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

[John Grehan]

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

Not sure I understand that because in the orangutan analysis there were
character conflicts giving different possible relationships among the
large bodies hominoids.

"Yet I still don't understand or find any reference demanding characters
to be restricted to the ingroup for the analysis to work."

Well, one can do an analysis, but even with the cladistic terminology it
just becomes a phenetic exercise in my opinion.

"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."

Exactly, there is no way to know what it is. By including it in the
analysis just muddies the phylogenetic waters.

"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..."

Yes that is pretty much true. I will make a subjective allowance for a
character state that is very rare in the outgroup - although if I were
strict about the procedure I would not. 


" but I find no recommendation to eliminate such a characters in the
book (above) or in the literature; and the book is about cladism!"

Perhaps I am wrong about that, in which case I retract the assertion,
although I maintain my position that the inclusion of character states
in the outgroup as well as the ingroup to analyze ingroup relationships
is phenetics pure and simple. 

"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."

Yes

"I cannot remember of any published justification for this, and I am
concerned about the bias potentially introduced by this method."

It's called a cladistic bias!

I sometimes wonder how may 'cladists' out there are really closet
pheneticists.

John Grehan