Models of nucleotide substitution

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Models of nucleotide substitution are mathematical equations built to predict the probability (or proportion) of nucleotide change expected in a sequence.

Jukes and Cantor's one-parameter model

JC69 is the simplest of the models of nucleotide substitution.[1] The model assumes that all nucleotides has the same rate () of change to any other nucleotides. The probability that any nucleotide remains the same from time 0 to time 1 is;

must be read; probability (or proportion, in this case it is equivalent) that becomes at time . For the probability that any nucleotide changes to any other nucleotide we write . The probability for time is;

The second part of the equation denotes the probability that the nucleotide was changed from time 0 and 1, but then got back to its initial states on time 2. The model can be rewritten in a differential equation with the solution;

Or if we want to know the probability of nuleotide to change to nucleotide ;

With time, the probability will approach 0.25 (25%).

Kimura's two-parameters model

Mostly known under the name K80, this model was developed by Kimura in 1980 as it became clear that all nucleotides substitutions weren't occurring at an equal rate. Most often, transitions (changes between A and G or C and T) are more common than transversions.[2]

Further Reading

  • Yang, Z. (2006). Computational Molecular Evolution. Oxford University Press.


  1. Jukes, T.H. and Cantor, C.R. (1969). "Evolution of protein molecules". In Munro, H.N. (editor). Mammalian protein metabolism. Academic Press, New York. pp. 21–123.
  2. Kimura, M. (1980). "A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences". Journal of Molecular Evolution. 16: 111–120.