Re: Prolacertiformes and Protorosauria

[Mike Habib <habib@jhmi.edu>]

David Peters wrote:

> re: the more robust tree question: The tree that has the fewest mpts  
> and survives the most decay tests is the more robust tree. Is it  
> not? In other words, the tree in which sister taxa share the most  
> synapomorphies is the more robust tree, yes?

The number of MPTs is not actually a particularly strong measure of  
the robustness of the tree.  Surviving decay tests is a better  
indicator, but it still doesn't actually tell you if your dataset is  
stronger than another dataset - it indicates whether or not you are  
confident reporting the MPT in question, relative to the next-most  
parsimonious trees.  Decay tests are mostly a way of approaching the  
issue that biological systems are not actually parsimonious.  If you  
can relax the parsimony requirement a great deal, and still recover  
the same topology, then the tree is at least robust to that particular  
assumption.

However, those indices do not answer the question of preference of  
topology *between* datasets - when two different matrices produce  
different topologies, then decay indices alone are not particular  
informative.  If one of the matrices produces many MPTs, with  
sensitivity to decay tests, then that particular analysis is  
hypothesizing a lack of resolution - such a result essentially  
indicates that we don't have a good idea of the answer.  If the  
competing matrix finds few MPTs, containing clades robust to decay  
tests, then we have the opposite result: that analysis would support  
the conclusion that we have high confidence in the relationships.  The  
problem is that, without additional information, we have no way of  
judging which hypothesis is correct: a lack of knowledge result is no  
less plausible than a presence of knowledge result.

Cheers,

--Mike


Michael Habib, M.S.
PhD. Candidate
Center for Functional Anatomy and Evolution
Johns Hopkins School of Medicine
1830 E. Monument Street
Baltimore, MD 21205
(443) 280-0181
habib@jhmi.edu