The augmentation algorithm and molecular phylogenetic trees

Summary The augmentation procedure of G.W. Moore leads to correct estimates of the total number of nucleotide substitutions separating two genes descendent from a common ancestor provided the data base is sufficiently dense. These estimates are in agreement with the true distance values from simulations of known evolutionary pathways. The estimates, on the average, are unbiased: they neither overaugment nor underaugment seriously. The variance of the population of augmented distance values reflects accurately the variance of the population of true distance values and is thus not abnormally large due to procedural defects in the algorithm.The augmented distances are in agreement with stochastic models tested on real data when the latter take proper account of the restricted mutability of codons resulting from natural selection.When the experimental data base is not dense, the augmented distance values and population variance may underestimate both the true distance values and their variance. This has a logical consequence that there exist significant and numerous errors in the ancestral sequences reconstructed by the parsimony principle from such data bases.The restrictions, resulting from natural selection, on the mutability of different nucleotide sites is shown to bear critically on the accuracy of estimates of the total number of nucleotide replacements made by stochastic models.