Traits, states and cladists

[Jason at]

>In a good data matrix of (morphological) characters, what we call
>"character states" are actually not different states of one character, but
>homologous (characters).

If they are in the same column you have already made the decision, right or
wrong, that they are homologous. I fail to see what difference the semantic
distinction will do to the concept of homology.

Sometimes one of the "states" is apomorphic
>and another plesiomorphic; in this case they are very useful for a
>phylogenetic-taxonomic study. Sometimes there are no apomorphies,
>and then we are appending phenetic noise to our analysis.

How would you determine if a character is apomorphic or plesiomorphic a
priori? In any case if a character only had a plesiomorphic state if would
be a waste of time adding it to the matrix. If all your taxa had the same
state what could you possibly achieve by adding this to the analysis?

>this is best for our computing: no distrust, no dobts, no suspicions
>about the resulting phylogeny reconstruction / classification.

A phylogenetic reconstruction and the data used to derive it are, in my
book, always under suspicion.


Cheers

Jason

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