Human and ape phylogeny

[pierre deleporte]

A 17:39 04/04/2003 +0200, René Zaragüeta-Bagils wrote :
>Hi,
>I agree with John Grehan's arguments. But I should not focus only on this
>paper:
>
>- Molecular characters are NEVER polarized (so they are phenetic, in
>Grehan's sense)

Phenetics can certainly not be defined as "no polarization".
And molecular characters are polarized by the outgroup criterion when 
treated with parsimony.

>- The more general problem is that Farris' optimization (= cladistic
>computer programs) is flawed. Cladistics is supposed to be a way of testing
>a conjecture (initial hypothesis) of hierarchical relationships. However,
>Farris' optimization produces no hierarchies, but unrooted trees (something
>that some Americans call "networks"). There is only an isomorphism (~
>equivalence) between rooted trees and hierarchies. So an outgroup is needed,
>not because of cladistics, but because of Farris' implementation of
>cladistics used in computer programs.
>
>- Farris' optimization is flawed in (at least) another sense: if your
>hypothesis proposes a grouping of, say, animals having a tail, your computer
>program may tell you that there is a group characterized by... ABSENCE of
>tail. However, you never made this hypothesis. It is your computer program's
>hypothesis!
>
>There are other problems with Farris' optimization.
>
>A solution, nevertheless, exists: three-taxon analysis.
>
>René
>
>René Zaragüeta-Bagils
>Département Histoire de la Terre UMR 8569
>Equipe SICC (Systématique, Informatique, Cladistique et Chronologie)
>Muséum national d'Histoire naturelle
>8 rue Buffon
>75005 Paris - France


Hi René,

Farris optimization, or Wagner trees, or standard parsimony analysis, is 
not "flawed", it just fits a particular model of evolution. You can allow 
character reversals, and thus reversals can tend to "support" a clade, for 
instance apomorphic reversal to "loss of tail" can support a clade. If this 
agrees with your model of character evolution, it's OK. If not, use PAUP 
"stepmatrix" tool and weight character step costs against reverals, and so 
on for an illimited series of models with possible differential charcter 
steps weighting...
All depends on your model of character evolution.

But if you really like phenetics, use three-taxon analysis in its last 
versions : its a true, and unexpected, rediscovery of phenetics, by people 
initially dealing with "parsimony" in the "cladistic" school.  3TA 
implements no implicit or explicit notion of character evolution. Even the 
basic notion of homology by descent between similar character states is 
broken down by the splitting of characters into separate "three taxon 
statements" treated independently. Different states of a same character and 
different occurences of a same character state are split into peaces with 
no return.

This makes the method non-evolutionary, i.e. fitting no conceivable 
evolutionary process, and thus non-phylogenetic at all.

Phenetics did not care with evolution either, it was "overall similarity 
for overall similarity's sake", just so. Like 3TA is 3TA for 3TA's sake. 
Just so.

3TA has obviously no "flaw", and cannot have any flaw, merely because it 
has no model to implement, and thus provides no handle to evaluate its 
adequacy.

Reminds me of a least some version of "Panbiogeography"...   :-)

best,
Pierre


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