Estimation of phylogenetic relationships from DNA restriction patterns and selection of endonuclease cleavage sites

The distribution of cleavage sites and their related sequences have been analyzed for 54 restriction endonucleases in the genome of human mitochondrial DNA; in three papova viruses, BK, simian virus 40, and polyoma; and in three bacteriophages, phi X174, fd, and G4. The results show that the cleavage sites and related sequences for most of the restriction enzymes tested are distributed nonrandomly. These results (i) constitute prima facie evidence for the action of natural selection, either direct or indirect on the restriction sites, and (ii) suggest that estimates of phylogenetic relationship, based on a phenetic approach using restriction enzyme data, will be biased.