Fig. 5: Mutation and diversification over longer evolutionary timescales.

a Left: an example simulation showing the step-wise accumulation of  ~100 adaptive knock-out mutations in a community with \({{{\mathcal{R}}}}=100\), \({{{{\mathcal{R}}}}}_{0}=20\), \({{{{\mathcal{S}}}}} {*}/{{{\mathcal{R}}}}=0.9\), \({{{{\mathcal{S}}}}} {*}/{{{\mathcal{S}}}}=0.1\). Solid lines denote the abundance trajectories of 3 example lineages. Large points indicate extinction events in these lineages (red), diversification events (yellow), and mutation events that displace their parent strain (blue) in the highlighted lineages, while smaller points indicate analogous events for other species in the community. Dashed lines illustrate offshoots of the highlighted lineages that eventually went extinct. Right: Relative abundances of strains when they experienced mutation, diversification and extinction events, respectively. Lines denote histograms aggregated over 9 simulation runs. b Left: Total number of surviving strains over time. Gray lines denote replicate simulations for the same parameters in panel (a), while their average is shown in black. Right: Total number of strains related to another surviving strain through one or more in situ diversification events. c The probability of mutant-parent coexistence being maintained (i.e., both lineages surviving) as a function of time since initial divergence, over ten simulations. d The distribution of fitness effects at the start of the simulation (red) and after 90 accumulated mutations (blue), compared to the first-step predictions from Fig. 2 (black). e The probability that a mutation event leads to stable diversification as a function of time. Black points denote binned values aggregated over nine replicate simulations, while red point denotes the analogous result for 10⁴ first-step simulations.