Molecular evolution in papova viruses and in bacteriophages.

By comparing the DNA sequences of three eukaryotic papova viral genomes, we attempt to show the very close relative phylogeny among the viral species and their host species, and that therefore the viral species appear to have evolved with their hosts. A comparison of the DNA data also reveals that the rate of nucleotide substitutions at the third positions of codons is much faster than at the first and second positions, though the rate varies depending upon the genes. The estimated rates of amino acid substitutions in homologous genes among the three virus species appear to be considerably faster than the rates known for various vertebrate genes. The comparison reveals further that the rate of silent substitutions is faster than that of replacement substitutions. The DNA sequence data on bacteriophages phi X174 and G4 enable us to examine the patterns of nucleotide substitutions in overlapping genes as well as in nonoverlapping genes. It then becomes evident that overlapping genes have a quite different substitutional pattern with respect to the position of nucleotides in codons than do nonoverlapping sequences. In nonoverlapping regions the third positions usually change the fastest among the three codon positions. This pattern does not apply to overlapping genes, which are coded in the same region but with different reading frames. It will be shown that the younger of the two overlapping genes appears to be very tolerant to nucleotide substitutions at any codon position. Further more, the rate of substitution at each nucleotide site appears to be determined by the rate of the corresponding site in the older of the two overlapping genes.