The molecular evolution of cytochrome c in eukaryotes

Summary Using many more cytochrome sequences than previously available, we have confirmed: 1, the eukaryotic cytochromes c diverged from a common ancestor; 2, the ancestral eukaryotic cytochrome c was not greatly different in character from those present today; 3, fixations are non-randomly distributed among the codons, there being evidence for at least four classes of variability; 4, there are similar classes of variability when the data are considered according to the nucleotide position within the codon; 5, the number of covarions (concomitantly variable codons) in mammalian cytochrome c genes is about 12 and the same value has been obtained for dicotyledonous plants as well; 6, all of the hyper- and most highly variable codons are for external residues, nearly 60 per cent of the invariable codons are for internal residues and nearly half of the codons for internal residues are invariable; 7, the first nucleotide position of a codon is more likely and the second position less likely to fix mutations than would be expected on the basis of the number of ways that alternative amino acids can be reached; 8, the character of nucleotide replacements is enormously non-random, with GA interchanges representing 42% of those observed in the first nucleotide position, but the observation does not stem from a bias in the DNA strand receiving the mutation, nor from the presence of a compositional equilibrium, nor from a bias in the frequency with which different nucleotides mutate, but rather from a bias in the acceptability of an alternative nucleotide as circumscribed by the functional acceptability of the new amino acid encoded; and 9, the unit evolutionary period is approximately 150 million years/observable (amino acid changing) nucleotide replacement/cytochrome c covarion in two diverging lines.Wherever non-randomness has been observed, it has always been consistent with the consideration that an alternative amino acid at any location is more likely to be acceptable the more closely it resembles the present amino acid in its physico-chemical properties.Finally, in no case did the a priori assumption of a biologically realistic phylogeny lead to any observations or conclusions that were in any way significantly different from those obtained when the phylogeny was based solely upon the sequences, proving that the earlier results were not a consequence of some internal circularity.