Estimating the total number of nucleotide substitutions since the common ancestor of a pair of homologous genes: Comparison of several methods and three beta hemoglobin messenger RNA's

Summary

The mRNA sequences of beta hemoglobin for human, mouse and rabbit were examined. Observations included the following: (1) there is a significant bias against the use of codons only one nucleotide different from terminating codons; (2) less than 4% of the codons end in adenine; (3), guanine is the most common third position nucleotide but it never follows a second position cytosine; (4) nearest neighbor (doublet) nucleotides are non-random with the greatest contributor to non-randomness being the third position suggesting that codon choice for a given amino acid rather than a choice among amino acids is the more important contributor; (5) the CG dinucleotide is even rarer in positions other than the first and second of the codon than it is in those two, suggesting that the need for arginine has in fact elevated the CG frequency in those positions; (6) 77 per cent of the nucleotides are unsubstituted among these three taxa, which could be a sampling effect, but there is strong evidence that about one-third of them are in fact unsubstitutable because of selective constrainsts; (7) the two longest stretches of unsubstituted nucleotides (32 and 35 consecutive nucleotides) surround the points of the two non-coding insertion sequences; (8) over half the substitutions occur in the third nucleotide position of the codons; (9) silent (non-amino acid changing) substitutions occur at about four times the rate of non-silent substitutions on the basis of their relative opportunity to occur; (10) silent substitutions occur slightly but significantly more often in codons that also have non-silent substitutions than independence of the two events would predict; (11) substitutions occur in adjacent nucleotides significantly more often than chance would predict; (12) among four-fold degenerate codons, third position transitions (principally cytosine-uracil interchanges) outnumber transversions by two to one although the reverse ratio would be expected.

The analysis of these messengers provided an opportunity to evaluate the random evolutionary hit (REH) theory. I observed that: (1) the REH theory is premised upon five assumptions, all false; (2) the theory leads to contradictory estimates of the number of varions; (3) the REH values are underestimates; (4) the REH values frequently violate the triangle inequality; (5) the REH values, contrary to claim, are not concordant either with accepted point mutations (PAMs) or augmented distances; (6) the REH values are more likely than values uncorrected for multiple substitutions to give incorrect phylogenies; and (7) the REH values have statistical problems probably associated with a large variance in its fundamental parameter, r_e. From this I conclude that REH theory is not suitable for its intended purpose of estimating from protein sequences of nucleotide substitutions since the common ancestor of two gene products.