Pleiotropy and expression levels of adjacent genes do not explain enhancer evolutionary rate variations. Comparisons of D (A) and D/d4 (B) for mouse forebrain (FB), midbrain (MB), limb (LM), and heart (HT) enhancers after controlling for the enhancer pleiotropy and the expression level of adjacent genes. Only specific enhancers are included in the analysis. The values of upper quartile, median, and lower quartile are indicated in each box, whereas the bars outside the box indicate semi-quartile ranges. Pairwise comparisons showing significant difference in D or D/d4 are connected with gray lines (***P≦0.001 by Mann-Whitney U test).