[Taxacom] Reproducibility of phylogenetic analysis

Richard Zander Richard.Zander at mobot.org
Wed Jan 27 10:13:47 CST 2010

Well, Dick, I think we need to go beyond patterns. The particular
processes and the particular historical events that lead to patterns and
clustering in nature should be a focus. Doubtless patterns lead to and
guide study that might reveal processes and historical events. Patterns
also are convenient for classification, but surely knowledge (when such
can be had) of a process and/or an historical event should also inform
classification. Also, patterns of what? With morphological data we get
inferred clusters of shared homologous traits fixed at nodes in a
gradualist model of evolution, with molecular data we get inferred
genetic continuity and isolation events without relevance to taxa. Of
course, compared to these bad interpretations in phylogenetic analysis,
phenetics is refreshingly clean in what it is doing.

Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/resbot/
and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:

-----Original Message-----
From: Richard Jensen [mailto:rjensen at saintmarys.edu] 
Sent: Wednesday, January 27, 2010 9:54 AM
To: Richard Zander
Cc: Stephen Thorpe; Bob Mesibov; TAXACOM
Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis

I think the key is that analytic methods produce results that we wish to

interpret according to some set of a priori 
assumptions/hypotheses/guesses. What we get, as Stephen noted, is a 
function of what those assumptions etc. are. Are they a function of some

explicit process, or are they just one possible reflection of a 
particular set of assumptions? There are patterns in nature - the 
questions are: Can we detect them? If so, how do we detect them? How do 
we know when we have detected them? Can we explain them?

Dick J

Richard Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
Tel: 574-284-4674

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