How the footprint of history shapes the evolution of digital organisms

Gould’s thought experiment of “replaying life’s tape” provides a conceptual framework for experiments that quantify the contributions of adaptation, chance, and history to evolutionary outcomes. For example, we can empirically measure how varying the depth of history in one environment influences subsequent evolution in a new environment. Can this “footprint of history”—the genomic legacy of prior adaptation—grow too deep to overcome? Can it constrain adaptation, even with intense selection in the new environment? We investigated these questions using digital organisms. Specifically, we evolved ten populations from one ancestor under identical conditions. We then replayed evolution from three time points in each population’s history (corresponding to shallow, intermediate, and deep history) in two new environments (one similar and one dissimilar to the prior environment). We measured the contributions of adaptation, chance, and history to the among-lineage variation in fitness and genome length in both new environments. In both environments, variation in genome length depended largely on history and chance, not adaptation, indicating weak selection. By contrast, adaptation, chance, and history all contributed to variation in fitness. Crucially, whether the depth of history affected adaptation depended on the environment. When the ancestral and new environments overlapped, history was as important as adaptation to the fitness achieved in the new environment for the populations with the deepest history. However, when the ancestral and novel environments favored different traits, adaptation overwhelmed even deep history. This experimental design for assessing the influence of the depth of history is promising for both biological and digital systems.