Parsimony is one of the principles of phylogenetic tree reconstruction in which the phylogeny of a group of species or genes is inferred to be the branching pattern that requires the smallest number of evolutionary changes (1). Of course, no one knows whether evolution actually occurred in this way, but the parsimony principle appears to work reasonably well, particularly for comparisons of closely related species or genes, but it tends to lose its effectiveness in comparison to more remotely related species or genes. For the latter comparisons, hidden mutational changes (due to reverse mutations) have accumulated to such an extent that the parsimony principle cannot detect all changes.
The merit of using the parsimony principle is that we can infer the amino acid or nucleotide sequences of all the intermediate stages in the continuous lineage between the ancestor and the present species. The intermediate stages may be trustworthy, however, only when closely-related genes are compared.
