Molecular taxonomy: on way out?

[John Grehan]

> Behalf Of pierre deleporte
> >Not if they are treated as apomorpies.
> 
> But they are NOT, John, they are not!
> 
> Of course, contemporaneous phylogeneticians accept the outgroup
criterion
> for rooting the trees, hence optimizing the plesiomorphy-apomorphy
> polarization for most of the data, and this is done by the algorithm
> during
> the analysis. 

Exactly - and that's the problem. Somehow a mindless algorithm can do
what the systematist/taxonomist is too lazy or too ignorant to do. Why
bother putting anything in that is not prima face a derived character?
If one limits the data to derived states then all the algorithm has to
do is chose between competing relationships that may be theorized by
those derived characters.

Everybody knows that (a few hours training is sufficient).

'Everybody' may know a procedure (cookbook) but that does not meant to
say that the ingredients are any better for it.


> But yo seem to reject the outgroup criterion, and you pretend to
polarize
> every character a priori, and put only what you consider reliable
> apomorphies into the data matrix.

Of course! I would be stupid to do otherwise. For example, the presence
of a single incisive foramen is unique to orangutans and humans among
the extant hominoids (apes and humans). Is it a reliable apomorphy. In
this I can say yes as every extant primate skull for about 300 species
is known and none have turned up this feature. So I would use the
character unhesitatingly. I do not need a mindless algorithm to include
and polarize the character. It is that simple.

> If I understand well, your criterion is that a character(-state) never
> present in ougroups is a reliable apomorphy 

Yes - as also elaborated above.

(all what I could pick out of
> your different messages on the topic, including your practice in the
Pongo
> debate).
> Well, if this is correct, you are implementing yourself the outgroup
> criterion you reject in other peoples' approaches! Don't reject your
own
> practice when nicely performed by algorithms.

The point is that my practice is not performed by algorithms as the
algorithmis cannot study the individual character qualities to evaluate
them for inclusion. It can only mimic the process after the characters
have been presented.

> Also, it seems that you don't put into the data matrix
characters(-states)
> which happen to be present in some outgroups.
> Well, if this is correct,  you are implementing a clique analysis some
> way!
> (I doubt that Nelson would approve that...). i.e. you are cool-bloodly
> killing non-completely congruent characters, hence denying the
possibility
> that they may be convergent at some high level in the phylogeny, but
> informative at a lower level. Have you any justification for this?

I don't worry abut what Nelson would or would not approve of with
respect to range of representation, but at an ideal level I would prefer
no representation of a character whatsoever. However, that is only a
preference. It is not absolute. I have accepted, for example, the
argument that thick molar enamel is derived for humans and orangutans,
but not a shared derived character that also the single species of New
World monkey and a genus of Old World monkeys that have thick dental
enamel. I take the view that these are parallelisms. I know one can play
with this in algorithms, but for my analysis I would treat the character
state as absent in the outgroup.
> 
Without
> implementing the outgroup criterion, of course, because you deny it
for
> molecules, hence you should'nt use it for morphology. 

No I do not deny it for molecules, I just note that molecular biologists
do not restrict their sequences to those for which they can individually
demonstrate derived homology

> Or do you rather look carefully at characters, in the blank of the
eyes,
> and get some intuitive illumination?

Ha, ha.

> Or do you implement some model of morphological character evolution?
Which
> one and why? And if so, why reject molecular model-based analyses?

Because they do not demonstrate derived states for each of their
characters before the analysis. They do not demonstrate that a
particular sequence in the outgroup is unchanged and therefore primitive
with respect to the ingroup.

> Another commentator correctly pointed that characters cannot be
'phenetic'
> (shear nonsense of course, but this has been repeatedly explained to
you
> on
> this list since years now).

I agree that individual characters can not be phenetic, but one can have
a group of characters that provide a measure of overall similarity and
dumping a cladistic algorithm on top of them does not change the dirt
below. 

> 
>  > ...and I am interested to be shown to be wrong
> 
> Well, just done once more, in my view (or prove ME wrong, for once,
> instead
> of merely repeating your point).

We are both perhaps guilty of repetition and boredom. Don't respond that
the matter will fade away...

> And you don't say how you deal with contradictions between your
different
> putative synapomorphies, possibly pointing to different and mutally
> incompatible clades: what is your optimality criterion, and why not
let
> the
> algorityhm implement it for you?

I have no problem with using algorithms to chose between different
putative synapmomorpheis. I have never said otherwise. I know that there
are theorists who froth at the mouth over different algorithms. Me - I
don't really care.

> Not to mention your possible criteria for a priori ordering all the
> multistate characters: any rule? (don't say outgroup, it cannot work
> beyond
> two states).

One can start with the outgroup and use that for orientation. For
example, the outgroup (gibbons and monkeys) have the closest distance
between nipples. A wider distance is found within the ingroup - great
apes and monkeys. So one can make the prediction that wider is more
derived than narrower and from that postulate a sequence in which
orangutans are most unlike the outgroup, then humans, then African apes.

> A great difficulty in the debate is your quite unique, very personal
> version of 'cladistic analysis'. I really know of nobody performing
> phylogeny inference that way (and certainly not Nelson, one of your
pet
> references: he doesn't and never did as far as I know, certainly not
> character assassination!).

Well, who knows? I get some responding off list saying that they agree
with me. As for nelson, perhaps he would not agree with all of my views
on cladistics, but then again he apparently does agree with my critique
of molecular techniques being pseudo-cladistic. Everyone is entitled to
their choice.

John Grehan