A population genetic model of selection that maintains specific trinucleotides at a specific location

Periodic appearances of specific trinucleotides along the DNA sequence have been reported in the chicken core DNA and the phenomenon has been suggested to be related to the supercoiling of DNA around nucleosomes. A population genetic model is constructed in which selection is operating to maintain specific trinucleotides at a specific location on the DNA sequence. Assuming low mutation rates, equilibrium probabilities of the appearances of respective trinucleotides were computed. Vague patterns appeared if the product of the effective size and the selection coefficient was 0.1-2.0. The genetic load and substitution rates in the equilibrium state were also computed. When the model was applied to the chicken DNA data, the product of the effective size and the selection coefficient was estimated to be 0.1-0.2. With this intensity of selection, the substitution rate was hardly different from that in the case without selection. However, the genetic load became fairly large. Considering the large number of times that DNA coils about nucleosomes, the number of trinucleotide sites must be very large, and thus the total load might be too large. Epistasis among these sites to reduce the total load is suggested to exist if selection is responsible for this periodic pattern observed in the chicken core DNA.