The logical basis of phylogenetic taxonomy

Systematic Biology
Paul C Sereno

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 ...Continue Reading

References

Nov 25, 1977·Journal of Molecular Evolution·W W de JungD Boulter
Jul 1, 1988·Journal of Neurosurgery·K L BernardoC L Roper
Apr 1, 1997·Thorax·D C Currie
Jun 23, 1999·Proceedings of the National Academy of Sciences of the United States of America·J C Avise, G C Johns
Dec 16, 2000·Biological Reviews of the Cambridge Philosophical Society·M J Benton
May 12, 2001·Environmental Science & Technology·R YanC Zheng
Jun 1, 1997·Systematic Biology·H B ShafferM L McKnight
May 3, 2002·Nature·H Charles J Godfray
Jun 18, 2002·Systematic Biology·P D CantinoM S Lee
Jun 18, 2002·Systematic Biology·Paul C Sereno
Jan 24, 2003·Nature·Xing XuXiangke Du
Feb 18, 2004·Systematic Biology·Michel Laurin, Jason S Anderson
Jan 1, 1994·Trends in Ecology & Evolution·K de Queiroz, J Gauthier
Jan 1, 1998·Trends in Ecology & Evolution·M S Lee

Citations

Mar 26, 2011·Briefings in Bioinformatics·Ahmed Ragab Nabhan, Indra Neil Sarkar
Jun 9, 2010·Systematic Biology·Christopher A BrochuLlewellyn D Densmore
Aug 11, 2016·Anais Da Academia Brasileira De Ciências·Lúcio Roberto-DA-SilvaSérgio Dias-DA-Silva
May 31, 2006·Development Genes and Evolution·Ronald A Jenner
Oct 25, 2006·Systematic Biology·Yann Bertrand, Mikael Härlin
Mar 24, 2017·Nature·Matthew G BaronPaul M Barrett
Nov 17, 2007·Nature Reviews. Genetics·Rudolf A Raff
Oct 20, 2005·The Cochrane Database of Systematic Reviews·W SomboonpornR Bell
Apr 21, 2006·The Cochrane Database of Systematic Reviews·T M WinzenbergG Jones
Apr 22, 2008·The Cochrane Database of Systematic Reviews·P ManningT J Lasserson
Jan 23, 2009·The Cochrane Database of Systematic Reviews·Christopher J Cates, Toby J Lasserson
Nov 10, 2009·Biological Reviews of the Cambridge Philosophical Society·Max C LangerFernando E Novas
Jul 25, 2019·Anais Da Academia Brasileira De Ciências·Bernardo J González RigaLucio M Ibiricu
Jan 17, 2020·The Anatomical Record : Advances in Integrative Anatomy and Evolutionary Biology·Ashley W PoustFengjiao Zhang
Nov 17, 2020·PeerJ·Yuqing YangPascal Godefroit
Jan 1, 2021·PLoS Biology·Katherine L BryantRogier B Mars

Related Concepts

Taxonomy
Logic
Phylogeny

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