Fig. 4

Interferon-stimulated genes have a higher whole-gene dN/dS value and more codons under positive selection than other genes. a Top: M0 is a codon model in PAML where all codons in an alignment are assigned to a single estimated dN/dS value. Below: box plot of the whole gene average dN/dS values determined by M0 in each category. *p-value < 0.05. a Top: The M8 model of codon evolution, as explained in the legend to Fig. 3a. Below: box plot of percentage of codon sites per gene in the dN/dS > 1 bin in the M8 model. *p-value < 0.05; ***p-value < 0.001. C Top: M2, a simple model that allows for positive selection, places all codons into one of three bins: a bin at dN/dS < 1 (conserved), a bin at dN/dS = 1 (neutral), and a bin at dN/dS > 1 (positive selection). The double-sided arrow indicates that the dN/dS value of this bin is optimized in the fitting of the data to the model. Below: box plot of the proportion of codon sites per gene in the dN/dS < 1 bin in model M2. *p-value < 0.05