Based on their studies of hemoglobin amino acid sequences, Emile Zuckerandl and Linus Pauling (1965), suggested that the rates of amino acid substitution were approximately constant for any protein across all evolutionary lineages. They called this idea the molecular clock, and it stands as one of the oldest and most intense controversies in molecular evolution. The existence of a universal molecular clock would allow for easy dating of phylogenetic divergence of organisms and simplify the process of reconstruction of their evolutionary histories. Yet studies of evolution at morphological and physiological levels have shown that evolution proceeds at an uneven pace when separate lineages are compared, and that the rate of evolution can vary greatly for a single lineage through time (Eldredge and Gould 1972).

Data published shortly after the original proposal of a universal molecular clock supported the hypothesis. Ohta and Kimura (1971) showed that at least "as a first approximation," the rate of amino acid substitution is constant for hemoglobins and cytochrome c across a variety of vertebrates. This early evidence of rate constancy was supported by Kimura’s (1968) neutral theory, which holds that the majority of evolutionary change at the molecular level is caused not by positive selection on advantageous alleles, but rather by random drift of selectively neutral mutations. These mutations should accumulate at a relatively constant rate, and would not be subject to the pattern of punctuated equilibrium shown for morphological traits by Eldrige and Gould (1972).

Ochman and Wilson (1987) reported evidence for the existence of a universal molecular clock by examining the evolution of bacteria. They first established phylogenetic relationships among the bacterial species in question through geologic evidence relating to both the bacteria themselves and ecologically significant events with which the bacteria are tied. For example, species of Rhizobium and Bradyrhizobium live in or near the nodules of the roots of legumes and a few other flowering plants, where they fix atmospheric nitrogen. Nearly all legumes have such a symbiotic relationship, so the authors estimate the date of the appearance of legumes (100-120 MYA) as a minimum time for the existence of these species of bacteria. They place the maximum boundary at the time of the origin of roots, about 415 MYA based on geologic evidence.

If these dates were more exact, they could have been used to calculate rate of change from the exact time of divergence. However, the uncertainty in divergence time led them to use the relative rate test (Sarich and Wilson 1973), which is use to determining relative rates of sequence divergence when the timing of divergence is unknown. This determination is accomplished by comparing the sequence of each taxon to a known outgroup of all of the taxa of interest. By examining 21 kb of protein coding nuclear DNA, they arrived at a silent substitution rate of 0.7-0.8%/My, a rate similar to the rate observed in a wide variety of nuclear genes in mammals, invertebrates and flowering plants. The average substitution rate for 16S rRNA in eubacteria was 1%/50 My, and the substitution rate for 5S rRNA was 1%/25 My, both of which correspond quite closely with rates of divergence measured in eukaryotes. Ochman and Wilson interpret these data to support a universal molecular clock, at least for synonymous substitutions.

Despite the evidence presented by Ochman and Wilson, the vast majority of evidence supports the belief that there is no universal molecular clock. Using DNA-DNA hybridization studies of species with clear divergence times based on the geological record, Britten (1986) showed that higher primates and birds have significantly slower rates of divergence than the Drosophila, sea urchin and rodents he examined. Latter studies have reached the same concluding as Britten with regards to a lack of a universal molecular clock.

A variety of studies on primates have suggested that apes and humans have slower rates of evolution than Old World monkey lineages. Many of these data are summarized by Li (1993) who noted that the original conclusion of a "hominoid rate slowdown" (based on protein sequences) used incorrect estimates of divergence times of the groups involved. More recent studies have focused on DNA sequences of pseudogenes, introns and flanking regions (Li 1993). Using New World monkeys as an outgroup, relative rate tests were performed on the sequences of Old World monkey and human sequences, revealing a consistent, statistically significantly slower rate of evolution in humans.

Variation in rates of evolution is not limited solely to vertebrates, or even to animals. Gaut et al. (1992) examined gene sequences for the chloroplast gene rbcL (the large subunit of ribulose-1,5-bisphosphate carboxylase-oxygenase, Rubisco) from 35 monocotyledonous plants. Using Magnolia macrophylla (a dicot) as an outgroup they found that 307 of 595 (51.6%) possible species pairs showed different rates of change. The fastest evolving group, grasses, was shown to have an overall rate of evolution five times faster and a silent site rate eight times faster than palms, the slowest group.

These three studies are a small part of the total documentation of rate heterogeneity observed among variety of evolutionary lineages. While these studies clearly indicate that no universal molecular clock exists, there is good evidence that a molecular clock can exist for certain lineages. (Such a clock is known as a local clock.) O’hUigin and Li (1992) compared 28 genes in common between muroids (rats and mice), hamsters and humans. The authors first used the hamster as an outgroup to test the rates of divergence of mice and rats. The relative rate test showed an overall substitution rates of 31.1% ± 1.0% and 32.4% ± 1.0%, respectively. These are not significantly different, indicating that the molecular clock has been uniform for these two species. They then used humans as an outgroup to test the substitution rates of hamsters with comparison to mice and rats. The substitution rates were 51.6% ± 1.4%, 53.5% ± 1.4%, and 52.7% ± 1.4% respectively, none of which are statistically different from one another. Apparently, a molecular clock can exist, if only locally.


Eldredge, N. AND S. J. Gould. 1972. Punctuated equilibria: An alternative to phyletic gradualism. Pp 82-115 In T. J. M. Schoph, ed. Models in Paleobiology. Freeman, Cooper and Company, San Fransisco.

Gaut, B. S., S. V. Muse, W. D. Clark, and M. T. Clegg. 1992. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J. Mol. Evol. 35:292-303.

Kimura, M. 1968. Evolutionary rate at the molecular level. Nature. 217:624-626.

Li, W.-H. 1993. So, what about the molecular clock hypothesis? Curr. Opin. Gen. Dev. 3:896-901.

Ochman, H. and A. C. Wilson. 1987. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26:74-86.

O’hUigin, C. and W.-H. Li. 1992. The molecular clock ticks regularly in muroid rodents and hamsters. J. Mol. Evol. 35:377-384.

Ohta, T. and M. Kimura. 1971. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1:18-25.

Sarich, V. M. and A. C. Wilson. 1973. Generation time and genomic evolution in primates. Science. 179:1200-1203.

Zuckerkandl, E. and L. Pauling. 1956. Evolutionary divergence and convergence in proteins. Pp 97-165 In V. Bryson, and H. J. Vogel, eds. Evolving genes and proteins. Academic Press, New York.

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