Stochastic versus augmented maximum parsimony method for estimating superimposed mutations in the divergent evolution of protein sequences. Methods tested on cytochrome c amino acid sequences.

Two ways of estimating superimposed fixed mutations in the divergent descent of proteins are examined. One method counts these in terms of a Poisson process operating within selective constraints. The other uses the maximum parsimony method to connect the contemporary sequences through intervening ancestral sequences in an evolutionary tree, and then, from the distribution of fixed mutations in dense regions of this genealogy, estimates how many fixations should be added to sparse regions. An algorithm is described which determines such augmented distances. The two methods yield similar estimates of genetic divergence when tested on a series of cytochrome c amino acid sequences. Within those constraints imposed by Darwinian selection, the dynamic behavior of the evolutionary divergence of proteins is described by the probabilistic pathways of the stochastic model. The parsimony model provides a valid Aufbau-Prinzip for examining which of those pathways occurred along a particular lineage. Concordance of the numerical magnitudes of genetic divergence estimates made by the two methods reveals them as logically consistent complements, not as mutually exclusive antagonists. Both methods indicate that cytochrome c has evolved in a non-uniform manner over geological time and more rapidly than previously estimated.