3TA (was Human and ape phylogeny)

David Williams dmw at NHM.AC.UK
Thu Apr 10 08:55:15 CDT 2003

Pierre argues from the perspective that certain things 'must' be satisfied,
and certain other things 'must' be true (his musings on 'models of
character evolution' and 'phenetics', as examples). He argues that because
such and such a thing looks 'true' then indeed it must be true. The
relationship between phenetics (however conceived) and three -item data,
and the relationship between 'certain models of character evolution' and
three-item data seem to be constructions of Pierre's (and various other
critiques). None of them have substance beyond the sociological (phenetics
= bad, no model of character evolution = bad; and, somewhat alarmingly,
mirror previous critiques of panbiogeography, basically sociological).
Then, of course, we descend into philosophy...

My interest in three-item data has nothing to do with any of the above and
is almost painfully simple. What might be the answer to the simple two
character problem AB(CD) + AC(BD)? As far as I am aware most (all?) methods
yield no result, or return the same two trees, as if the solution to 2 + 2
= 2 + 2. I see the answer as A(BCD) [2 + 2 = 4]. I need no method, no
matrix, no program (all my MSc students suggest the same answer as well,
before they learn that computer programs know better). Now, to me,
something is wrong.


At 16:37 09/04/2003 +0200, you wrote:
>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?

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