More on the 'cladistics' of sequences

SKÁLA Zdenek skala at INCOMA.CZ
Mon Jun 7 16:54:30 CDT 2004

pierre (quoting Swofford and Farris - correctly I believe :-):

..given that one can always make a mistake in choosing "the" outgroup (i.e. 
choose a taxon that is in fact a member of the ingroup at stake), it's 
preferable to take into account several putative outgroups in the analysis, 
in order to try and minimize the risk.
If they all fall into the same place on the optimal topology, there is no 
ambiguity in rooting. ...

True, but note an interesting point: in searching for an outgroup we are doing so in an phenetic way (=overall similarity, no polarization). This is perhaps unavoidable (no cladogram topology is known a priori) but still a thing that is a bit discrediting the cladistic way of thinking. If there is no limitation for phenetic selection of outgroup, why not to use it more widely in the whole tree construction, somebody could say. One could start with 2 taxa, add 1 as "outgroup", then add next one etc. etc. ending with a "cladogram" constructed by succesive phenetic addition of taxa.

Zdenek Skala

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