Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration

Advocates of cladistic parsimony methods have invoked the philosophy of Kar l Popper in an attempt to argue for the superiority of those methods over p hylogenetic methods based on Ronald Fisher's statistical principle of likel ihood. We argue that the concept of likelihood in general, and its applicat ion to problems of phylogenetic inference in particular, are highly compati ble with Popper's philosophy. Examination of Popper's writings reveals that his concept of corroboration is, in fact, based on likelihood. Moreover, b ecause probabilistic assumptions are necessary for calculating the probabil ities that define Popper's corroboration, likelihood methods of phylogeneti c inference- with their explicit probabilistic basis- are easily reconciled with his concept. In contrast, cladistic parsimony methods, at least as de scribed by certain advocates of those methods, are less easily reconciled w ith Popper's concept of corroboration. If those methods are interpreted as lacking probabilistic assumptions, then they are incompatible with corrobor ation. Conversely, if parsimony methods are to be considered compatible wit h corroboration, then they must be interpreted as carrying implicit probabi listic assumptions. Thus, the non-probabilistic interpretation of cladistic parsimony favored by some advocates of those methods is contradicted by an attempt by the same authors to justify parsimony methods in terms of Poppe r's concept of corroboration. In addition to being compatible with Popperia n corroboration, the likelihood approach to phylogenetic inference permits researchers to test the assumptions of their analytical methods (models) in a way that is consistent with Popper's ideas about the provisional nature of background knowledge.