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Making alignments

Guy A. Hoelzer hoelzer at med.unr.edu
Wed Jan 21 13:32:51 EST 1998

In article <6a575g$gpa at net.bio.net>, Joe Staton <jstaton at oeb.harvard.edu> wrote:

> The model of evolution is another consideration, altogether (i.e.,
> parsimony) which MAY be more robust to giving information about
> evolutionary patterns even if not completely correct. (no flames please)

I think the question of robustness to model assumptions is still a wide
open question.  At this point, everone I talk to seems to think that their
approach (MP vs. ML) is more robust, but I am not aware of any direct
comparisons.  However, we are now able to test the basic assumptions of
the MP model without resorting to induction as is currently done in the ML
approach.  This is a "shameless plug", but I think it is on point.  I have
been involved in the development of a method called Relative Apparent
Synapomorphy Analysis (RASA), which deductively measures matrix
hierarchy.  If hierarchy is present, and was caused by phylogenetic
history, then MP will tend to give you the right tree.  IMHO, phylogenetic
history is the only process that can create matrix hierarchy.  Processes
like convergent selection or homoplastic evolution destroy that
hierarchy.  In fact, if there is lots of good, clean hierarchy in the
matrix, nearly every method with minimal evolutionary model assumptions
(e.g., NJ, UPGMA) tend to get the tree correct.  IMHO, the value of ML in
phylogeny estimation will eventually be greatly improved by reducing
reliance on inductive procedures.

Guy Hoelzer                              e-mail:  hoelzer at med.unr.edu
Department of Biology                    phone:   702-784-4860
University of Nevada Reno                fax:     702-784-1302
Reno, NV  89557

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