Fig. 3.

Phage populations adapted to the same host show high within-group similarity. a Representative normalized growth curves of the three hosts when infected by four phage populations at a virus particle per cell ratio of 3. Phage populations shown are the ancestral (Anc), evolved in the optimal host (MIT9515 #1), and evolved in sub-optimal hosts (MED4 #3, WH8102 #2). Y-axis shows the fluorescence levels of infected cultures divided by the fluorescence of the uninfected culture, i.e, normalized culture fluorescence. Blue shading shows normalized fluorescence on the tenth day post infection, which was used for further analyses. Each curve is the average of three infection assays, error bars correspond to standard deviations. b Normalized cell densities of all infected cyanobacterial cultures at 10 days post infection. Lower values indicate more rapid declines in the infected host population, i.e. increased fitness (Supplementary Figure 1). Rows correspond to viral populations, columns are for infections of specific hosts at 0.1 and 3 viral particles/cell. Each box is the average of three infection assays. Symbols next to the population number denote the populations shown in panel a. c The phenotypic distance tree is based on the infection profile of each population (i.e., values of each row in panel b). Colors and numbering correspond to panel b. d Genomic maps show increased diversity in populations evolved in sub-optimal hosts. Positions along the genome are shown on the x-axis; horizontal lines correspond to specific populations. Vertical lines correspond to identified mutations, and their length corresponds to the mutation frequency within the population. e Genotypic distance tree reveals lower distance in populations evolved in MIT9515. The tree was constructed based on pair-wise genetic distances between phage populations. Colors and numbering correspond to panel b. Raw data can be found in Supplementary Table 2 and Supplementary File 1