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Systematic Biology 2005 54(4):595-619; doi:10.1080/106351591007453
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© 2005 Society of Systematic Biologists

The Logical Basis of Phylogenetic Taxonomy

Paul C. Sereno

Department of Organismal Biology and Anatomy, University of Chicago 1027 E. 57th Street, Chicago, Illinois, 60637, USA E-mail: dinosaur{at}uchicago.edu

Edited by Mike Lee: Associate Editor


  Abstract

Phylogenetic taxonomy, like modern Linnean taxonomy, was modeled on a phylogenetic tree rather than a cladogram and, like its predecessor, perpetuates the use of morphology as a means of recognizing clades. Both practices have generated confusion in graphical representation, operational terminology, and definitional rationale in phylogenetic taxonomy, the history of which is traced. The following points are made: (1) cladograms, rather than trees or hybrid cladogram-trees, provide the framework for the simplest graphical depiction of phylogenetic definitions; (2) a complete notational scheme for phylogenetic definitions is presented that distinguishes symbolic notation from shorthand and longhand versions; (3) phylogenetic definitions are composed of three components (paradigm, specifier, qualifier) arranged in two fundamental patterns—node and stem; (4) apomorphies do not constitute a fundamental definitional pattern but rather serve to qualify a stem-based definition (as do time and geographic range); (5) formulation of phylogenetic definitions involves three heuristic criteria (stability, simplicity, prior use); (6) reasoned definitional revision is encouraged and better defined (textual substitution, first-and second-order revision); and (7) a database, TaxonSearch, allows rapid recall of taxonomic and definitional information.

Keywords: Content; definition; node; notation; PhyloCode; stem; taxonomy; TaxonSearch

Received September 13, 2004; Revised December 9, 2004; Accepted March 18, 2005
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