MAXIMUM LIKELIHOOD INFERENCE OF PHYLOGENETIC TREES, WITH SPECIAL REFERENCE TO A POISSON PROCESS MODEL OF DNA SUBSTITUTION AND TO PARSIMONY ANALYSES

Maximum likelihood inference is discussed, and some of its advantages and dis- advantages are noted. The application of maximum likelihood inference to phylogenetics is examined, and a simple Poisson process model of DNA substitution is used as one example. Further examples follow from the clarification of implicit models underlying traditional "par- simony" and "compatibility" analyses. From the elucidation of these models and analyses, it is seen that Poisson process analysis gives a statistically consistent estimate of phylogeny, and that parsimony methods do indeed have a maximum likelihood foundation but give potentially incorrect estimates of phylogeny. The maximum likelihood formulation provides a common framework within which these analyses are discussed and compared. (Phylogenetic inference; maximum likelihood inference; Poisson process model; parsimony analysis; DNA substitution.)

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