Fig. 4: Successful mutations drive extinctions of metabolically distant species.

a Schematic showing the extinction of an unrelated species (blue) after a beneficial knockout mutation (orange) invades. In this example, the displaced species and the mutant share one common resource, but not the one targeted by the knock-out mutation. b Average number of extinctions after the invasion of a successful mutant, as a function of niche saturation \({{{{\mathcal{S}}}}} {*}/{{{\mathcal{R}}}}\); parent strains are excluded from the extinction tally. Inset: full distribution of extinctions for the starred parameters, compared to a Poisson distribution with the same fraction of zero counts. Points denote the averages over 10⁴ simulation runs with the same base parameters as Fig. 3. c Distribution of the number of resources jointly utilized by the displaced species and the invading mutant (parent strains excluded). Points denote the results of simulations with \({{{{\mathcal{S}}}}} {*}/{{{\mathcal{R}}}}=0.9\). Gray curves show the analogous background distribution between the mutant and all other species in the community, regardless of whether they become extinct. d Probability of extinction as a function of initial relative abundance for the starred point in panel (b). e The fold change in probability that the displaced species uses the same resource targeted by the mutant (i.e., the resource being knocked in or out), relative to the background distribution of resource use in the population. Points denote means and standard errors for knock-in and knock-out mutations as a function of \({{{{\mathcal{R}}}}}_{0}\) for \({{{{\mathcal{S}}}}} {*}/{{{\mathcal{R}}}}=0.8\), with the the remaining parameters the same as panel (b).