Human and ape phylogeny

[René Zaragüeta Bagils]

Salut Pierre,

C'est déjà bien que ça discute en France...

(Characters are considered binary, to simplify the discussion).

Pierre Deleporte wrote:
"Farris optimization, or Wagner trees, or standard parsimony analysis, is
not "flawed", it just fits a particular model of evolution"
Re:
Standard parsimony analysis does not produce a hierarchy, so it follows
logically that it cannot fit any model of evolution, because evolution is
supposed to produce hierarchies.

Pierre Deleporte wrote:
"Phenetics can certainly not be defined as "no polarization".
And molecular characters are polarized by the outgroup criterion when
treated with parsimony."
Re:
The "outgroup criterion" is a technique (I would prefer to say a patch) to
correct the problem: standard parsimony produces no hierarchies
so you must choose on quite obscure grounds the 'correct' outgroup. This is
flagrant with molecular characters.
(For people not used to three-taxon analysis (3TA) : 3TA produces
hierarchies, that is, rooted trees, and no outgroup is needed.  3TA tests
these conjectures in a particular way, different (more consistent and
precise) from standard parsimony).

Pierre Deleporte wrote:
"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"
 Re:
This is not the point. Cladistic characters are classificatory concepts that
partition individuals into instances of the concept an non-instances of the
concept. Absence cannot be an instance of a concept. So grouping by
non-instances of concepts is logically inconsistent. "Reversals" can only be
a posteriori interpretations of the presence of several non-instances of
concepts in a clade. Reversals are not homoplasies (refuted conjectures of
instances of classificatory concepts) but non-instances of concepts (or
absences, or plesiomorphies). So it is logically inconsistent to optimize
"reversals" because they cannot be "apomorphic", by definition (except in
phenetics...)

Pierre Deleporte wrote:
"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 occurrences of a same character state are split into
peaces with no return."
Re:
I do not agree, but it should be too long to explain why characters are not
"splitted..." in 3TA.
However, how do you interpret the "basic notion of homology
by descent with modification" for absences? If someone calls me to announce
me an heritage of an absence of money from my old aunt, I should think it
is, at best, a joke.

Pierre Deleporte wrote:
"But if you really like phenetics, use three-taxon analysis in its last
versions [...] This makes the method non-evolutionary, i.e. fitting no
conceivable evolutionary process, and thus non-phylogenetic at all."
Re:
What do you mean by "last versions"? I do not agree with "modified
three-taxon analysis" because it is as phenetic as standard parsimony (it
optimizes absences). But I do not agree either with your "scala naturae"
model of evolution of ideas concerning three-taxon analysis.
Perhaps in other areas or fields you are "forced" to agree with , or
believe, someone's ideas, even if they are phenetic. It seems to me that it
is you who like phenetics (e.g. when you say that "apomorphic reversal to
'loss of tail' can support a clade")
However, how can absences evolve (=transform, I guess you should say) in
your model? What
do you mean by the evolution of the "lack of a tail"? How can, for instance,
natural selection work on the absence of something? How can you distinguish
between the 'transformation' of the absence of a tail to the presence of a
tail and the 'transformation' of the absence of a leg to the presence of a
tail?

Pierre Deleporte wrote:
"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."
Re:
This is exactly the point concerning standard parsimony. If you make a
conjecture of
homology based on the presence of a feature (as everybody does), then why a
computer program
tells you that the absence characterizes a group if you didn't make the
conjecture? Cladistics is supposed to test your conjectures, not computers'
ones (unless PCs and Macs are delivered with evolutionnary models installed
:-)).
Optimizing instances and non-instances of characters at the same time is
simply phenetic (just so). Organisms grouped together because they lack
something live in a phenetic world (or a pre-evolutionary one...).

A final question to the so-called "strict cladists" and to Pierre: Has
anybody ever been criticised because his character definitions where not
consistent with a particular theory of evolution or model? It has never
happened to me, and I have never seen this kind of criticisms. People
criticize my characters on topological grounds or on quality of
descriptions, even on taxonomic sampling grounds, etc. I work on teleosts:
can anybody tell me what cannot be
coded because it doesn't evolve? Or everything, however described, evolves?
As Jorge Wagensberg* has put it (modified): If evolution is always the
answer,
what is the question?

* Wagensberg, J., 2002: Si la naturaleza es la respuesta, cual era la
pregunta? Metatemas-Tusquets, Barcelona, Catalonia, 126pp.

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
rzb at mnhn.fr