Generalized Frequency Coding: A Method of Preparing Polymorphic Multistate Characters for Phylogenetic Analysis

A new method of coding polymorphic multistate characters for phylogenetic analysis is presented. By dividing such characters into subcharacters, their frequency distributions can be represented with discrete states. Differential weighting is used to counter the effect of representing one character w...

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Bibliographic Details
Published in:Systematic biology 2001-04, Vol.50 (2), p.156-169
Main Authors: Smith, Eric N., Gutberlet, Ronald L., Wiens, J.
Format: Article
Language:English
Subjects:
Animals
Biological taxonomies
Biometry - methods
Cladistics
Classification
Data coding
Databases, Genetic
Datasets
Frequency distribution
Generalized frequency coding
Genetics
Methods
Parsimony
phylogenetic systematics
Phylogenetics
Phylogeny
polymorphic multistate characters
Polymorphism, Genetic
step matrix coding
Taxa
Term weighting
Viperidae - classification
Viperidae - genetics
Zoology
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Description
Summary:A new method of coding polymorphic multistate characters for phylogenetic analysis is presented. By dividing such characters into subcharacters, their frequency distributions can be represented with discrete states. Differential weighting is used to counter the effect of representing one character with multiple characters. The new method, generalized frequency coding (GFC), is potentially superior to previously used methods in that it incorporates more information and is applicable to both qualitative and quantitative characters. When applied to a previously published data set that includes both types of polymorphic multistate characters, the method performed well, as assessed with g1 and nonparametric bootstrap statistics and giving results congruent with those of other studies. The data set was also used to compare GFC with both gap-weighting and Manhattan distance step matrix coding. On these grounds and for philosophical reasons, we consider GFC to be a better estimator of phylogeny.
ISSN:1063-5157
1076-836X
DOI:10.1080/10635150121392