Analysis of the diversity around nonsynonymous substitutions; response: number of 4-fold degenerate polymorphisms around nonsynonymous substitutions.

A generalized linear mixed model with Poisson distribution used to compare the diversity around nonsynonymous substitutions along the D. pseudoobscura+D. persimilis lineage in relation to recombination rates measured in the Flagstaff cross. Measures were taken 60 kb from the site in either direction (120 kb total) in nonoverlapping bins of 1,000 bp. Identity of the substitution was included as a random effect. Proportion nonsynonymous is the proportion nonsynonymous substitutions fixed along the D. pseudoobscura+D. persimilis lineage for each 1,000 bp window. Absolute distance is the absolute distance from the focal nonsynonymous substitution. Neutral mutation rate is the average divergence at 4-fold degenerate sites between D. lowei–D. persimilis for the 1,000 bp window. An asterisk indicates significance at an α of 0.05. All effects in the model were standardized to mean zero and unit standard deviation. Estimates given in the table must be interpreted to take this into account. Using the example of eligible bases, our model predicts that for each standard deviation increase in eligible bases above the mean, there is a 0.213679 increase in the log of the number of polymorphisms. Table S12 gives the mean and standard deviation for each factor in the model.