Abstract
The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary ‘dead end’, there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that duplicated GRNs might provide polyploids with better chances to acquire the drastic changes necessary to adapt to challenging conditions, thus endowing DOs with increased adaptive potential under extinction events. In contrast, under stable environments, random mutations might easily render the GRN less well adapted to such environments, a phenomenon that is exacerbated in duplicated, more complex GRNs. We believe that our results provide some additional insights into how genome duplication and polyploidy might help organisms to compete for novel niches and survive ecological turmoil, and confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome some of the traditional limitations of evolution experiments with model organisms.
Highlights
Polyploidy, or the duplication of entire genomes, is a common phenomenon in the evolutionary history of many eukaryotic organisms, especially plants
Studying the impact of whole genome duplication (WGD) on the evolution of Digital Organisms (DOs) under different environmental conditions To study the putative effect of WGDs on the evolution of DOs under challenging environmental conditions, we have simulated the evolution of clonal populations of DOs under two different scenarios of food availability and specific rates of WGD and nucleotide substitution
It is inherent to the system that DOs with different genomic makeups and encoded gene regulatory networks (GRNs) can have very different responses to the same amount of food removal, which makes it hard to summarize the results, except for evaluating overall success when putting polyploids and non-polyploids in competition
Summary
Polyploidy, or the duplication of entire genomes, is a common phenomenon in the evolutionary history of many eukaryotic organisms, especially plants. The significance of whole genome duplication for evolution. Arthur Zwaenepoel and Eshchar Mizrachi for helpful discussions. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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