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Time (in 1 x 105 generations)

Figure 8.9 The probability that a nucleotide site retains its original base pair under the Jukes-Cantor model of nucleotide substitution. If a nucleotide site originally has a G base, for example, the probability of the same base being present declines steadily over time. If a nucleotide site was initially not a G (it was an A, C, or T), the probability that a G is present at the site increases over time. The probability that a given base is present always converges to 25% because that is the probability of sampling a given base at random if the probability of substitution to each nucleotide is equal. In the top panel a = 1 x 10-6 whereas in the bottom panel a = 1 x 10-5.

-Initially G

The exponent can be removed from this equation by taking the natural logarithm of the right side and the equation rearranged to give

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