Fig. 3: Mutational spectra and selection within the host.
From: Pneumococcal within-host diversity during colonization, transmission and treatment
a, The relative fraction of different single-nucleotide base changes found within the host in 1,627 samples involving only a single pneumococcal lineage compared to those changes observed between hosts inferred using ancestral state reconstruction. b, dN/dS ratios for genes found to be under significant selection (adjusted P < 0.05) within the host in 1,592 samples using the Poisson individual gene model in the dNdScv R package. Error bars indicate the 95% confidence intervals of the coefficient in the regression. The grey line indicates a dN/dS ratio of one, indicating the separation of positive and negative selection. c, An example of the within-host variant allele frequencies over five consecutive samples, taken from a single infant colonized with a single pneumococcal lineage (GPSC 47), which is not a common ‘epidemic’ lineage. Each coloured line indicates the frequency of a different within-host variant.
