Adaptation under prolonged resource exhaustion is characterized by high levels of convergence and frequent historical contingency

Escherichia coli are non-sporulating bacteria that possess an ability to enter a state called Long-Term Stationary Phase (LTSP), which allows them to survive very prolonged resource exhaustion. In July of 2015 an LTSP experiment was launched in our laboratory, in which five independent populations were established via inoculation into fresh media and have not been provided with any external nutrients ever since. We found that genetic adaptation under LTSP occurs in an extremely convergent manner, across independently evolving populations. Within each population, we observe the early establishment of lineages - subpopulations that descend from a common ancestors and co-exist within a population, alongside other lineages, evolving independently from them. The high convergence with which mutations occur and the observed lineage structure have provided us with an opportunity to ask how contingent evolution under LTSP is. In other words, we could ask how often a certain locus is significantly more likely to be mutated on the background of specific or non-specific mutations to a second locus. We found very high levels of contingency with approximately a third of convergently mutated loci participating in contingent loci pairs. Contingent pairs of loci are significantly more likely than expected by chance to have known functional relationships. This indicates that the contingencies we identified are likely biologically meaningful, and that pairs of contingent loci are more likely to be functionally related, even when no such relationship is currently known.