Fig. 3.

The same genes of a bacterial species repeatedly undergo change or loss of function during infection by different strains. Our statistical framework defines genes that undergo change or loss of function repeatedly in a statically significant number of strains as undergoing adaptive change or loss of function, respectively. (a) Upper panel: Boxplots of the fractions of adaptively changed genes out of all changed genes in the different strains of each species. The number above the bar represents the number of strains included for that bacterial species. Lower panel: The mean similarity between the lists of genes undergoing change or loss of function in different strains of each species as measured by the Mean Jaccard Index (Materials and Methods). The number above the bar represents the number of studies included for that bacterial species. (b) Upper panel and lower panel as in (a), for genes undergoing loss of function. For most strains, there is no relationship between the fraction of genes undergoing adaptive change/loss of function and the similarity between strains of a species. Names of bacterial species are as in figure 1b.