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Re: Evolution programs (was: Reevolving bones)

On Wed, 7 May 1997, Thomas R. Holtz, Jr. wrote:

> >
> >This is exactly what I had in mind. Have the evolution program generate an
> >"ecosystem" of virtual dinosaurs, hand the dinosaurs over to the
> >systematists, then see whether the trees the systematists come up with match
> >the trees that the computers constructed when they generated the virtual
> >dinosaurs. Even more interesting: Set the parameters of the programs to
> >generate trees with no reversals, lots of reversals, no homoplasies, lots of
> >homoplasies, strict parsimony, no parsimony, and so forth, and see whether
> >the methodology can consistently pick them out. Or see just what it does do
> >with such trees. This could go any number of ways...
> >
> Okay, let's see it.
> This would be an excellent experiment, and could easily get the team that
> runs it several papers (a short one in Science or Nature, a longer one in
> Systematic Biology or similar journal).
> But, why dinosaurs?  Why not (for example) muppets or other imaginary taxon?
> The results should be interesting. And, given the fact that no one has done
> this yet (to my knowledge), we have no way of knowing a priori the results
> of such an experiment.
> Any takers?  People working on a comp sci masters: this is prime thesis
> material!

It has been done. Though the models that were evolved were in the form of 
molecular data rather than morphological data. Anyway the basic result 
was that parsimony analysis can fail, when the underlying phylogeny had a 
low "stemminess"  and or was highly  pectinate (a hennigian comb). 
"Steminess" refers to the length of the branches of the terminal taxa 
compared to the length of the branches that connect them (stems). If 
stemminess is low the terminal branches will be long and the stems short, 
vice versa if stemminess is high. Its like comparing a tuft of grass to 
an ordinary bush. Unfortuneately this appears to be the case with my 
beloved stereospondyls, a rapid radiation producing highly autapomorphic 
branches with little to connect them, resulting in a rather unstable tree 

Some references are

Debry, R. W. 1992. The consistency of several phylogenetic - inference 
methods under varying evolutionary rates. Molecular Biology and Evolution 
9, 537-551.

Felsenstein, J. 1988. Phylogenies from from molecular sequences: 
inference and reliability. Annual Reviews in Genetics 22, 521-565.

A good simple (but short) review of this work is in 

Smith, A. B. 1994. Systematics and the fossil record. Blackwell 
Scientific Publications.  


Adam Yates