Molecular Clocks


Molecules such as proteins and DNA evolve over time as a consequence of the fixation of mutations to DNA. Molecular evolution has been shown to be approximately constant across species, a phenomenon known as the molecular clock.

Keywords: rate of molecular evolution; evolutionary history; DNA; protein

Figure 1.

Testing the molecular clock hypothesis using maximum likelihood methods. There are two topologies showing the relationships among six species (A–F). The topology on the left was constructed subject to the constraint of a strict molecular clock. By contrast, the tree on the right is not constrained by the assumption of strict clock‐like evolution and differences in length of lineages from the common ancestor reflect variation in the process of nucleotide substitution among lineages.

Figure 2.

The relative rate test. There are three taxa: A, B and C. If there is a molecular clock (i.e. different lineages evolve at similar rates) then the genetic distance between A and C (KAC) should equal the genetic distance between B and C (KBC).

Figure 3.

Relationship between rate of mtDNA sequence divergence (in % change per million years) and body size (in kg) for various vertebrates. Solid circles are homeotherms and crosses are poikilotherms. Solid lines approximate the relationship between rate of molecular evolution and body size. Dashed line represents the hypothesis of rate constancy. Redrawn from data presented in Martin and Palumbi .

Figure 4.

Steps for calibrating a molecular clock for a single gene or protein. For a given set of taxa with (a) known divergence times, gene sequences are determined and (b) aligned so that it is possible to determine (c) the number of sequence differences that distinguish the taxa. The proportional differences between pairs of taxa are (d) transformed using an appropriate model of sequence evolution to estimate genetic distance between species. The genetic distances are (e) plotted against divergence time and the slope of the line estimates the rate of sequence evolution.

Figure 5.

Graph of the average (± 1 standard deviation) genetic distance between lineages of animals with known divergence times (from Doolittle et al., ). Genetic distances are based on comparison of homologous protein sequences. Data: 1, humans versus mouse; 2, eutheria versus marsupials; 3, mammals versus birds and reptiles; 4, amniotes versus amphibians; 5, tetrapods versus fish; 6, gnathostomes versus agnathans; 7, chordates versus echinoderms.

Figure 6.

Two different evolutionary histories for a group of eight taxa inferred using a molecular clock to reconstruct the duration of individual lineages. Dashed horizontal lines are regular time intervals. Numbers indicate number of lineages present at a given time. In the left tree, branching events occur over the entire time period; by contrast, the right tree shows that most extant lineages originated in a brief period of time.



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Further Reading

Avise JC (1994) Molecular Markers, Natural History and Evolution. New York: Chapman and Hall.

Bromham L (2003) Molecular clocks and explosive radiations. Journal of Molecular Evolution 57(suppl. 1): S13–S20.

Ho SY and Larson G (2006) Molecular clocks: when times are a‐changin. Trends Genetics 22: 79–83.

Kumar S (2005) Molecular clocks: four decades of evolution. Nature Reviews Genetics 6: 654–662.

Nei M (1985) Molecular Evolutionary Genetics. New York: Columbia University Press.

Takahata N (1996) Neutral theory of molecular evolution. Current Opinion in Genetics and Development 6: 767–772.

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How to Cite close
Martin, Andrew Peter(Dec 2007) Molecular Clocks. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001669.pub2]