Experimental environments were configured to be well-mixed, mimicking a chemostat. They were initialized with a single resource available. When consumed, this resource created a byproduct also available for consumption, which in turn created yet another byproduct upon consumption, and so on. In total, environments had a potential for 50 resources, 49 of which were created exclusively as byproducts of one another. Conversion rate between resource and byproduct was 1:1, which is equivalent to an environment without any energy loss between trophic levels. This enabled me to study the effects of recurring perturbations isolated from the well-known constraint that energetics impose on food chains [1]. The grid was set to 100 x 100 cells, thus allowing for a population of up to 10 000 organisms.

Each experiment was seeded with a single ancestor organism, capable of self-replication but no tasks, and digital populations evolved at a mutation rate of 0.0025 mutations per copied instruction for around 5000 generations. Because evolution is a stochastic process, communities evolving from identical conditions may develop differently. Therefore, experiments were replicated by evolving 20 different communities under identical conditions.

I exposed digital communities to a period of recurring perturbations, where each perturbation event consisted of an instantaneous removal of a fraction of all organisms from the population. Intensity of perturbations was varied by altering the fraction of organisms removed and the average waiting time between perturbation events (see thesis for details on how perturbation intensity was calculated). Each community was perturbed 100 times, and timing of perturbations were random.

Cross-feeding chain length was defined for each organism as the bottom-most resource it consumed (in cross-feeding interactions, the initial resource is the top-most resource, and each consecutive byproduct is considered one level lower).

I tracked lineages of organisms surviving the perturbations, to see how their cross-feeding chains evolved. I compared ancestors born before perturbations (red dot) to its descendants a few hundred generations after perturbations stopped (blue dots).

Continue to Findings & Conclusion or go back to Digital evolution. 

1. Hutchinson, G. E., 1959. Homage to Santa Rosalia, or why are there so many kinds of animals? American Naturalist 93 (870), 137–145.