Selection Acts Coherently on Cellular Functions
(A) Correlations in ν, dN/dS, and relative dN/dS (normalized as described in Methods) were obtained for the 109,405 gene-pairs with a COG functional category annotation (16 categories, excluding “general” or “unknown” function). Of these pairs, 10,377 have the same COG function, accounting for a proportion of ∼0.09 of the total (plotted as a solid gray line). Pairs were binned according to correlation-percentile in groups of ten percentile points except for the last three (90%–95%, 95%–99%, 99%–100%). Shown is the fraction with common function in each bin. To avoid potential bias, percentiles were calculated separately for genes present in different numbers of species (15 bins ranging from 16 to 30 species).
(B) Gene families under the same model of evolution have highly correlated selective signatures. Correlations in ν were obtained for all pairs of simulated gene families, with or without branch variation in dN/dS, and with dN/dS chosen randomly from within ±1 standard deviation of the mean of the observed dN/dS values (range: 0.005–0.26). The distribution of correlations is shown for pairs of gene families with branch variation in dN/dS and that are replicates of the same evolutionary model (light blue). The distribution of all pairwise correlations—including gene families with or without branch variation, and pairs from the same or different models—is also shown (gray).