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Re: True cladograms & Black swans



>
>I have now read several papers on the subject of verifying cladograms, and
>they all seem to agree that there is an irreducible fraction--about 15-20%--of
>cladograms that, despite best efforts and perfectly correct analysis, turn out
>incorrect, that is, do not match the control phylogeny. Long branch
>convergence is one way that may give rise to incorrect cladograms; so is
>choice of representative species. The problem that worries me is how to
>identify and fix those 15-20%. There doesn't seem to be a handle on that yet.


Sure there is.  Some of the tests are even included as standard procedures
in the newest version of PAUP.  Try this:


Faith, D.P., and P.S. Cranston.  1991.  Could a cladogram this short have
arisen by chance alone?  On permutation tests for cladistic structure.
Cladistics, 7:1-28.

Hillis, D.M.  1995.  Approaches for assessing phylogenetic accuracy.
Systematic Biology, 44:3-16.

Also - could you explain what you mean by 15 - 20 percent inaccuracy?  Are
you talking about trees that are wrong overall, or a percentage of nodes
within trees that are wrong? These are very different things.



chris


-=--=--=--=--=--=--=--=--=--=
Christopher Brochu, Ph.D.

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

phone:  312-922-9410, ext. 469
fax:  312-922-9566

cbrochu@fmppr.fmnh.org