Encyclopedia of Scientific Dating Methods

Living Edition
| Editors: W. Jack Rink, Jeroen Thompson

Molecular Rate Variation (Molecular Clocks)

Living reference work entry
DOI: https://doi.org/10.1007/978-94-007-6326-5_89-2

Molecular Rate Variation

The rate of molecular evolution is the rate at which substitutions accumulate in an organism’s genome. Rates of molecular evolution can vary dramatically, for example, the rate of molecular evolution in some viruses is around one substitution per base pair per 1,000 years (Pagán et al. 2010), while in mammals the rate is around one substitution per base pair per 1,000 million years (Nabholz et al. 2008). Even closely related plants and animals can have rates of molecular evolution that vary by more than an order of magnitude (Thomas et al. 2006; Smith and Donoghue 2008; Welch et al. 2008; Lanfear et al. 2013). Accounting for molecular rate variation is important in methods that use molecular sequence data to date the divergences between species (molecular dating).

There has been a great deal of research into the causes of variation in rates of molecular evolution. This research has identified a range of factors which may cause variation in the rate of molecular...

Keywords

Natural Selection Mutation Rate Genetic Drift Oxygen Radical Effective Population Size 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Bibliography

  1. Bromham, L., 2011. The genome as a life-history character: why rate of molecular evolution varies between mammal species. Philosophical Transactions of the Royal Society, B: Biological Sciences, 366, 2503–2513.CrossRefGoogle Scholar
  2. Charlesworth, J., and Eyre-Walker, A., 2007. The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations. Proceedings of the National Academy of Sciences of the United States of America, 104, 16992–16997.CrossRefGoogle Scholar
  3. Davies, T. J., Savolainen, V., Chase, M. W., Moat, J., and Barraclough, T. G., 2004. Environmental energy and evolutionary rates in flowering plants. Proceedings of the Biological Sciences, 271, 2195–2200.CrossRefGoogle Scholar
  4. de Visser, J. A. G. M., Zeyl, C. W., Gerrish, P. J., Blanchard, J. L., and Lenski, R. E., 1999. Diminishing returns from mutation supply rate in asexual populations. Science, 283, 404–406.CrossRefGoogle Scholar
  5. Galtier, N., Blier, P. U., and Nabholz, B., 2009. Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds. Mitochondrion, 9, 51–57.CrossRefGoogle Scholar
  6. Hodgkinson, A., and Eyre-Walker, A., 2011. Variation in the mutation rate across mammalian genomes. Nature Reviews. Genetics, 12, 756–766.CrossRefGoogle Scholar
  7. Joyner-Matos, J., Bean, L. C., Richardson, H. L., Sammeli, T., and Baer, C. F., 2011. No evidence of elevated germline mutation accumulation under oxidative stress in Caenorhabditis elegans. Genetics, 189, 1439–1447.CrossRefGoogle Scholar
  8. Lanfear, R., Thomas, J. A., Welch, J. J., Brey, T., and Bromham, L., 2007. Metabolic rate does not calibrate the molecular clock. Proceedings of the National Academy of Sciences of the United States of America, 104, 15388–15393.CrossRefGoogle Scholar
  9. Lanfear, R., Ho, S. Y. W., Jonathan Davies, T., Moles, A. T., Aarssen, L., Swenson, N. G., Warman, L., Zanne, A. E., and Allen, A. P., 2013. Taller plants have lower rates of molecular evolution. Nature Communications, 4, 1879.CrossRefGoogle Scholar
  10. 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, 1773–1787.CrossRefGoogle Scholar
  11. Lartillot, N., and Poujol, R., 2011. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Molecular Biology and Evolution, 28, 729–744.CrossRefGoogle Scholar
  12. Lourenço, J. M., Glémin, S., Chiari, Y., Galtier, N., 2013. The determinants of the molecular substitution process in turtles. Journal of Evolutionary Biology, 26(1), 38–50.Google Scholar
  13. Lynch, M., 2010. Evolution of the mutation rate. Trends in Genetics, 26, 345–352.CrossRefGoogle Scholar
  14. Lynch, M., 2011. The lower bound to the evolution of mutation rates. Genome Biology and Evolution, 3, 1107–1118.CrossRefGoogle Scholar
  15. Martin, A. P., and Palumbi, S. R., 1993. Body size, metabolic rate, generation time, and the molecular clock. Proceedings of the National Academy of Sciences of the United States of America, 90, 4087–4091.CrossRefGoogle Scholar
  16. Moran, N. A., 1996. Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proceedings of the National Academy of Sciences of the United States of America, 93, 2873–2878.CrossRefGoogle Scholar
  17. Nabholz, B., Glémin, S., and Galtier, N., 2008. Strong variations of mitochondrial mutation rate across mammals – the longevity hypothesis. Molecular Biology and Evolution, 25, 120–130.CrossRefGoogle Scholar
  18. Pagán, I., Firth, C., and Holmes, E. C., 2010. Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus Tobamovirus. Journal of Molecular Evolution, 71, 298–307.CrossRefGoogle Scholar
  19. Smith, S. A., and Donoghue, M. J., 2008. Rates of molecular evolution are linked to life history in flowering plants. Science, 322, 86–89.CrossRefGoogle Scholar
  20. Thomas, J. A., Welch, J. J., Woolfit, M., and Bromham, L., 2006. There is no universal molecular clock for invertebrates, but rate variation does not scale with body size. Proceedings of the National Academy of Sciences of the United States of America, 103, 7366–7371.CrossRefGoogle Scholar
  21. Thomas, J. A., Welch, J. J., Lanfear, R., and Bromham, L., 2010. A generation time effect on the rate of molecular evolution in invertebrates. Molecular Biology and Evolution, 27, 1173–1180.CrossRefGoogle Scholar
  22. Welch, J. J., Bininda-Emonds, O. R. P., and Bromham, L., 2008. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evolutionary Biology, 8, 53.CrossRefGoogle Scholar
  23. Woolfit, M., 2009. Effective population size and the rate and pattern of nucleotide substitutions. Biology Letters, 5, 417–420.CrossRefGoogle Scholar
  24. Woolfit, M., and Bromham, L., 2003. Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes. Molecular Biology and Evolution, 20, 1545–1555.CrossRefGoogle Scholar
  25. Woolfit, M., and Bromham, L., 2005. Population size and molecular evolution on islands. Proceedings of the Biological Sciences, 272, 2277–2282.CrossRefGoogle Scholar
  26. Wright, S., 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 United States of America, 103, 7718–7722.CrossRefGoogle Scholar
  27. Wright, S. D., Gillman, L. N., Ross, H. A., and Keeling, D. J., 2009. Slower tempo of microevolution in island birds: implications for conservation biology. Evolution, 63, 2275–2287.CrossRefGoogle Scholar
  28. Wright, S. D., Ross, H. A., Keeling, D. J., McBride, P., and Gillman, L. N., 2011. Thermal energy and the rate of genetic evolution in marine fishes. Evolutionary Ecology, 25, 525–530.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Ecology, Evolution, and GeneticsThe Australian National UniversityCanberraAustralia