[Taxacom] base alignment

pierre deleporte pierre.deleporte at univ-rennes1.fr
Tue Aug 29 07:24:31 CDT 2006

A 13:56 28/08/2006 -0400, John Grehan wrote:

>(Deleporte): discussions allowed me to understand that what you mean by 
>characters" is the set (or 'clique' in jargon) of completely
>'compatible' characters (= homoplasy-free characters) as resulting from a 
>compatibility analysis ('clique analysis') at a higher phylogenetic level
>J.G.: No that is not correct. By cladistic character I mean any characters
>(states) that can be shown to be unique to ingroup members.

Sorry but this is exactly the definition of compatible characters: no 
homoplasy between the ingroup (taken as a whole) and any outgroup. It seems 
that I am correct.

>J. G.: Such character relationships within the ingroup may not be completely
>compatible at all - hence the need for an analytical procedure to then
>determine which cluster of putatively derived characters is best
>supported (whether through parsimony or any other tree building
>procedure one might use).

Right, but now you have to specify which procedure you will use for the 
ingroup: compatibility analysis or otherwise?
Please note that using compatibility analysis outside (your prior selection 
of putative "cladistic characters"), and standard parsimony inside, would 
be logically inconsistent: your results would differ according to the 
phylogenetic level of delineation of your ingroup versus outgroups. In the 
extreme, analysing the data matrix of "Life" would leave you with no room 
for prior selectioin of "cladistic (copmpatible) characters at all... the 
logical inconsistence seems obvious enough.

>J. G.: It's not my fault that others don't do this (which makes me wonder if
>they are really pheneticists). But as to 'never' I might suggest this is
>not correct.

Some people perform(ed) compatibility analysis. I merely suggest that 
nobody calls compatible characters "cladistic characters" like you do. 
Please quote some paper using this terminology (just one)...

If you define standard cladists as "pheneticists", hence all cladists I 
know are "pheneticists".
If you define "cladistic characters" as compatible ones, hence no 
molecularist I know, and no morpho-anatomist either, is performing analysis 
of "cladistic characters".

Maybe this whole planet is "pheneticist", except yourself. But for 
everybody I know "phenetic" means classifying on the basis of overall 
similarity of taxa, not selecting compatible characters.
Of course you can go on as far as you like in devising personal acceptions 
of this sort.
I simply suggest that this does not help communication.


Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 63
Télécopie : 02 99 61 81 88

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