Three-item analysis: Hierarchical representation and treatment of missing and inapplicable data

Abstract Matrix-based methods, including parsimony programs, represent and treat missing data in the same way, such that every character-state is possible, and inapplicable data, such that every character state is impossible. This is because the hierarchical nature of homology assessments cannot be represented in taxon–character matrices. We show that the hierarchical representation of hypotheses of homology used in three-item analysis permits the accurate treatment of missing and inapplicable data.

[1]  L. Grande,et al.  A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy : an empirical search for interconnected patterns of natural history , 1998 .

[2]  J. Hawkins,et al.  Primary Homology Assessment, Characters and Character States , 1997, Cladistics : the international journal of the Willi Hennig Society.

[3]  Régine Vignes-Lebbe,et al.  Hierarchical representation of hypotheses of homology , 2007 .

[4]  David M. Williams.  Homologues and Homology, Phenetics and Cladistics: 150 Years of Progress , 2004 .

[5]  G. Nelson,et al.  Three-Area Statements: Standard Assumptions for Biogeographic Analysis , 1991 .

[6]  Gottlob Frege,et al.  Écrits logiques et philosophiques , 1971 .

[7]  James M. Clark,et al.  PROBLEMS DUE TO MISSING DATA IN PHYLOGENETIC ANALYSES INCLUDING FOSSILS: A CRITICAL REVIEW , 2003 .

[8]  A. Kluge.  THREE‐TAXON TRANSFORMATION IN PHYLOGENETIC INFERENCE: AMBIGUITY AND DISTORTION AS REGARDS EXPLANATORY POWER , 1993 .

[9]  J. Freudenstein.  Characters, states, and homology. , 2005, Systematic biology.

[10]  Michel Launay,et al.  Conjectures et réfutations : la croissance du savoir scientifique , 1985 .

[11]  Dong-Chan Lee,et al.  A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems , 1999, Cladistics : the international journal of the Willi Hennig Society.

[12]  Mark Wilkinson,et al.  THREE‐TAXON STATEMENTS: WHEN IS A PARSIMONY ANALYSIS ALSO A CLIQUE ANALYSIS? , 1994 .

[13]  G. Nelson,et al.  3 – HOMOLOGY AND SYSTEMATICS , 1994 .

[14]  H. Lelièvre,et al.  Temporal information, fossil record and phylogeny , 2008 .

[15]  R. E. Strauss,et al.  EVALUATION OF THE PRINCIPAL-COMPONENT AND EXPECTATION-MAXIMIZATION METHODS FOR ESTIMATING MISSING DATA IN MORPHOMETRIC STUDIES , 2003 .

[16]  Jacques Lebbe,et al.  Representation des concepts en biologie et en medecine. Introduction a l'analyse des connaissances et a l'identification assistee par ordinateur , 1991 .

[17]  Gareth Nelson,et al.  Information Content and Fractional Weight of Three-Item Statements , 1992 .

[18]  V. Schawaroch,et al.  THREE STEPS OF HOMOLOGY ASSESSMENT , 1996, Cladistics : the international journal of the Willi Hennig Society.

[19]  René Descartes.  Discours de la methode : pour bien conduire sa raison, et chercher la verité dans les sciences, plus, La dioptrique, Les meteores, et, La geometrie qui sont des essais de cette methode , 1986 .

[20]  N. Platnick,et al.  THREE‐TAXON STATEMENTS: A MORE PRECISE USE OF PARSIMONY? , 1991 .

[21]  Norman I. Platnick,et al.  CHARACTER OPTIMIZATION AND WEIGHTING: DIFFERENCES BETWEEN THE STANDARD AND THREE‐TAXON APPROACHES TO PHYLOGENETIC INFERENCE , 1993, Cladistics : the international journal of the Willi Hennig Society.

[22]  N. Platnick.  Philosophy and the Transformation of Cladistics , 1979 .

[23]  Mário C. C. Pinna.  CONCEPTS AND TESTS OF HOMOLOGY IN THE CLADISTIC PARADIGM , 1991 .

[24]  W. Maddison.  Missing Data versus Missing Characters in Phylogenetic Analysis , 1993 .

[25]  C Patterson,et al.  Significance of Fossils in Determining Evolutionary Relationships , 1981 .

[26]  F. Pleijel.  ON CHARACTER CODING FOR PHYLOGENY RECONSTRUCTION , 1995 .

[27]  David M. Williams,et al.  Milestones in Systematics , 2004 .

[28]  Gareth Nelson,et al.  Systematics and Biogeography: Cladistics and Vicariance , 1981 .

[29]  P. Tassy,et al.  Temporal paralogy, cladograms, and the quality of the fossil record , 2004 .

[30]  I. Kitching.  Cladistics: The Theory and Practice of Parsimony Analysis , 1998 .