Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The modern molecular clock

Nature Reviews Genetics volume 4, pages 216–224 (2003)Cite this article

Key Points

  • 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.

Abstract

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, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Selectionist, neutral and nearly neutral theories.
Figure 2: A molecular clock for the Hawaiian islands.

References

  1. 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.

    Article  CAS  Google Scholar 

  2. Korber, B. et al.Timing the ancestor of the HIV-1 pandemic strains. Science 288, 1789–1796 (2000).

    Article  CAS  PubMed  Google Scholar 

  3. Zuckerkandl, E. & Pauling, L. in Horizons in Biochemistry (eds Kasha, M. & Pullman, B.) 189–225 (Academic Press, New York, 1962).

    Google Scholar 

  4. Kimura, M. & Ohta, T. On the rate of molecular evolution. J. Mol. Evol. 1, 1–17 (1971).

    Article  CAS  PubMed  Google Scholar 

  5. Dickerson, R. E. The structure of cytochrome c and rates of molecular evolution. J. Mol. Evol. 1, 26–45 (1971).

    Article  CAS  PubMed  Google Scholar 

  6. 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).

    Article  CAS  PubMed  Google Scholar 

  7. Smith, N. H. & Eyre-Walker, A. Adaptive protein evolution inDrosophila. Nature 415, 1022–1024 (2002).

    Article  CAS  PubMed  Google Scholar 

  8. King, J. L. & Jukes, T. H. Non-Darwinian evolution. Science 164, 788–798 (1969).

    Article  CAS  PubMed  Google Scholar 

  9. 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'.

    Google Scholar 

  10. 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).

    Article  CAS  PubMed  Google Scholar 

  11. Gillespie, J. H. The Causes of Molecular Evolution (Oxford University Press, Oxford, UK, 1991).

    Google Scholar 

  12. 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.

    Article  CAS  PubMed  Google Scholar 

  13. 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).

    Article  CAS  PubMed  Google Scholar 

  14. Cutler, D. J. Estimating divergence times in the presence of an overdispersed molecular clock. Mol. Biol. Evol. 17, 1647–1660 (2000).

    Article  CAS  PubMed  Google Scholar 

  15. 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.

  16. Fitch, W. M. Rate of change of concomitantly variable codons. J. Mol. Evol. 1, 84–96 (1971).

    Article  CAS  PubMed  Google Scholar 

  17. 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).

    Article  CAS  PubMed  Google Scholar 

  18. 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).

    Article  CAS  PubMed  Google Scholar 

  19. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 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).

    Article  PubMed  Google Scholar 

  21. Wyles, J. S., Kunkel, J. G. & Wilson, A. C. Birds, behavior, and anatomical evolution. Proc. Natl Acad. Sci. USA 80, 4394–4397 (1983).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ohta, T. & Kimura, M. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1, 18–25 (1971).

    Article  CAS  Google Scholar 

  23. Ohta, T. Very slightly deleterious mutations and the molecular clock. J. Mol. Evol. 26, 1–6 (1987).

    Article  CAS  PubMed  Google Scholar 

  24. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Felsenstein, J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376 (1981).

    Article  CAS  PubMed  Google Scholar 

  26. Rambaut, A. & Bromham, L. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15, 442–448 (1998).

    Article  CAS  PubMed  Google Scholar 

  27. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. 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).

    Article  CAS  PubMed  Google Scholar 

  29. 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Ota, R. & Penny, D. Estimating changes in mutational mechanisms of evolution. J. Mol. Evol. (in the press).

  31. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. 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).

    Article  CAS  PubMed  Google Scholar 

  33. Chao, L. & Cox, E. C. Competition between high and low mutating strains ofEscherichia coli. Evolution 37, 125–134 (1983).

    Article  PubMed  Google Scholar 

  34. Rand, D. M. Thermal habit, metabolic rate and the evolution of mitochondrial DNA. Trends Ecol. Evol. 9, 125–131 (1994).

    Article  CAS  PubMed  Google Scholar 

  35. 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Martin, A. P. Metabolic rate and directional nucleotide substitution in animal mitochondrial DNA. Mol. Biol. Evol. 12, 1124–1131 (1995).

    CAS  PubMed  Google Scholar 

  37. Bromham, L., Rambaut, A. & Harvey, P. H. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43, 610–621 (1996).

    Article  CAS  PubMed  Google Scholar 

  38. Bromham, L. Molecular clocks in reptiles: life history influences rate of molecular evolution. Mol. Biol. Evol. 19, 302–309. (2002).

    Article  CAS  PubMed  Google Scholar 

  39. 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).

    Article  CAS  PubMed  Google Scholar 

  40. 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).

    Article  CAS  PubMed  Google Scholar 

  41. 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).

    Article  Google Scholar 

  42. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Johnson, K. P. & Seger, J. Elevated rates of nonsynonymous substitution in island birds. Mol. Biol. Evol. 18, 874–881 (2001).

    Article  CAS  PubMed  Google Scholar 

  44. 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).

    Article  CAS  PubMed  Google Scholar 

  45. Moran, N. A. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl Acad. Sci. USA 93, 2873–2878 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Barraclough, T. G. & Savolainen, V. Evolutionary rates and species diversity in flowering plants. Evolution 55, 677–683 (2001).

    Article  CAS  PubMed  Google Scholar 

  47. 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).

    Article  CAS  PubMed  Google Scholar 

  48. 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).

    Article  CAS  PubMed  Google Scholar 

  49. Bromham, L. Molecular clocks and explosive radiations. J. Mol. Evol. (in the press).

  50. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Tajima, F. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135, 599–607 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Kumar, S. & Hedges, S. B. A molecular timescale for vertebrate evolution. Nature 392, 917–920 (1998).

    Article  CAS  PubMed  Google Scholar 

  53. Nei, M. & Glazko, G. V. Estimation of divergence times for a few mammalian and several primate species. J. Hered. 93, 157–164 (2002).

    Article  CAS  PubMed  Google Scholar 

  54. Takezaki, N., Rzhetsky, A. & Nei, M. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12, 823–833 (1995).

    CAS  PubMed  Google Scholar 

  55. 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).

    Article  CAS  Google Scholar 

  56. Sanderson, M. J. A nonparametric approach to estimating divergence times in the absence of rate constancy. J. Mol. Evol. 14, 1218–1231 (1997).

    Article  CAS  Google Scholar 

  57. 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.

    Article  CAS  PubMed  Google Scholar 

  58. 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).

    Article  PubMed  Google Scholar 

  59. Rannala, B. Identifiability of parameters in MCMC Bayesian inference of phylogeny. Syst. Biol. 51, 754–760 (2002).

    Article  PubMed  Google Scholar 

  60. Bromham, L. The human zoo: endogenous retroviruses in the human genome. Trends Ecol. Evol. 17, 91–97 (2002).

    Article  Google Scholar 

  61. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 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).

    Article  CAS  PubMed  Google Scholar 

  64. 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.

  65. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Rambaut, A. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16, 395–399 (2000).

    Article  CAS  PubMed  Google Scholar 

  67. Page, R. D. M. & Holmes, E. C. Molecular Evolution: a Phylogenetic Approach (Blackwell Science, Oxford, UK, 1998).

    Google Scholar 

  68. 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.

    Article  CAS  PubMed  Google Scholar 

  69. Conway Morris, S. Early metazoan evolution: reconciling paleontology and molecular biology. Am. Zool. 38, 867–877 (1998).

    Article  Google Scholar 

  70. Valentine, J., Jablonski, D. & Erwin, D. Fossils, molecules and embryos: new perspectives on the Cambrian explosion. Development 126, 851–859 (1999).

    CAS  PubMed  Google Scholar 

  71. Carroll, R. C. Towards a new evolutionary synthesis. Trends Ecol. Evol. 15, 27–32 (2000).

    Article  CAS  PubMed  Google Scholar 

  72. Kimura, M. The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, UK, 1983).

    Book  Google Scholar 

Download references

Acknowledgements

We thank A. Rambaut and A. Eyre-Walker for helpful comments.

Author information

Authors and Affiliations

  1. Centre for the Study of Evolution, School of Biological Sciences, University of Sussex, Falmer, BN1 9QG, Brighton, UK

    Lindell Bromham

  2. Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand

    David Penny

Authors
  1. Lindell Bromham
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David Penny
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lindell Bromham.

Related links

Related links

FURTHER INFORMATION

University of Sussex Centre for the Study of Evolution

Allan Wilson Centre for Molecular Ecology and Evolution

Glossary

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.

MACROEVOLUTION

Evolution at, or above, the level of species; the patterns and processes of diversification and extinction of species over evolutionary time.

MICROEVOLUTION

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.

ECTOTHERM

A 'cold-blooded' organism, such as a reptile, for which body temperature is dependent on the environment.

ENDOTHERM

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).

FIXATION

An increase in allele frequency to the point at which all individuals in a population are homozygous.

EUSOCIALITY

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.

VARIANCE

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.

Rights and permissions

Reprints and Permissions

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

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrg1020

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing