Data from: Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates

Synonymous codon usage (SCU) patterns are shaped by a balance between mutation, drift, and natural selection. To date, detection of translational selection in vertebrates has proven to be a challenging task, obscured by small long-term effective population sizes in larger animals and the existence of isochores in some species. The consensus is that, in such species, natural selection is either completely ineffective at overcoming mutational pressures and genetic drift or perhaps is effective but so weak that it is not detectable. The aim of this research is to understand the interplay between mutation, selection, and genetic drift in vertebrates. We observe that although variation in mutational bias is undoubtedly the dominant force influencing codon usage, translational selection acts as a weak additional factor influencing synonymous codon usage. These observations indicate that translational selection is a widespread phenomenon in vertebrates and is not limited to a few species.Supplementary Figure 1Plots of axis 1 versus axis 2 of correspondence analyses, using RSCU values and raw codon counts, respectively. Blue points indicate non­‐highly expressed genes. Red points indicate highly expressed genes.SupplementaryFigure1.pdfSupplementary Table 1Correspondence analysis of RSCU values and raw codon counts. The "Axis 0 inertia" column is the amount of inertia that is explained by the principal axis. The "Axis 1 inertia" column is the amount of interia that is explained by the next biggest CA axis. These results demonstrate that there is a single major trend that determines synonymous codon usage in vertebrates.SupplementaryTable1.pdfSupplementary Table 2Spearman correlations. Spearman correlation comparing Axis 1 versus GC3 , and axis 1 versus expression level.SupplementaryTable2.pd