[Taxacom] Methodological plurality [was cladistic analysis for morphological characters -- UPGMA is not cladistics]

David Campbell pleuronaia at gmail.com
Mon Nov 19 16:04:19 CST 2012

> That line of reasoning makes using multiple methods a sensitivity
> analysis. It would be the equivalent of using only one alternative set
> of parameters. There is quite an extensive literature on sensitivity
> analyses, but I can’t recall ever seeing such a limited test of
> parameter space being considered sufficient.

I think I see where I misunderstood you.  What is a "method"?  Testing
across a varied range of parameter space could be classified as a
"method" of analysis, specifically analyzing for sensitivity.  If
"method" is thought of very broadly, then mutliple methods is a useful
approach, in contrast to the "here's the tree produced by my favorite
phylogenetic black box method, therefore all other classifications are
wrong" approach.  Multiple methods for assessing phylogenetic trees
are hopefully fairly redundant, assuming that the method in used is
appropriate for the data set.  However, arbitrary selection of a
single method would be even less informative.  What is needed is a
consideration of what methods of analysis, testing for support, etc.
are likely to be most appropriate for a given data set, why different
data sets might give different results, why different methods might
give different results, etc.

So "I ran parsimony and Bayesian analyses under a single set of
parameters apiece and got similar/different trees" is not all that
informative, whereas "I ran phylogenetic analyses using a wide range
of parameter space and consistently obtain high support for clades A,
B, and C" is more informative.  Yet both could be described as using
multiple methods-the difference is "methods of what?"

Dr. David Campbell
Visiting Professor
Department of Natural Sciences
Gardner-Webb University
Boiling Springs NC 28017

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