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Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast

Figure 6

SNP data support the compensatory evolution hypothesis.

Data [39] on allele frequencies in a sample of S. cerevisiae strains was used to test the hypotheses that low and high occupancy sequences maintain their local G+C content due to weak selection. Theory predicts that allele frequencies of deleterious mutations would tend to be smaller than frequencies of neutral mutations and that SNPs representing beneficial mutations would be frequently observed at higher allele frequencies. A) Classifying SNPs. Major and minor alleles at SNPs representing postulated A/T gain and A/T loss at low and high occupancy loci were determined as illustrated. Loci with G/C flanking context were analyzed separately. B–E) Allele frequencies. The groups of SNPs were compared by computing the fraction of SNPs with minor allele frequency smaller than 20%. Shown is the fraction of rare alleles in cases of A/T gain, A/T loss and A/T neutral polymorphisms in non G/C contexts in low occupancy sequences (B), non G/C contexts in high occupancy sequences (C), G/C contexts in low occupancy sequences (D), G/C contexts in high occupancy sequences (E). The data show A/T losing SNPs tend to be rarer than neutral SNPs and A/T gaining SNPs in low occupancy sequences. The opposite behavior is observed at high occupancy sequences or at G/C contexts, confirming the predictions of our evolutionary model.

Figure 6

doi: https://doi.org/10.1371/journal.pcbi.1001039.g006