DNA evolution under weak selection

Some DNA data show patterns of variation not expected under the neutral the ory. Here, the independent multicodon (IMC) model, a nearly neutral mutatio n model assuming no interaction among codons, was studied when population s ize changes using computer simulation. Patterns of variation expected under the model were investigated using statistics for the neutrality tests. The average dispersion index is more than one when population size changes slo wly but it never becomes large. The diversity at linked silent site decreas es when the strength of selection is intermediate and the reduction is larg er when population size changes slowly. Tajima's (1989. Genetics 123, 585-5 95) D is generally negative. Rejections by the Tajima's test occur more fre quently if population size changes quickly but the effect of selection is c onfounded with the size change itself in this case. If we apply the test of McDonald and Kreitman (1991. Nature 351, 652-654), the rejection is always in the direction of excess replacement polymorphisms. The rejection probab ility decreases as the rate of population size changes decreases. These res ults show that the predictions of the IMC model are consistent with the pat tern observed in mitochondrial DNA data but not consistent with some data o f nuclear DNA. Interaction among codons or variable selection would be nece ssary to explain such cases. (C) 2000 Elsevier Science B.V. All rights rese rved.