Rates of molecular evolution can be remarkably constant over time, producing a molecular clock.
The constancy of rates was explained by the neutral theory by assuming that most changes to DNA or protein sequences are neutral — that is, driven by drift not selection.
The neutral theory has been refined to allow for the effect of population size on the chance of mutations of small selective effect being fixed in a population (the nearly neutral theory).
The molecular clock is a 'sloppy' clock: theory predicts that the rate of molecular evolution will be influenced by mutation rate, patterns of selection and population size.
Stochastic fluctuations in substitution rate over time in lineages (residual effects) make molecular date estimates imprecise.
Variation in rate between lineages can cause substantial bias in molecular date estimates.
Attempts to use molecular clocks to date evolutionary divergences must account for these sources of imprecision and bias, and variation in rates must be expressed in confidence intervals around date estimates.
The discovery of the molecular clock — a relatively constant rate of molecular evolution — provided an insight into the mechanisms of molecular evolution, and created one of the most useful new tools in biology. The unexpected constancy of rate was explained by assuming that most changes to genes are effectively neutral. Theory predicts several sources of variation in the rate of molecular evolution. However, even an approximate clock allows time estimates of events in evolutionary history, which provides a method for testing a wide range of biological hypotheses ranging from the origins of the animal kingdom to the emergence of new viral epidemics.
This is a preview of subscription content
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Smith, A. B. & Peterson, K. J. Dating the time of origin of major clades: molecular clocks and the fossil record. Annu. Rev. Earth Planet. Sci. 30, 65–88 (2002). A review of the controversy surrounding dates for the Cambrian explosion of animal phyla and the early Tertiary radiation of modern mammals and birds. Written by a palaeontologist and a molecular geneticist, this review takes a critical look at the reliability of both fossil and molecular dates.
Korber, B. et al.Timing the ancestor of the HIV-1 pandemic strains. Science 288, 1789–1796 (2000).
Zuckerkandl, E. & Pauling, L. in Horizons in Biochemistry (eds Kasha, M. & Pullman, B.) 189–225 (Academic Press, New York, 1962).
Kimura, M. & Ohta, T. On the rate of molecular evolution. J. Mol. Evol. 1, 1–17 (1971).
Dickerson, R. E. The structure of cytochrome c and rates of molecular evolution. J. Mol. Evol. 1, 26–45 (1971).
Penny, D., McComish, B. J., Charleston, M. A. & Hendy, M. D. Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 53, 711–723 (2001).
Smith, N. H. & Eyre-Walker, A. Adaptive protein evolution inDrosophila. Nature 415, 1022–1024 (2002).
King, J. L. & Jukes, T. H. Non-Darwinian evolution. Science 164, 788–798 (1969).
Darwin, C. The Origin of Species by Means of Natural Selection 6th edn Ch. 4 64 (John Murray, London, 1872). Remarkably prescient exposition of the processes of evolution, including a pre-genetic description of the neutral theory, pre-emptively rebutting rumours that neutral evolution is 'non–Darwinian'.
Fleischer, R. C., McIntosh, C. E. & Tarr, C. L. Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar based ages of the Hawaiian islands to estimate molecular evolutionary rates. Mol. Ecol. 7, 533–545 (1998).
Gillespie, J. H. The Causes of Molecular Evolution (Oxford University Press, Oxford, UK, 1991).
Zheng, Q. On the dispersion index of a Markovian molecular clock. Math. Biosci. 172, 115–128 (2001). This gives a statistical view of the expected variability in rates that occur when the simple probabilistic models of molecular evolution are allowed to increase in complexity.
Bickel, D. R. Implications of fluctuations in substitution rates: impact on the uncertainty of branch lengths and on relative-rate tests. J. Mol. Evol. 50, 381–390 (2000).
Cutler, D. J. Estimating divergence times in the presence of an overdispersed molecular clock. Mol. Biol. Evol. 17, 1647–1660 (2000).
Bastolla, U., Porto, M., Roman, H. E. & Vendruscolo, M. Lack of self-averaging in neutral evolution of proteins. Phys. Rev. Lett. 89, article no. 208101 (2002). This original paper follows the evolution of protein sequences that are restricted in their predicted tertiary structure. It shows, using basic biochemical principles, that the variability in rates of a molecular clock is expected to be higher than for a simple Poisson process.
Fitch, W. M. Rate of change of concomitantly variable codons. J. Mol. Evol. 1, 84–96 (1971).
Swanson, K. W., Irwin, D. M. & Wilson, A. C. Stomach lysozyme gene of the langur monkey: tests for convergence and positive selection. J. Mol. Evol. 33, 418–425 (1991).
Zhang, J. Z., Zhang, Y. P. & Rosenberg, H. F. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nature Genet. 30, 411–415 (2002).
Papadopoulos, D. et al. Genomic evolution during a 10,000-generation experiment with bacteria. Proc. Natl Acad. Sci. USA 96, 3807–3812 (1999). A laboratory experiment comparing rates of morphological and molecular evolution in bacterial populations. Although adaptive phenotypic evolution was fastest at the beginning, DNA substitutions accumulated steadily through the experiment, indicating that the molecular clock is decoupled from the pace of adaptive evolution.
Bromham, L., Woolfit, M., Lee, M. S. Y. & Rambaut, A. Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution 56, 1921–1930 (2002).
Wyles, J. S., Kunkel, J. G. & Wilson, A. C. Birds, behavior, and anatomical evolution. Proc. Natl Acad. Sci. USA 80, 4394–4397 (1983).
Ohta, T. & Kimura, M. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1, 18–25 (1971).
Ohta, T. Very slightly deleterious mutations and the molecular clock. J. Mol. Evol. 26, 1–6 (1987).
Ohta, T. Near-neutrality in evolution of genes and gene regulation. Proc. Natl Acad. Sci. USA 99, 16134–16137 (2002). The most recent exposition of the nearly-neutral model, in which the effects of weak selection depend both on the selection coefficient of the mutation and the size of the population in which the mutant occurs.
Felsenstein, J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376 (1981).
Rambaut, A. & Bromham, L. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15, 442–448 (1998).
Bromham, L., Rambaut, A., Fortey, R., Cooper, A. & Penny, D. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proc. Natl Acad. Sci. USA 95, 12386–12389 (1998).
Bromham, L. D., Rambaut, A., Hendy, M. D. & Penny, D. he power of relative rates tests depends on the data. J. Mol. Evol. 50, 296–301 (2000).
Drake, J., Charlesworth, B., Charlesworth, D. & Crow, J. Rates of spontaneous mutation. Genetics 148, 1667–1686 (1998). Observable mutation rates, when measured per genome per generation, are remarkably similar across widely divergent organisms, indicating that natural selection might shape optimum mutation rates.
Ota, R. & Penny, D. Estimating changes in mutational mechanisms of evolution. J. Mol. Evol. (in the press).
Hart, R. W. & Setlow, R. B. Correlation between deoxyribonucleic acid excision-repair and life-span in a number of mammal species. Proc. Natl Acad. Sci. USA 71, 2169–2173 (1974).
Li, W. -H., Ellesworth, D. L., Krushkal, J., Chang, B. H. -J. & Hewett-Emmett, D. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol. 5, 182–187 (1996).
Chao, L. & Cox, E. C. Competition between high and low mutating strains ofEscherichia coli. Evolution 37, 125–134 (1983).
Rand, D. M. Thermal habit, metabolic rate and the evolution of mitochondrial DNA. Trends Ecol. Evol. 9, 125–131 (1994).
Martin, A. P. & Palumbi, S. R. Body size, metabolic rate, generation time and the molecular clock. Proc. Natl Acad. Sci. USA 90, 4087–4091 (1993). Showed a relationship between body size and the rate of molecular evolution for vertebrates using estimates of absolute substitution rates. This paper showed that the life history of a species must influence the rate of molecular evolution.
Martin, A. P. Metabolic rate and directional nucleotide substitution in animal mitochondrial DNA. Mol. Biol. Evol. 12, 1124–1131 (1995).
Bromham, L., Rambaut, A. & Harvey, P. H. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43, 610–621 (1996).
Bromham, L. Molecular clocks in reptiles: life history influences rate of molecular evolution. Mol. Biol. Evol. 19, 302–309. (2002).
Mooers, A. Ø. & Harvey, P. H. Metabolic rate, generation time and the rate of molecular evolution in birds. Mol. Phylogenet. Evol. 3, 344–350 (1994).
Bromham, L. & Cardillo, M. Testing the link between the latitudinal gradient in species richness and rates of molecular evolution. J. Evol. Biol. 16, 200–207 (2003).
Held, C. No evidence for slow-down of molecular substitution rates at subzero temperatures in Antarctic serolid isopods (Crustacea, Isopoda, Serolidae). Polar Biol. 24, 497–501 (2001).
Bielas, J. H. & Heddle, J. A. Proliferation is necessary for both repair and mutation in transgenic mouse cells. Proc. Natl Acad. Sci. USA 97, 11391–11396 (2000).
Johnson, K. P. & Seger, J. Elevated rates of nonsynonymous substitution in island birds. Mol. Biol. Evol. 18, 874–881 (2001).
Schmitz, J. & Moritz, R. F. A. Sociality and the rate of rDNA sequence evolution in wasps (Vespidae) and honeybees Apis. J. Mol. Evol. 47, 606–612 (1998).
Moran, N. A. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl Acad. Sci. USA 93, 2873–2878 (1996).
Barraclough, T. G. & Savolainen, V. Evolutionary rates and species diversity in flowering plants. Evolution 55, 677–683 (2001).
Doolittle, R. F., Feng, D. F., Tsang, S., Cho, G. & Little, E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470–477 (1996).
Bromham, L. D., Phillips, M. J. & Penny, D. Growing up with dinosaurs: molecular dates and the mammalian radiation. Trends Ecol. Evol. 14, 113–118 (1999).
Bromham, L. Molecular clocks and explosive radiations. J. Mol. Evol. (in the press).
Wu, C. -I. & Li, W. -H. Evidence for higher rates of nucleotide substitutions in rodents than in man. Proc. Natl Acad. Sci. USA 82, 1741–1745 (1985).
Tajima, F. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135, 599–607 (1993).
Kumar, S. & Hedges, S. B. A molecular timescale for vertebrate evolution. Nature 392, 917–920 (1998).
Nei, M. & Glazko, G. V. Estimation of divergence times for a few mammalian and several primate species. J. Hered. 93, 157–164 (2002).
Takezaki, N., Rzhetsky, A. & Nei, M. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12, 823–833 (1995).
Bromham, L. D. & Hendy, M. D. Can fast early rates reconcile molecular dates to the Cambrian explosion? Proc. R. Soc. Lond. B 267, 1041–1047 (2000).
Sanderson, M. J. A nonparametric approach to estimating divergence times in the absence of rate constancy. J. Mol. Evol. 14, 1218–1231 (1997).
Kishino, H., Thorne, J. L. & Bruno, W. J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18, 352–361 (2001). This paper outlined new Bayesian methods for estimating dates of divergence if rates of molecular evolution vary between lineages, by allowing the mutation rate to vary with time, and averages its estimates over a range of alternatives.
Aris-Brosou, S. & Yang, Z. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst. Biol. 51, 703–714 (2002).
Rannala, B. Identifiability of parameters in MCMC Bayesian inference of phylogeny. Syst. Biol. 51, 754–760 (2002).
Bromham, L. The human zoo: endogenous retroviruses in the human genome. Trends Ecol. Evol. 17, 91–97 (2002).
Tristem, M. Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the Human Genome Mapping Project database. J. Virol. 74, 3715–3730 (2000).
Shankarappa, R. et al. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73, 10489–10502 (1999).
Twiddy, S. S., Holmes, E. C. & Rambaut, A. Inferring the rate and time-scale of dengue virus evolution. Mol. Biol. Evol. 20, 122–129 (2003).
Drummond, A., Pybus, O. G. & Rambaut, A. Inference of viral evolutionary rates from molecular sequences. Adv. Parasitol. (in the press). A review of the methods used to estimate substitution rates in viruses, including estimating molecular dates when rates vary.
Fitch, W. M., Leiter, J. M., Li, X. Q. & Palese, P. Positive Darwinian evolution in human influenza A viruses. Proc. Natl Acad. Sci. USA 88, 4270–4274 (1991).
Rambaut, A. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16, 395–399 (2000).
Page, R. D. M. & Holmes, E. C. Molecular Evolution: a Phylogenetic Approach (Blackwell Science, Oxford, UK, 1998).
Madsen, O. et al.Parallel adaptive radiations in two major clades of placental mammals. Nature 409, 610–614 (2001). Used the quartet method which uses several calibration dates to allow for differences in substitution rate between lineages to support the hypothesis that modern mammals arose long before the final extinction of the dinosaurs.
Conway Morris, S. Early metazoan evolution: reconciling paleontology and molecular biology. Am. Zool. 38, 867–877 (1998).
Valentine, J., Jablonski, D. & Erwin, D. Fossils, molecules and embryos: new perspectives on the Cambrian explosion. Development 126, 851–859 (1999).
Carroll, R. C. Towards a new evolutionary synthesis. Trends Ecol. Evol. 15, 27–32 (2000).
Kimura, M. The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, UK, 1983).
We thank A. Rambaut and A. Eyre-Walker for helpful comments.
- MAXIMUM LIKELIHOOD
The maximum-likelihood method takes a model of sequence evolution (essentially a set of parameters that describe the pattern of substitutions) and searches for the combination of parameter values that gives the greatest probability of obtaining the observed sequences.
- BAYESIAN APPROACH
A method that selects the tree that has the greatest posterior probability (the probability that the tree is correct), under a specific model of substitution.
- POISSON DISTRIBUTION
A discrete frequency distribution of the number of independent events per time interval, for which the mean value is equal to the variance.
Evolution at, or above, the level of species; the patterns and processes of diversification and extinction of species over evolutionary time.
The process of evolution in populations: changing allele frequencies over generations, due to selection or drift.
- HOX GENE COMPLEX
A group of linked regulatory genes that are involved in patterning the animal body axis during development.
- LIFE HISTORY
The reproductive strategy of an organism.
A 'cold-blooded' organism, such as a reptile, for which body temperature is dependent on the environment.
A 'warm-blooded' organism, such as a mammal or bird, for which body temperature is maintained independently of the environment.
- EFFECTIVE POPULATION SIZE
(Ne). The equivalent number of breeding adults in a population after adjusting for complicating factors, such as reproductive dynamics. It is usually less that the actual number of living or reproducing individuals (the census population size N).
An increase in allele frequency to the point at which all individuals in a population are homozygous.
A life-history strategy in which only a subset of members of a group produce their own offspring, and others act as non-reproductive helpers, as in honeybees or naked molerats.
- GENETIC DRIFT
The random fluctuation that occurs in allele frequencies as genes are transmitted from one generation to the next. This is because allele frequencies in any sample of gametes that perpetuate the population might not represent those of the adults in the previous generation.
A measure of the variation around the central class of a distribution (the average squared deviation of the observations from their mean value).
- RELATIVE RATES TEST
A test for variation in the rate of molecular evolution between lineages, which compares the distance between each of a pair of taxa and an outgroup to determine the relative amount of change in each lineage since their last common ancestor.
- TAJIMA TEST
A test for variation in the rate of molecular evolution between lineages, based on the expectation that under a uniform rate of substitution, the number of sites at which the amino-acid or nucleotide state is shared by the outgroup and only one of the two ingroups should be equal for both ingroups.
- LIKELIHOOD RATIO TEST
A method for hypothesis testing. The maximum of the likelihood that the data fit a full model of the data (in this case, multiple substitution rates) is compared with the maximum of the likelihood that the data fit a restricted model (a single substitution rate) and the likelihood ratio (LR) test statistic is computed. If the LR is significant, the full model provides a better fit to the data than does the restricted model.
About this article
Cite this article
Bromham, L., Penny, D. The modern molecular clock . Nat Rev Genet 4, 216–224 (2003). https://doi.org/10.1038/nrg1020
Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama
BMC Ecology and Evolution (2021)
Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes
BMC Ecology and Evolution (2021)
Cell Death Discovery (2021)
Nature Reviews Microbiology (2021)
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution
Nature Microbiology (2021)