Fig. 4

Comparison of CDC values between asexual and sexual oribatid mite species. Boxplots show CDC values of three asexual (blue) and three sexual (red) oribatid mite species for (a) 3545 nuclear orthologous genes (involving 10,635 CDC values for both asexual and sexual species) and (b) ten mitochondrial orthologous genes (involving 30 CDC values for both asexual and sexual species). CDC measures the deviation of observed from expected codon usage and allows for inference of the effectiveness of purifying selection acting on synonymous sites. A lower CDC value corresponds to more ‘relaxed’ selection on codon usage bias (see ‘Methods’). For nuclear orthologs, per-gene CDC was slightly but significantly higher in asexual species (gene effect P < 0.001, reproductive mode effect P = 0.008, interaction P = 0.616; permutation ANOVA). For mitochondrial orthologs, per-gene CDC differed more strongly between reproductive modes (gene effect P = 0.002, reproductive mode effect P < 0.001, interaction P = 0.960; permutation ANOVA). Significant differences in CDC are marked with asterisks (***P < 0.001 and **P < 0.01). Whiskers correspond to 1.5 times the interquartile range