Reading the molecular clock from the decay of internal symmetry of a gene

The closely related serum albumin, alpha-fetoprotein, and vitamin D-binding proteins are derived from a common ancestor, which itself was the result of a triplication of an ancestral gene. We have aligned the sequences of these proteins against themselves to assess the degree to which the ancestral 3-fold symmetry has been retained; in a dot plot, relics of the molecular symmetry appear as a series of alignments parallel to the main diagonal. The decay of internal symmetry reflects the rate of change of a gene in a single line of evolutionary descent. We examined 11 serum albumins, 2 ceruloplasmins, 3 alpha-fetoproteins, and 3 vitamin D-binding proteins. We have found that ceruloplasmin evolves at the same rate in human and rat, whereas albumin, alpha-fetoprotein, and vitamin D-binding protein evolve at different rates. The human genes had the highest alignment scores, indicating the most preserved ancestral features. We conclude that the molecular clock may run at different rates for the same gene in different species.