Models of DNA Substitution
See main article: Models of DNA evolution for more formal descriptions of the DNA models.
Models of DNA evolution were first proposed in 1969 by Jukes and Cantor, assuming equal transition rates as well as equal equilibrium frequencies for all bases. In 1980 Kimura introduced a model with two parameters: one for the transition and one for the transversion rate and in 1981, Felsenstein made a model in which the substitution rate corresponds to the equilibrium frequency of the target nucleotide. Hasegawa, Kishino and Yano (HKY) unified the two last models to a six parameter model. In the 1990s, models similar to HKY were developed and refined by several researchers.
For DNA substitution models, mainly mechanistic models (as described above) are employed. The small number of parameters to estimate makes this feasible, but also DNA is often highly optimized for specific purposes (e.g. fast expression or stability) depending on the organism and the type of gene, making it necessary to adjust the model to these circumstances.
Read more about this topic: Substitution Model
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