Molecular Evolution: Rates


The rate of molecular evolution varies dramatically between taxa, for example, some viruses have a rate of genome evolution a million times faster than mammals. Although some rate variation may be due to random fluctuations or locus‐specific effects, studies have revealed strong and predictable patterns in the differences in the rate of molecular evolution between species. In particular, large, long‐lived organisms with low reproductive output tend to have slower rates of molecular evolution than related species with shorter lives, faster generations or higher fecundity. Studies of the variation in the rate of molecular evolution between species may reveal the mechansims underlying these differences, and can inform analyses that seek to derive information on evolutionary history and processes from molecular data.

Key Concepts:

  • The number of genetic differences between lineages increases with the time since their separation, but differences do not accrue in the same rate in all lineages.

  • Variation in the rate of molecular evolution can be compared between species by comparing absolute rates, derived from laboratory experiments or estimated by comparing sequences where the age of the divergence is known.

  • A more common approach is to compare the relative rate differences between species by comparing the number of sequence changes that have accumulated since they last shared a common ancestor.

  • Mutation rate varies between species, at least in part due to the action of selection finding a balance between the competing costs of DNA repair and mutation.

  • Many mutations arise from DNA replication errors, so the more times DNA is copied per unit time, the higher the mutation rate will be.

  • Rates of molecular evolution in many taxa scale with body size, possibly because smaller‐bodied taxa go through more genome replications per unit time, a hypothesis referred to as the generation time effect.

  • Metabolic rate has been suggested to play a role in species differences in mutation rate, on the assumption that species with higher mass‐specific metabolic rate will suffer more DNA damage per unit time, though there is little direct evidence for this hypothesis.

  • Natural selection might play a role in fine‐tuning mutation rates to fit different life history strategies, for example, reducing mutation rates in large, long‐lived organisms.

Keywords: molecular clock; substitution; mutation; relative rates; generation time; metabolic rate; longevity; population size

Figure 1.

Relative rates test. The genetic distances between each of a pair of taxa (A and B) and an outgroup (C) can be used to compare the amount of evolution along lineages A and B since their last common ancestor (O).



Amemiya CT, Alfoldi J, Lee AP et al. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature 496: 311–316.

Baer C, Miyamoto MM and Denver DR (2007) Mutation rate variation in multicellular eukaryotes: causes and consequences. Nature Reviews Genetics 8: 619–631.

Barraclough TG and Savolainen V (2001) Evolutionary rates and species diversity in flowering plants. Evolution 55: 677–683.

Bromham L (2002) Molecular clocks in reptiles: life history influences rate of molecular evolution. Molecular Biology and Evolution 19: 302–309.

Bromham L (2009) Why do species vary in their rate of molecular evolution? Biology Letters 5: 401–404.

Bromham L and Leys R (2005) Sociality and rate of molecular evolution. Molecular Biology and Evolution 22(6): 1393–1402.

Bromham L and Penny D (2003) The modern molecular clock. Nature Reviews Genetics 4: 216–224.

Bromham L, Rambaut A and Harvey PH (1996) Determinants of rate variation in mammalian DNA sequence evolution. Journal of Molecular Evolution 43(6): 610–621.

Charlesworth B (2009) Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics 10: 195–205.

Denamur E and Matic I (2006) Evolution of mutation rates in bacteria. Molecular Microbiology 60: 820–827.

Dowle E, Morgan‐Richards M and Trewick S (2013) Molecular evolution and the latitudinal biodiversity gradient. Heredity 110: 501–510.

Duchene D and Bromham L (2013) Rates of molecular evolution and diversification in plants: chloroplast substitution rates correlate with species richness in the Proteaceae. BMC Evolutionary Biology 13: 65.

Ellegren H (2007) Characteristics, causes and evolutionary consequences of male‐biased mutation. Proceedings of the Royal Society B: Biological Sciences 274(1606): 1–10.

Eo SH and DeWoody JA (2010) Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles. Proceedings of the Royal Society B: Biological Sciences 277: 3587–3592.

Estabrook G, Smith G and Dowling T (2007) Body mass and temperature influence rates of mitochondrial DNA evolution in North American cyprinid fish. Evolution 61(5): 1176–1187.

Fleischer RC, McIntosh CE and Tarr CL (1998) Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K‐Ar based ages of the Hawaiian islands to estimate molecular evolutionary rates. Molecular Ecology 7: 533–545.

Galtier N, Jobson RW, Nabholz B, Glemin S and Blier PU (2009) Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution. Biology Letters 5(3): 413–416.

Gillooly JF, Allen AP, West GB and Brown JH (2005) The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proceedings of the National Academy of Sciences of the USA 102(1): 140–145.

Goldie X, Gillman L, Crisp M and Wright S (2010) Evolutionary speed limited by water in arid Australia. Proceedings of the Royal Society B: Biological Sciences 277(1694): 2645–2653.

Goldie X, Lanfear R and Bromham L (2011) Diversification and the rate of molecular evolution: no evidence of a link in mammals. BMC Evolutionary Biology 11: 286.

Halligan DL and Keightley PD (2009) Spontaneous mutation accumulation studies in evolutionary genetics. Annual Review of Ecology, Evolution, and Systematics 40(1): 151–172.

Holmes EC (2009) The evolutionary genetics of emerging viruses. Annual Review of Ecology, Evolution, and Systematics 40: 353–372.

Janecka J, Chowdhary B and Murphy W (2012) Exploring the correlations between sequence evolution rate and phenotypic divergence across the Mammalian tree provides insights into adaptive evolution. Journal of Biosciences 37(5): 897–909.

Joyner‐Matos J, Bean LC, Richardson HL, Sammeli T and Baer CF (2011) No evidence of elevated germline mutation accumulation under oxidative stress in Caenorhabditis elegans. Genetics 189(4): 1439–1447.

Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.

Lancaster LT (2010) Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages. BMC Evolutionary Biology 10(1): 162.

Lanfear R, Ho SYW, Davies TJ et al. (2013) Taller plants have lower rates of molecular evolution: the rate of mitosis hypothesis. Nature Communications 4: 1879. DOI: 10.1038/ncomms2836

Lanfear R, Ho SYW, Love D and Bromham L (2010) Mutation rate influences diversification rate in birds. Proceedings of the National Academy of Sciences of the USA 107(47): 20423–20428.

Lanfear R, Thomas JA, Welch JJ and Bromham L (2007) Metabolic rate does not calibrate the molecular clock. Proceedings of the National Academy of Sciences of the USA 104: 15388–15393.

Lanfear R, Welch JJ and Bromham L (2010) Watching the clock: studying variation in rates of molecular evolution. Trends in Ecology and Evolution 25(9): 495–503.

Larsson N‐Gr (2010) Somatic mitochondrial DNA mutations in mammalian aging. Annual Review of Biochemistry 79(1): 683–706.

Lartillot N and Delsuc F (2012) Joint reconstruction of divergence times and life‐history evolution in placental mammals using a phylogenetic covariance model. Evolution 66(6): 1773–1787.

Li W‐H, Ellesworth DL, Krushkal J, Chang BH‐J and Hewett‐Emmett D (1996) Rates of nucleotide substitution in primates and rodents and the generation‐time effect hypothesis. Molecular Phylogenetics and Evolution 5(1): 182–187.

Lourenco J, Glemin S, Chiari Y and Galtier N (2012) The determinants of the molecular substitution process in turtles. Journal of Evolutionary Biology 26(1): 38–50.

Lynch M (2010) Evolution of the mutation rate. Trends in Genetics 26(8): 345–352.

Martin AP and Palumbi SR (1993) Body size, metabolic rate, generation time and the molecular clock. Proceedings of the National Academy of Sciences of the USA 90: 4087–4091.

Mooers AO and Harvey PH (1994) Metabolic rate, generation time and the rate of molecular evolution in birds. Molecular Phylogenetics and Evolution 3: 344–350.

Nabholz B, Glemin S and Galtier N (2008) Strong variations of mitochondrial mutation rate across mammals – the longevity hypothesis. Molecular Biology and Evolution 25: 120–130.

Pagel M, Venditti C and Meade A (2006) Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science 314(5796): 119–121.

Rand DM (2001) The units of selection on mitochondrial DNA. Annual Review of Ecology and Systematics 32: 415–448.

Reha‐Krantz LJ (2010) DNA polymerase proofreading: Multiple roles maintain genome stability. Biochimica et Biophysica Acta 1804(5): 1049–1063.

Romiguier J, Ranwez V, Douzery E and Galtier N (2013) Genomic evidence for large, long‐lived ancestors to placental mammals. Molecular Biology and Evolution 30(1): 5–13.

Santos JC (2012) Fast molecular evolution associated with high active metabolic rates in poison frogs. Molecular Biology and Evolution 29(8): 2001–2018.

Steiper ME and Seiffert ER (2012) Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of early primate evolution. Proceedings of the National Academy of Sciences of the USA 109(16): 6006–6011.

Thomas JA, Welch JJ, Lanfear R and Bromham L (2010) A generation time effect on the rate of molecular evolution in invertebrates. Molecular Biology and Evolution 27(5): 1173–1180.

Venditti C and Pagel M (2009) Speciation as an active force in promoting genetic evolution. Trends in Ecology and Evolution 25(1): 14–20.

Webster AJ, Payne RJH and Pagel M (2003) Molecular phylogenies link rates of evolution and speciation. Science 301: 478.

Welch JJ (2004) Accumulating Dobzhansky‐Muller incompatibilities: reconciling theory and data. Evolution 58(6): 1145–1156.

Welch JJ, Bininda‐Emonds ORP and Bromham L (2008) Correlates of substitution rate variation in mammalian protein‐coding sequences. BMC Evolutionary Biology 8: 53.

Woolfit M (2009) Effective population size and the rate and pattern of nucleotide substitutions. Biology Letters 5(3): 417–420.

Wright S, Ross H, Jeanette Keeling D, McBride P and Gillman L (2011) Thermal energy and the rate of genetic evolution in marine fishes. Evolutionary Ecology 25(2): 525–530.

Wright SD, Keeling J and Gillman L (2006) The road from Santa Rosalia: a faster tempo of evolution in tropical climates. Proceedings of the National Academy of Sciences of the USA 103: 7718–7722.

Further Reading

Bromham L (2008) Reading the Story in DNA: A Beginner's Guide to Molecular Evolution. Oxford: Oxford University Press.

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

Lynch M (2007) The Origins of Genome Architecture. Sunderland, MA: Sinauer Associates.

Maynard Smith J (1998) Evolutionary Genetics, 2nd edn. Oxford, UK: Oxford University Press.

Page RDM and Holmes EC (1998) Molecular Evolution: A Phylogenetic Approach. Oxford: Blackwell Science.

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Bromham, Lindell(Sep 2013) Molecular Evolution: Rates. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001802.pub3]