Comparison of the silent third position GC composition (GC3s) to the effective number of codons (Nc) across 327 budding yeast species shows that a significant portion of the genes in many species’ genomes deviate substantially from the neutral expectation. A) Distribution of the percentage of genes that deviate more than 10% (purple bars) or 20% (blue bars) from the neutral expectation. Almost half of the genomes have 10% or more of their genes deviate at the 20% threshold (159 / 327), and almost all of the genomes do so at the 10% threshold (309 / 327). B) The genome of the yeast Alloascoidea hylecoeti shows a high correlation between GC3s and Nc (R-squared value = 0.762), in line with neutral expectations. The neutral expectation (i.e., the expectation when the only influence is GC mutational bias and genetic drift) of the effective number of codons for a given GC content of third positions in a genome is indicated by the black line. C) In contrast, the genome of Saccharomyces cerevisiae shows a lack of correlation between GC3s and Nc (R-squared value = -4.027) and does not conform with the neutral expectation.

https://doi.org/10.1371/journal.pgen.1009824.g001