plesio- and apomorphies -- and these two terms don't 
make any sense without evolution --, then it's cladistics.

> Using cladistics to refer to phylogeny implicitly appears to be in error, 
> as I
> understand this.

Even though the pattern cladists tried to deny it, cladistics preassumes 
evolution.