Table 1.
State variables and parameters of the IBM.
Fig 1.
Trade-off based compatibility function .
The left panel shows how varies with |gα − gβ| for fixed values of gν;
is high when gα and gβ have similar values and low otherwise. The right panel shows how
varies with gν for fixed values of |gα − gβ|;
is high for high values of gν and low otherwise.
Fig 2.
Trade-off based virulence function .
The left panel shows how varies with gβ for fixed values of gν;
is high for high values of gβ and low otherwise. The right panel shows how
varies with gν for fixed values of gβ;
is high for low values of gν and low otherwise.
Fig 3.
Infection dynamics of B28 virus and E. coli.
Infection experiments performed as plate reader assays for different virus to host ratios (VHR). Optical density at 600 nm (OD600) was monitored to serve as a proxy for the host abundance. The growth curve of E. coli without virus infection (control) is shown in red. Plotted curves: mean values (n = 8 and ncontrol = 11) shown as solid lines and standard deviaitons shown as shading, with the vertical dashed line denoting the time (t = 3.5 hr) for viral infection.
Fig 4.
Model’s sensitivity to environmental parameters.
Population dynamics for hosts (a-c) and viruses (d-f) for varying virus to host ratios (VHR), total phosphorous content (P, μmol-P L−1) and washout rate (ω, h−1). Plotted curves: ensemble averages from 100 runs lasting T = 36 h, with standard deviations shown as shading.
Fig 5.
Model’s sensitivity to evolution in organism traits.
Sensitivity of host (a-d) and virus dynamics (e-h) to mutation probability in host traits (πh), virus traits (πv), standard deviation in mutation for host traits (σh) and standard deviation in mutation for virus traits (σv). Plotted curves: ensemble averages from 100 runs lasting T = 36 h, with standard deviations shown as shading.
Fig 6.
Model’s sensitivity to trade-off-based vs random infection processes.
Host (a-d, i-l) and virus population dynamics (e-h, m-p) shown for closed systems and open systems with washout rate 0.2 h−1 for genotypic compatibility and genotypic virulence (,
, upper left), genotypic compatibility and random virulence (
,
, upper right), random compatibility and genotyipc virulence (
,
, lower left) and random compatibility and random virulence (
,
, lower right). Ensemble averages of 100 simulations (lines) with standard deviation (shaded areas) lasting for T = 720 h are shown. Sub-panels show virus dynamics on adjusted y-axis scales.