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Fig. 1 | BMC Ecology and Evolution

Fig. 1

From: Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana

Fig. 1

Data collection and the context-independent selection on synonymous mutations in Arabidopsis thaliana. a Definition of derived alleles based on two outgroup species (Sp2 and Sp3). Two cases of ancestral (orange background) or non-ancestral (blue background) states were shown. The base letters of derived alleles were colored in red. b Derived allele frequencies (DAF) of CDS mutations of different categories. These categories include synonymous, nonsynonymous and nonsense mutations as well as the synonymous mutations that cause changes in tAI value. P values are calculated from Wilcoxon rank sum tests (“tAI up” versus “tAI down”, “nonsynonymous” versus “all synonymous”, and “nonsense” versus “all synonymous”). ***Represents p-value < 0.001. Multiple testing correction was performed to adjust the p-value. Length of multiple testing correction was set to the number of tests performed. “syn” represents synonymous, “nsy” represents nonsynonymous. c Definition of two types of synonymous mutations according to the change in tAI value. Codons with higher tAI values have more available tRNAs. d Spearman correlation between the tAI change (Y-axis: delta tAI) of the synonymous mutations and the conservation level of host genes (X-axis). The synonymous mutation sites are ranked according to the dN/dS ratios. Note that the X-axis (1 to 50) is the rank number rather than the exact value of dN/dS. Circle represents mean and error bar represents standard error

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