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Fig. 2 | BMC Biology

Fig. 2

From: Crossing fitness valleys via double substitutions within codons

Fig. 2

Null models that are used to infer selection on double substitutions through the DF measure. a The selection on double substitutions is inferred by comparing the DF for codons and their respective null models (NM1 and NM2). Two adjacent codons are illustrated, and the nucleotide position within the codon is indicated, according to the reading frame. The two null models are artificial codons constructed by considering positions from two adjacent codons, denoted codon i (indicated in green) and codon ii (indicated in orange). b The first configuration of the null model NM1. A constant second codon position in codon i, followed by a fourfold degenerate site in the third codon position of codon i which is followed by a twofold degenerate site in the first position of codon ii. All substitutions are synonymous (S). Substitution in a fourfold degenerate site is indicated by blue shading of the mutated codon position, and cyan shading indicates a substitution in a twofold degenerate site. c The second configuration of the null model NM1. A fourfold degenerate site in the third codon i position followed by a twofold degenerate site in the first position of codon ii, which is followed by a constant base in the second codon position of codon ii. All substitutions are synonymous (S). Substitution in a fourfold degenerate site is indicated by blue shading of the mutated codon position, and cyan shading indicates a substitution in a twofold degenerate site. d Null model NM2. A fourfold degenerate site in the third position of codon i followed by a constant first codon position in codon ii and by a fourfold degenerate site in the third codon ii position (skipping the second position of codon ii). All substitutions are synonymous (S), and substitutions in the fourfold degenerate sites are indicated by blue shading of the mutated codon position. e Comparison of DF between the two null models, NM1 (adjacent synonymous substitutions) as in b and c and NM2 (non-adjacent synonymous substitutions) as in d. The difference between the two distributions is significant according to t test (p value = 0.0038) but not significant under the U test (p value = 0.104)

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