Correcting parsimonious trees for unseen nucleotide substitutions: the effect of dense branching as exemplified by ribonuclease.

In a study of mammalian ribonuclease evolutionary rates, we applied the Fitch-Bruschi correction to reduce the bias caused by an unequal sampling of taxa in different lineages. The correction was clearly appropriate but only up to a point. The analysis showed that the sampling of taxa within the pecora was sufficiently intense that no correction for unseen, amino acid-changing, nucleotide substitutions was required. It was also found that the ribonuclease gene was duplicated at least twice at the origin of the pecoran branch of the artiodactyls.