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Quantification of the success of phylogenetic inference in simulations
Author(s) -
Simmons Mark P.,
Webb Colleen T.
Publication year - 2006
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.1096-0031.2006.00105.x
Subject(s) - phylogenetic tree , synapomorphy , tree (set theory) , context (archaeology) , inference , clade , contrast (vision) , resolution (logic) , mathematics , artificial intelligence , computer science , topology (electrical circuits) , algorithm , biology , combinatorics , paleontology , biochemistry , gene
For phylogenetic simulation studies, the accuracy of topological reconstruction obtained from different data matrices or different methods of phylogenetic inference generally needs to be quantified. Two components of performance within this context are: (1) how the inferred tree topology matches or conflicts with the correct tree topology, and (2) the branch support assigned to both correctly and incorrectly resolved clades. We present a method (averaged overall success of resolution) that incorporates both of these components. Branch support is incorporated in the averaged overall success of resolution by linearly scaling the observed support relative to that conferred by uncontradicted synapomorphies. We believe that this method represents an improvement relative to the commonly used approaches of quantifying the percentage of clades that are correctly resolved in the inferred trees or presenting the Robinson–Foulds distance between the inferred trees and the correct tree. In contrast to Bremer support, the averaged overall success of resolution may be applied equally well to distance, likelihood and parsimony analyses. © The Willi Hennig Society 2006.