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

[Richard Zander]

Since we are discussing morphological data sets, because the characters
have already been selected as conservative, the data set is already
constructed to reflect the relationships that the taxonomists who
described the taxa intended. Any differences from the relationships
inherent in the descriptions of taxa are not intended by the original
describer and so are probably caused by atomization of traits that are
preselected to be taxonomically linked. The morphological cladogram is a
mechanical way to generate a natural key in a better way than by brain
power alone. Any surprising differences from what might be expected from
a natural key are artifacts. IMO.

The phylogenetic waters are a fierce baptism for the credulous.

 

* * * * * * * * * * * *
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA  
Web sites: http://www.mobot.org/plantscience/resbot/ and
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm


-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Sergio Vargas
Sent: Friday, August 12, 2011 3:00 PM
To: taxacom at mailman.nhm.ku.edu; jgrehan at sciencebuff.org
Subject: Re: [Taxacom] clique analysis in texbooks (was: Evolution of,
,human-ape relationships...)


So I got it right! Finally. Then, and I've mentioned this before, the
Human-Orangutan hypothesis can be viewed as a phylogenetic tree
conditional only on characters which polarity can be decisively
determined, often a priori.

I see several potential problems for a tree inferred using John Grehan's
method of character pre-selection:

1. as an explanatory hypothesis, such a tree is worse than a tree
resulting from a matrix also including characters which polarity cannot
be decisively determined because the second tree would also provide an
explanation for these, say bad, characters as well. Thus the second tree
will have a higher explanatory power than  the first one.

2. from a testing perspective the first tree (JGs) is less thoroughly
tested than the second one because characters that could potentially
falsate (not sure how you write this word) the topology are not being
used, even if the analytical method can handle them without problems and
no cladistic textbook (unless Wiley and Brooks are "closet pheneticists"
which will be scary) or published work recommend to exclude them from
the analysis.

3. because of the way the character matrix is constructed, it seems that
it is really hard to add new characters to the matrix, which means that
the conclusions of the analysis are protected against future testing:
you can always take characters out (those that do not fulfil JGs
criterion of character selection) but never, or only very rarely, you
can add characters to the matrix. Moreover, if you ignore JGs criterion
of character selection you are "muddying the phylogenetic waters" and
your matrix is phenetic, therefore irrelevant. If you use DNA characters
you are a "molecular theorist", whatever that means.

I guess these problems make a tree inferred using this method a bad
hypothesis when compared with an hypothesis that does not require
excluding potentially relevant information and does not pose obstacles
to further testing.

sergio