Fig. 2

Transcriptional regulation contributes significantly more to protein level divergence compared to translational regulation. a Inter-species divergence in translation efficiency. A scatter plot comparing translation efficiency (TE) between human and chimpanzee. Each data point represents a gene, position along each axis indicates log₂ translation efficiency of each species, and the color of each data point indicates whether the gene is significantly diverged between species in translation efficiency at a significance cut-off of FWER 0.05 (blue: significant, gray: not significant). b An example gene, Profilin 1 (PFN1), which shows human–chimpanzee divergence in translation efficiency. Level of protein translation (blue) and RNA transcription (red) are shown in log₂RPKM. Each data point represents an individual human or chimpanzee sample. c Divergence between human and chimpanzee at the transcript level occurs more frequently than that of translation efficiency. Quantile-quantile plot of –log₁₀(p values) derived from testing for divergence between human and chimpanzee for each trait of interest (RNA: transcript level, TE: translation efficiency). For each molecular trait, observed p value (y-axis) is plotted against the null expectation (i.e. uniform distribution of p values) (x-axis). The red line marks the expected results from a scenario where no divergence is observed. d Divergence between human and chimpanzee at the transcript level is greater than that of translation efficiency. Boxplots comparing effect size (absolute log₂ ratio) of human-chimpanzee divergence (RNA: transcript level, TE: translation efficiency). Only genes that are diverged in protein levels were considered in this analysis. e Between human and chimpanzee, inter-species divergence in translation efficiency contributes little to inter-species divergence in protein level. Proportion of inter-species divergence propagated from translation level to the protein level (y-axis) was estimated using coefficient of determination (r²) between translation level divergence and protein level divergence. Each r² was calculated for a subset of genes each defined by an FDR cut-off (x-axis) for divergence in protein level. These coefficients (r²) were calculated either with (red) or without (black) accounting for the effects from the transcript level