Fig. 4

A selection-mutation model for synonymous codon use in kinetoplastids explains relative synonymous codon use with ~90 % accuracy and recapitulates the difference in the nitrogen cost of genes. a The average mRNA nitrogen content per codon for 3003 orthologous genes in the Kinetoplastida. b The average nitrogen content per double-stranded codon (dsDNA) for the genes in a. c Empirical codon use probabilities (expressed as percentages) plotted against themselves. d The average mRNA nitrogen content per codon for sequences simulated using synonymous codon use probabilities derived from fitting the selection-mutation model to the observed sequence data. e The average nitrogen content per double-stranded codon for the genes in d. f The synonymous codon use probabilities inferred using the selection-mutation model plotted against the empirical codon use probabilities expressed as percentages. Dot colour corresponds to nitrogen availability group. L_N R² = 0.92, M_N R² = 0.88, H_N R² = 0.90