Alternative Methods of Phylogenetic Inference and Their Interrelationship

Abstract

A probabilistic model of evolution in a character is presented. It involves 2 character states, 0 and 1. The population may have a 3rd state, 01, in which there is polymorphism for both character states. There are 3 evolutionary events in the model: origination of state 1, reversion from state 1 and loss of polymorphism, plus an event corresponding to total misinterpretation of the character by the taxonomist. The maximum likelihood method of estimating the phylogeny is described. When the probabilities of the 4 events are taken to be extreme, then depending on their relative sizes under different circumstances 4 different phylogenetic inference methods emerge as maximum likelihood methods: the Camin-Sokal parsimony method, Farris''s Dollo parsimony method and the Estabrook-Johnson-McMorris compatibility method. A new method, the polymorphism parsimony method, also emerges. It explains parallelism and convergence by persistence of character-state polymorphism after a unique origin of the derived character state and attempts to find that evolutionary tree which requires the least extent of polymorphism. Details of implementation of the polymorphism parsimony method are given. Some variants of the evolutionary model, involving unrooted character state trees, are discussed. The use of the model to resolve a paradox which arises when the Dollo parsimony method is applied to multiple-state characters is briefly considered.