More on the 'cladistics' of sequences

[pierre deleporte]

Hi David, nice to read from you.
I was guessing when you'd pop out !

A 10:55 11/06/2004 +0100, David Williams wrote:
>  Perhaps this is what leads Pierre, for example, to conclude that “Some 
> ‘cladists’ effectively rediscovered phenetics (Jaccard index). They 
> belong to some trends of the ‘pattern cladistics’ school, which is not 
> evolutionary, thus you shouldn't bother if your own goal is phylogeny 
> inference”, an assertion based on no evidence or published source, as far 
> as I am aware, and entirely of his own making.

Yes, I confess, I'm a great mythomaniac, and I invented the following:
Carine and Scotland, 1999, Cladistics. "Taxic and transformational 
homology: different ways of seeing". (the method exposed there is M3ta = 
modified three taxon analysis, a pure invention of mine of course).

Not statisfied, I then went on inventing :
Kluge and Farris, 1999, Cladistics. "Taxic homology = overall similarity".

I then dreamt that I agreed with the second paper, particularly that M3ta 
"reinvented phenetics" (p. 207).

In my delirium, I even considered that the first authors did not even 
realized their reinvention,  because they believed that the difference 
between cladistics and phenetics was that phenetics could group on the 
basis of the absence of characters, ignoring that e.g. the phenetic Jaccard 
index allows for just that: phenetic clustering on the basis of presence, 
not absence, of characters.

Even worse: I forged the legend that Rieppel recently wrote in Syst Biol 
about ambiguity between evolutionary and positivist systematics in Hennig's 
own writings, hence duality in the cladistic school ("evolutionary" versus 
"pattern") is a fairly long lasting story.

David, I owe you a beer for demasking me  ;-).

>  Efforts to substantiate one methodology over another is ultimately 
> pointless.

Agreed in general, one can only judge a method according to the explicit 
theoretical context and goals. If any.

>  Thus, for example, to equate cladistics with parsimony methods is false.

All depends on your personal definition of cladistics. M3ta proponents call 
themselves cladists and implement phenetics, not parsimonious optimization 
of character state topological contiguity (in my delirious nightmares, of 
course).

>all numerical methods are all inherently phenetic (because of the matrix 
>and thus not phylogenetic)

Definitions...

>So
 What, if anything, are the entries in a matrix?

I fully agree that this was likely the point raised by John, behind 
problems of semantics, now largely surmounted I think (for me at least).

John's point, as I understand it, is: characters polymorphic in putative 
outgroups should be discarded. He himself uses some, but visibly feels 
uneasy with that.

Best,
Pierre


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