Logic of cladistics

Mike Zwick mezwick at ucdavis.edu
Thu Jun 9 17:37:57 EST 1994


In article <Cr5EA0.CBz at zoo.toronto.edu>, mes at zoo.toronto.edu (Mark Siddall)
wrote:

> 
> apologies for not continuing this thread immediately, I've been doing
> the proverbial chicken without a head thing recently...
> 
> ...the above also pertains to Eric's concerns regarding lack of 
> follow-up... (in article 1759 of this group)...
> 
> In article <2sri9k$eh4 at news.u.washington.edu> joe at evolution.u.washington.edu (Joe Felsenstein) writes:
> >
> >
> >"Cladists" (phylogenetic systematists of the Willi Hennig Society persuasion)
> >usually say you should look only at the most parsimonious tree or trees.  But
> >they acknowledge that these don't have a 100% probability of including the
> >true tree.   I can't quite put this together unless they believe that
> >a statistical approach would be valid, but that existing ones are not, so one
> >should avoid looking at the confidence intervals they suggest.  However I
> >don't hear that from cladists, but rather a complete rejection of the framework
> >of statistics instead.  Perhaps I miscontstrue.
> 
> I agree with Joe here that there is some strong resistance to the notion]
> of pursueing a statistical framework in cladistics (ASIDE: I actually
> like the word cladist... and am an ardent one :-) ...); witness 
> Carpenter's diatribe against all-things-random in the journal _Cladistics_
> about 2 yr ago.  Though defintitely a cladist myself, I don't fall into
> that group that eshews issues of probability and have even taken a stab
> at some of this myself (see below).  Perhaps the perspective is that
> there is a feeling that one cannot ever know the "true" phylogeny so 
> how does one go about looking to empirically measure the performance of
> a statistical approach to phylogeny reconstruction?
> Parsimony is seen by many (like myself) to be a logical "path of least
> resistance" approach to phylogeny reconstruction.  That is, why
> propose widespread convergence (for example) when there's a simpler
> explanation.
>    I think that one would likely find that those that resist a 
> probabilistic approach have their grounding in morphology and not in
> sequence data.

I have one question about the logic of cladistics.  Do you agree as other
"pattern cladists" have suggested (rather strongly among some that I have
had the opportunity to interact with), that their methodology is assumption
and process theory free i.e. that they are looking solely at pattern
(characters + parsimony and that is it)?  Would you agree with this
assertion?  

It has always seemed to me that by employing parsimony, one is making a
very specific assumption about the evolutionary process (assuming one
believes that the evolutionary process is what is responsibible for the
change of characters).
If for example, in the analysis of molecular characters, one knew that the
substitution process did not follow the process of parsimony, then would
one be justified in employing parsimony to analyze molecular data sets?  I
would think not - instead one would probably want to employ maximum
likelihood (with a specific model of molecular evolution for example).    

-- 
mike zwick
mezwick at ucdavis.edu
Department of Ecology and Evolution
Center for Population Biology



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