Fig. 3.

Species differences in the full DFE. (A) Shows the model-averaged discretized DFE, that is, the fraction of new mutations in each scaled fitness effect (N_es) category. Black bars indicate 95% confidence intervals on the estimated fraction, as estimated from model-averaged bootstrap replicates. (B) Violin plots show the shape parameter, b, the scale parameter, (C) S_d, for the gamma distribution of deleterious fitness effects per species, (D) α_DFE, the estimated fraction of substitutions inferred to be adaptive. Black diamonds are the inferred model-averaged parameters, while violins show the 95% confidence intervals, as estimated from model-averaged bootstrap replicates. In (E), we show the fraction of slightly deleterious (−1 < N_es < 0) mutations plotted against the ratio of 0- to 4-fold degenerate nucleotide diversity. Circles represent the fraction as inferred from the deleterious-only DFE model, diamonds represent the fraction as inferred from the full (advantageous and deleterious) DFE model. The dashed line indicates x = y. For P. abies, the diamond and circle overlap.