[Taxacom] clique analysis in texbooks (was: Evolution of, human-ape relationships...)

Sergio Vargas sevragorgia at gmail.com
Thu Aug 11 15:41:47 CDT 2011


>I can remember of no textbook recommending to implement clique analysis by hand through a priori rejecting characters (a procedure also known as "character assassination" among cladists) followed by standard parsimony optimisation, rather than using a dedicated computer program - e.g. the "CLIQUE" program in Felsenstein's phylogeny inference package PHYLIP, finding the largest clique of compatible characters (and it's free);

I don't think John Grehan is using compatibility to choose characters because his trees have CI<100, hence his matrices have homoplasic characters.

Yet I still don't understand or find any reference demanding characters to be restricted to the ingroup for the analysis to work. As I mentioned in an email before, if you have a character present in some taxa in the outgroup you will only experience a problem trying to reconstruct the polarity of the character, because that character will be equivocal. Actually, a rather well explained example of a case where the outgroup has both character states can be found in the Compleat Cladist (Chapter 3). If I have understood everything so far, John Grehan will discard such a character because it is not exclusively derived... (I forget the exact phrase), but I find no recommendation to eliminate such a characters in the book (above) or in the literature; and the book is about cladism! So instead of compatibility analysis I would say John Grehan restricts the character matrix to characters were the polarity can be decisively determined and discards characters that could yield equivocal polarity reconstructions. I cannot remember of any published justification for this, and I am concerned about the bias potentially introduced by this method.


Sergio Vargas R., M.Sc.
Dept. of Earth&  Environmental Sciences
Palaeontology&  Geobiology
Ludwig-Maximilians-Universität München
Richard-Wagner-Str. 10
80333 München
tel. +49 89 2180 17929
s.vargas at lrz.uni-muenchen.de
sevra at marinemolecularevolution.org

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