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

[John Grehan]

Yes I am asserting that 'my' form of cladistics is necessarily correct -
or at least more correct or better than some others. And I realize that
I am sticking my neck out on that and perhaps setting myself up for a
fall - in which case the orangutan evidence will not doubt be refuted
(and I am not using that term as a synonym of rejected as often occurs
in US language).



John Grehan 

-----Original Message-----
From: Don.Colless at csiro.au [mailto:Don.Colless at csiro.au] 
Sent: Saturday, August 13, 2011 3:06 AM
To: John Grehan
Cc: taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] clique analysis in texbooks (was: Evolution
of,human-ape relationships...)

 The reason a phenogram may not necessarily be incorrect follows from an
an analysis of character change under the evolutionary process. It would
hard to disagree with John's "presumption" , which is analytic,
logically neessary. I in turn presume that he is suggesting that his
form of cladistics is necessarily correct.

Donald H. Colless
CSIRO Ecosystem Sciences
GPO Box 1700
Canberra 2601
don.colless at csiro.au
tuz li munz est miens envirun
________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu
[taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
[jgrehan at sciencebuff.org]
Sent: 12 August 2011 19:52
To: taxacom
Subject: Re: [Taxacom] clique analysis in texbooks (was: Evolution of,
human-ape relationships...)

Presumably a phenetic analysis may not necessarily be phylogenetically
incorrect  on the basis that it gets the same answer as something that
is necessarily correct.

In our analysis of relationships among the large bodied hominoids
(humans and great apes) we used gibbons, and OW and NW monkeys as the
outgroup. These together with the large bodied hominoids these are
accepted by everyone as far as I know to form a monophyletic group based
on cladistic analyses. So we used that arrangement as the assumption for
our analysis, so our outgroup was not chosen by overall similarity.

The group was based on cladistic analysis against other groups.
Admittedly one has to work up every larger group by a further outgroup.
I suppose in the end the outgroup for life would be 'non-life' (I'll
leave it to others to lose sleep over that one).

John Grehan

-----Original Message-----
From: Don.Colless at csiro.au [mailto:Don.Colless at csiro.au]
Sent: Thursday, August 11, 2011 11:09 PM
To: John Grehan
Cc: taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] clique analysis in texbooks (was: Evolution
of,human-ape relationships...)

It's amusing to note how the term "phenetic" can be so pejorative! As I
have shown long ago, a phenetic analysis will not NECESSARILY  be
phylogenetically incorrect. But the chance is high that it will be
imperfect, especially if evolutionary rates vary considerably over
branches. However, I've never seen a good answer to the fact that
outgroups are chosen phenetically. Otherwise,we enter and endless
regress of analyses.

Donald H. Colless
CSIRO Ecosystem Sciences
GPO Box 1700
Canberra 2601
don.colless at csiro.au
tuz li munz est miens envirun
________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu
[taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
[jgrehan at sciencebuff.org]
Sent: 12 August 2011 06:52
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] clique analysis in texbooks (was: Evolution of,
human-ape relationships...)

"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




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