Cladistic Information, Leaf Stability and Supertree Construction
نویسنده
چکیده
This thesis is about phylogenetic trees mathematical graph structures which represent the pattern of evolution. More speci cally, it is concerned primarily with cladograms, the simplest type of phylogenetic tree, and the information they provide about the branching pattern of evolution. Although theoretical in orientation a real dataset is analysed in some detail and a user-friendly program provided. Many di erent measures have been proposed to measure the information content of phylogenetic trees. The problems associated with each method are illustrated and a new information theoretic family of measures is de ned. The quanti cation of the Cladistic Information Content of source trees, strict consensus trees, individual leaves and the root is then discussed in some detail and the utility of the measure as a criterion of strict consensus tree choice explored. Traditionally stability studies have focused on the stability of branches. I de ne a family of measures of the stability of individual leaves and the overall phylogenetic stability. Speci c measures are then compared and used to test published claims regarding the a ect of an early tetrapod on the stability of the inferred phylogenetic relationships. Supertree consensus methods allow the fusion of smaller subtrees, on partially overlapping set of leaves, to produce larger supertrees. The various problems associated with the fusion of compatible subtrees are reviewed and some additional solutions provided. The limitations of Matrix Representation with Parsimony (MRP), the most commonly used supertree consensus method which attempts to resolve con icts, are discussed. The Reduced supertree consensus method which removes and represents con icts but does not attempt to resolve them is then described and an attempt made to characterize the method. RadCon, a MacOS computer program which implements many of the methods discussed in this thesis, The RadCon Manual and some of the C++ source code is also provided.
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RadCon: phylogenetic tree comparison and consensus
SUMMARY RadCon is a Macintosh program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information Content of individual trees, the stability of leaves across a set of bootstrap trees, produce the strict basic Reduced Cladistic Consensus profile of a set of trees and convert a set of trees into its matrix representation for supertree construction. AVA...
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