Figure 3. J evolution (a) and evidence of the interdependency between λ and E. coli fitness during their coevolution (b-d).

(a) Phylogenetic reconstruction and relative abundance of λ genotypes isolated through time from a previously coevolved community (Meyer et al., 2012). Each letter and star indicate a non-synonymous mutation in J (see Supplementary file 1c for labels’ corresponding mutations). A genotype’s relative abundance on a given day is denoted by the fraction of the total height of the y-axis that it occupies (e.g. on day 9, frequency of ABC is 0.2 and A**C is 0.8; see Supplementary file 1d). The lineage WT-A-ABC-ABCDE eventually evolves OmpF function and fixes in the population; resistance in E. coli through malT^— rises to high frequencies between days 5 and 8 (Meyer et al., 2012). (b & c) Selection rates (per 24 hr) of phage genotypes on the two hosts. Each bar represents the mean of three experimental replicates. While mutation A is favored over wildtype (WT) λ in the presence of the ancestral host and not malT^—, AB only outcompetes A in the presence of malT^— and not the ancestral host. One tailed t-tests to test if the mean selection rate is significantly greater (or less) than zero: A vs WT with ancestor host- ${\displaystyle t=98.76,d.f.=2,\mathrm{p}<0.0001}$; A vs WT with malT^— - ${\displaystyle t=-4.99,d.f.=2,\mathrm{p}=0.0190}$; AB vs A with ancestor- ${\displaystyle t=3.4,d.f.=2,\mathrm{p}=0.0383}$; AB vs A with malT^— - ${\displaystyle t=-8.88,d.f.=2,\mathrm{p}=0.0062}$. (d) Selection rate (per 4 hr) of malT^– E. coli relative to its ancestor in the presence of λ from different stages of coevolution. Each competition was replicated three times. Lowercase letters denote significance via Tukey’s honest significance test, see Supplementary file 1g for pairwise p-values (ANOVA: F-ratio=111.22, d.f.=11, p<0.0001). One tailed t-tests were also used to test if the selection rate of malT^— was greater than zero WT: ${\displaystyle t=2.44,d.f.=2,\mathrm{p}=0.676}$; A: ${\displaystyle t=5.12,d.f.=2,\mathrm{p}=0.0181}$; ABC: ${\displaystyle t=26.59,d.f.=2,\mathrm{p}=0.0007}$; A**C: ${\displaystyle t=71.67,d.f.=2,\mathrm{p}<0.0001}$. This shows that malT^— is unlikely to evolve in the presence of WT λ but it becomes progressively more likely as λ gains mutations. Asterisks over all the competitions indicate significance level corresponding to the p-values. Error bars in all bar graphs represent one sample SD.

Figure 3—figure supplement 1. Competition assay of λ isolates from population D7.

Relative fitness of λ with two mutations (AB) to an OmpF⁺ λ with five mutations (ABCDE) on two host genotypes. This shows that AB outcompetes ABCDE in the presence of ancestral E. coli while ABCDE is favored over AB with malT^— E. coli. Selection rate (per 4 hr) is the difference in Malthusian growth rates of the competitors over 1 day with a value of 0 indicating no difference in fitness. Each bar represents mean of three replicate trials and error bars indicate one sample SD. (One-tailed t-test to test if the selection rate is greater (or less) than zero— ABCDE vs AB with ancestor host: ${\displaystyle t=-58.53,d.f.=2,\mathrm{p}<0.0001}$, ABCDE vs AB with malT^—: ${\displaystyle t=13.09,d.f.=2,\mathrm{p}=0.0029}$. Asterisks over the bar graphs indicate significance level corresponding to the p-values).