3TA (was Human and ape phylogeny)
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
>"solution." And, despite the appearance of phenograms as trees, they
>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
>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
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