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MONOPHYLY AND COMPARISONS BETWEEN TREES
Author(s) -
Wood Stephen W.
Publication year - 1994
Publication title -
cladistics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.323
H-Index - 92
eISSN - 1096-0031
pISSN - 0748-3007
DOI - 10.1111/j.1096-0031.1994.tb00184.x
Subject(s) - monophyly , mathematics , polyphyly , paraphyly , cluster (spacecraft) , tree (set theory) , combinatorics , statistics , phylogenetic tree , biology , computer science , clade , biochemistry , gene , programming language
— The Farris method for assessing the empirical status of groups, as either monophyletic, paraphyletic or polyphyletic, is discussed. The reasons for presenting the method in terms of the behaviour of abstract, rather than real, characters are upheld. The method (i) reflects the insight that monophyly and related terms are used in comparisons between trees, (ii) avoids the problems associated with definitions based on the exclusion of subgroups, (iii) avoids the contentious issue of inclusion vs. exclusion of a group's most recent common ancestor. The Farris method is shown to be equivalent to the cluster distortion method for comparing the shapes of a pair of trees. Descriptor variables for each cluster in a reference tree are mapped on to a comparison tree. If a cluster's descriptor requires homoplasy then the cluster is a nonmonophyletic group. If the cluster descriptors behave according to Wagner parsimony, the kind of nonmonophyletic group is determined by the kind of homoplasy exhibited by the descriptor variable. The single cluster distortion coefficient is shown to be equal to (1‐ri), where ri is the retention index of the descriptor variable on the comparison tree. The overall distortion coefficient acts as a tree comparison metric and is defined as (1‐RI) where RI is the ensemble retention index.