Positive selection is usually considered in the context of a higher rate of substitutions in non-synonymous as compared to synonymous sites in complete coding sequences of genes or individual positions. We show that genes conserved in eukaryota, coelomata, and bilateria, that is, proteins that arose earlier in evolution as compared to mammalia specific genes evolve slowly and are subjected to negative selection. This finding supports the notion that evolutionary rates progressively diminish with the age of a gene. The data suggests that in both intron-containing and intronless genes synonymous sites may be subject to some degree of selection that is indicative of a relative acceleration of amino-acid substitution, which could be due to a relaxation of functional constraints and/or directional selection.