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Re: Cladistics (was Sci. Am. - present)



>In a message dated 98-02-21 03:02:23 EST, cbrochu@fmppr.fmnh.org writes:
>
><< How would you "improve" a parsimony analysis?  I'm not trying to be
> patronizing - this is a serious question.  Given the principle of total
> evidence, the hypothesis that best matches all the available data is the
> preferred one - are you advocating some sort of significance test for
> character data?  If so, on what objective basis would this be based?  And
> bear in mind, switching to molecular data won't necessarily "improve" the
> analysis, except by adding additional relevant information. >>
>
>This carries the walloping untested assumption that nature is parsimonious. I
>don't believe this for a minute. At best, nature may be "not wildly
>unparsimonious."

Actually, it doesn't, since a parsimony analysis' primary goal is to derive
the best fit of the data - not to statistically estimate evolutionary
processes a priori.  If the assumption of absolute natural parsimony were
valid - which it is not - we would be horrified at the CI values we
routinely get.

The kind of assumption you're thinking about is valid for maximum
likelihood, wherein a priori assumptions of evolutionary mode are central
to the analysis.  In strict parsimony analysis, parsimony is used as a
matter of first principles, not as a model of evolution.





>
>In particular, therefore, I do not believe that nature necessarily strictly
>generates a cladogram with the least number of steps, only--in most cases--a
>cladogram with something fairly close to the least number of steps, and every
>so often, a cladogram with a considerably larger number of steps. The
>phylogenetic patterns found by cladistic analysis are all very nice, but
>nobody has shown that they correspond to reality--only that they sometimes
>correspond, to varying degrees (almost never exactly), with other patterns
>generated by other means or (shudder!) other cladistic analyses.

I'm sorry, but this is incorrect.  The accuracy of parsimony over a broad
range of conditions has been confirmed not only by simulations, but by
actual viral phylogenies generated in the laboratory.





Maybe they're
>real, or maybe they're all way off in some systematic way that we haven't yet
>discovered (such as consistently biased choice of outgroup or choice of
>representative taxa, or hidden assumptions about character-state polarity). In
>this sense, they're no better than the phylogenies generated by "old
>fashioned" methods, and not particularly more reliable. A cladist can no more
>show that his or her cladograms are correct than I can show that they're not;
>thus the whole exercise is pointless.

Well, given that you can say nothing in paleontology without some sort of
hypothesis for relationships, I hardly think the procedure is pointless.



chris


=-=-=-=-=-=-=-=-=-=-=-=-=-=
Christopher Brochu

Postdoctoral Research Scientist
Department of Geology
Field Museum of Natural History
Lake Shore Drive at Roosevelt Road
Chicago, IL  60605  USA

cbrochu@fmppr.fmnh.org