Abstract
Felsenstein (1985) developed a method for analyzing comparative data that calculates a set of mutually independent comparisons among the species. The method was designed to be used with phylogenies for which the true dichotomous branching pattern is known. However, available phylogenies often contain many incompletely resolved nodes, or nodes from which three or more branches emanate. This paper reports a generalization of Felsenstein's method that permits the analysis of incompletely resolved phylogenies. The method is general to any sort of phylogeny and, like Felsenstein's model can accommodate more than one model of evolutionary change. The method is implemented in a computer program which can make use of information on branch lengths, or, if branch length information is not available, an algorithm is used to calculate a set of branch lengths. The wider implications of the method are that it makes explicit the assumptions about unknown branching patterns and branch lengths that all comparative methods that are applied to incompletely resolved phylogenies must make.
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