3TA (was Human and ape phylogeny)

pierre deleporte pierre.deleporte at UNIV-RENNES1.FR
Wed Apr 9 16:37:00 CDT 2003

Thanks to Richard Jensen to confirm that phenetics were not intended as 
phylogenetic in the first place, and that they can perfectly be performed 
under different assumptions "e.g., including or ignoring negative matches 
when calculating association coefficients".

The proponents of 3TA generally deny this last point, oddly believing that 
phenetics obligatorily accept to group on the basis of negative matches, 
i.e. shared absence. They confound a characteristic of some options of 
phenetics with the method itself. They are eager "not to be phenetic", but 
they are satisfied in this respect when they group on positive matches 
only. Trained pheneticians will appreciate.

Of course phenetic analysis can fit some models of character evolution 
(typically clocklike evolution implying regular divergence), and of course 
the availability of a number of options is not a flaw in itself in any 
method (phylogenetic methods involve as many otions as evolutionary models).
The question is just not to forget arguing the choice of the option. If you 
get puzzled when the moment comes to argue your choice of options, you must 
severely question your problematic: which tool is best for which task in 
which theoretical framework ?

I just don't grasp the notion of "testable hypothesis of relationships" 
raised by Jensen, but this is another question.
Phenetics infer an optimal phenogram from a data matrix using some option, 
and that's it. There's no test involved.
You can of course deal with another data matrix or another option. There's 
still no test involved.
You can also have two data matrices involving different character sets for 
the same set of taxa. Just combine them in one data matrix and draw the 
phenogram. No test involved either.

What are phenetic tests, if any?


A 08:21 09/04/2003 -0500, Richard Jensen wrote :
>I can't help but think that phenetics is getting a bad rap here.  Phenetic
>analyses make no reference to apomorphic, plesiomorphic, synapomorphic, etc.
>with respect to characters.  Characters provide the information by which the
>analysis is conducted and a phenetic analysis will lead to a classification.
>And, it is a testable hypothesis of relationships.
>Sokal and Sneath never intended for phenetic analyses to be interpreted as
>phylogenetic or evolutionary classifications.  Colless noted that, with 
>assumptions, phenetic analyses would be expected to be good approxamations to
>such releationships and it has been suggested that in situations in which 
>is little homoplasy, phenetic analyses and cladistic analyses may yield 
>the same
>"solution."  And, despite the appearance of phenograms as trees, they 
>cannot be
>interpreted as rooted trees.  They represent sets and subsets in a nested
>Further, don't criticize phenetics for the many options available for 
>phenetic analyses.  Unless I have missed something important over the last 20
>years, there are a variety of approaches for conducting cladistic analyses and
>they typically yield different results for a single data matrix.  In other
>words, both approaches yield results that are dependent on a set of 
>choices made
>by the investigator.  The fundamental question is whether or not the choices
>made can be justified (e.g., including or ignoring negative matches when
>calculating association coefficients).
>pierre deleporte wrote:
> > Hi René, David, and taxacomers
> >

Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 66
Télécopie : 02 99 61 81 88

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