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STATISTICAL COVARIANCE AS A MEASURE OF PHYLOGENETIC RELATIONSHIP

Abstract— The method of parsimony in phylogenetic inference is often taken to mean two things: (1) that one should favor the genealogical hypothesis that minimizes the required number of homoplasies (matchings of independently evolved derived character states), and (2) that symplesiomorphies (matchings of primitive character states) have little or no evidential value for phylogenetic relationship. This paper shows both theses to be false by undermining recent likelihood arguments for them and by providing a more secure likelihood proof of a new method, which is incompatible with both (1) and (2).