A bayesian probability view of phylogenetic systematics

Abstract

The development of hypotheses in phylogenetic systematics involves two activities: (1) the construction of phylogenetic hypotheses, and (2) subjecting these hypotheses to critical tests. Both may be analyzed within the framework of Bayes’ theorem. Both are, in my view, inherently probabilistic and, as such, do not fit well into Popper’s rigidly deductive models of scientific methodology. Regarding item (1), phylogenetic hypotheses are constructed, wholly or in part, by applying an ordering principle of shared derived character states to M taxa out of a group of N taxa. In order to establish a rational basis for when to apply the ordering principle (when to believe it), the principle is analyzed in terms of a relative frequency model. Application of Bayes’ theorem to this model, first for M = 2, and then for M b 2, establishes a necessary condition for applying the ordering principle. As it turns out, the conditions under which one might rationally apply the principle vary markedly from one value of N (and M) to the next; this conclusion provides a good incentive for following a probabilistic approach when applying the ordering principle. The testing of phylogenetic hypotheses (item 2 above) is also viewed in terms of Bayes’ theorem. These probabilistic approaches contrast markedly with the strictly deductive view of scientific methodology developed by Popper. [Phylogenetic systematics; phyletics; phylogeny construction; Bayesian probability.]. © 1979 Oxford University Press.