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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.


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