MO640 - Exercises - DNA Evolution Models, Durand-lec-notes (2014), Felsenstein (2004)- chapters 11 and 13

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2. Two 100-character long DNA sequences differ in 15 positions, with 6 of them being transversions and 9 transitions. Admitting that their evolution follows the Kimura two-parameter model, find the transition and transversion rates multiplied by time.

Answer:

For the transversion rate (βΔt) we can use the first part of the developments below, taking into account that since each nucleotide can undergo two transversions, an observed frequency of 6/100 means that the probability pvxy is in fact 3/100.

Knowing the transversion rate we can use the second part of the development below to find the transition rate.

algebraic calculations


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