Forbidden synonymous substitutions in coding regions

In the evolution of highly conserved genes, a few "synonymous"substitutions at third bases that would not alter the protein sequence areforbidden or very rare, presumably as a result of functional requirementsof the gene or the messenger RNA. Another 10% or 20% of codons aresignificantly less variable by synonymous substitution than are themajority of codons. The changes that occur at the majority of third basesare subject to codon usage restrictions. These usage restrictions controlsequence similarities between very distant genes. For example, 70% of thirdbases are identical in calmodulin genes of man and trypanosome. Third-basesimilarities of distant genes for conserved proteins are mathematicallypredicted, on the basis of the G+C composition of third bases. Theseobservations indicate the need for reexamination of methods used tocalculate synonymous substitutions.