An example of logical consistency for loblolly pine between genes associated to phenotypes or environmental variables and gene categories that have average deviations from neutrality consistent with positive or negative selection. Error bars give 99% bootstrap confidence intervals for the direction of selection statistic (DoS), with yellow bars having confidence intervals excluding zero. Lines give average Tajima’s D for nonsynonymous (blue) and synonymous sites (green), as well as the proportion of genes associated to at least one phenotype (red). Shaded areas give null distributions (99% quantiles) generated via permutations of genes among categories (n = 10,000 permutations). All lines, including those forming the null distributions, were smoothed using lowess smoothing.