Fig. 4.

Nucleotide diversity near CpG sites is lower in lineages where positive selection has been inferred. Log₁₀(π) (with an offset of 0.001 to avoid undefined values) for the 1-kb window surrounding CpG sites where DNA methylation levels are taxonomically structured, and 1) we inferred no evidence for positive selection (pink: n = 16,907 sites) or 2) where positive selection was inferred on any baboon lineage (dark blue: n = 3,043 sites, based on the intersection set of the heuristic and OU approaches for multispecies lineages and results from the heuristic approach for single lineages). Log₁₀(π) for sites in dark blue are replotted in gray for lineages unaffected by putative positive selection and in light blue for lineages putatively affected by positive selection. Lineage-site combinations linked to positive selection (light blue) exhibit lower local nucleotide diversity than all other classes (Tukey’s Honestly Significant Difference test: P = 1.75 × 10⁻⁸ compared with sites with no evidence of positive selection [pink]; P = 0.0160 against the same sites, but with π averaged across all lineages [dark blue]; P = 5.00 × 10⁻⁹ against the same sites, but with π averaged across nonselected lineages only [gray]). π was calculated separately for each species prior to averaging, and is log transformed here for visualization purposes only. Box plots show median (black bar) and interquartile range (whiskers).