Fig. 6
Impact of the initial genotype frequencies on the evolutionary emergence of metabolic dependencies in populations of E. coli with two leaky amino acids. Here, we have shown the results of targeted in silico invasion experiments for a representative amino acid pair (lysine and isoleucine) (see also Fig. 4c). a 00, 01, and 10 simultaneously originate from 11 (i.e., WT) through genome streamlining and invade an existing population of 11 genotypes. b A small population of 10 and 00 invade a resident population of the 11 and 01. This simulates the second step of a two-step process for the loss of the leaky functions hypothesized in ref. 10 (see the main text for details and also Supplementary Fig. 8). c A small population of 01 and 10 invades a resident population of 11. This models an alternative scenario for the two-step loss of leaky functions leading to stable cross-feeders: Two partial producer mutant genotypes (01 and 10) simultaneously originate from 11, followed by the rise of the 00 genotype from 01 and/or 10 in a later stage. As shown here, cross-feeders can evolutionarily stabilize and coexist with 11 genotypes in the first step. Further analysis showed that cross-feeders are also resistant to invasion by 00 genotypes arising in the second step (see Supplementary Fig. 9). Dynamic plots in a–c show the sample evolutionary dynamics of the system for selected equal leakiness levels for both lysine and isoleucine. Pie charts show the equilibrium frequencies of each genotype starting from the initial genotype frequencies shown in each panel. These equilibrium frequencies are given only for the sustainable leakiness region (green region in Fig. 4c)
