Center for Plant Systems Biology, VIB, Ghent, Belgium.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
PLoS One. 2019 Jul 31;14(7):e0220257. doi: 10.1371/journal.pone.0220257. eCollection 2019.
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.
全基因组复制（WGD）在进化中的潜在作用存在争议。虽然有些人认为 WGD 主要是有害的，是进化的“死胡同”，但越来越多的证据表明，多倍体的长期建立可能与环境变化、压力条件或灭绝时期有关。然而，尽管进行了大量研究，但为什么以及多倍体有时能够在环境剧变时胜过非多倍体的机制基础仍然难以确定。在这里，我们改进了我们最近开发的基于生物启发的框架，将人工基因组与基于代理的系统结合起来，形成了所谓的数字生物体（DOs）群体，以研究在模拟不同强度和频率灭绝事件的不同环境情景下 WGD 对进化的影响。我们发现，在稳定的环境下，具有非复制基因组的 DOs 形成了大部分（如果不是全部）的种群，而具有复制基因组的 DOs 的数量在极具挑战性的环境下增加。在根据序列和编码基因调控网络（GRN）跟踪个体基因组的进化轨迹之后，我们提出复制的 GRN 可能为多倍体提供更好的机会获得适应挑战性条件所需的巨大变化，从而在灭绝事件中赋予 DOs 更高的适应潜力。相比之下，在稳定的环境下，随机突变可能很容易使 GRN 不太适应这种环境，这种现象在更复杂的复制 GRN 中更加严重。我们认为，我们的研究结果为基因组复制和多倍体如何帮助生物体竞争新的生态位和在生态动荡中生存提供了一些额外的见解，并证实了我们的计算模拟在研究 WGD 在进化和适应中的作用的有用性，有助于克服传统的进化实验模型生物的一些局限性。
