Pinho Ricardo, Garcia Victor, Feldman Marcus W
Department of Biological Sciences, Stanford University, Stanford, California, USA; PhD Program in Computational Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal.
Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
PLoS One. 2015 Apr 28;10(4):e0119972. doi: 10.1371/journal.pone.0119972. eCollection 2014.
Evolution requires phenotypic variation in a population of organisms for selection to function. Gene regulatory processes involved in organismal development affect the phenotypic diversity of organisms. Since only a fraction of all possible phenotypes are predicted to be accessed by the end of development, organisms may evolve strategies to use environmental cues and noise-like fluctuations to produce additional phenotypic diversity, and hence to enhance the speed of adaptation. We used a generic model of organismal development --gene regulatory networks-- to investigate how different levels of noise on gene expression states (i.e. phenotypes) may affect access to new, unique phenotypes, thereby affecting phenotypic diversity. We studied additional strategies that organisms might adopt to attain larger phenotypic diversity: either by augmenting their genome or the number of gene expression states. This was done for different types of gene regulatory networks that allow for distinct levels of regulatory influence on gene expression or are more likely to give rise to stable phenotypes. We found that if gene expression is binary, increasing noise levels generally decreases phenotype accessibility for all network types studied. If more gene expression states are considered, noise can moderately enhance the speed of discovery if three or four gene expression states are allowed, and if there are enough distinct regulatory networks in the population. These results were independent of the network types analyzed, and were robust to different implementations of noise. Hence, for noise to increase the number of accessible phenotypes in gene regulatory networks, very specific conditions need to be satisfied. If the number of distinct regulatory networks involved in organismal development is large enough, and the acquisition of more genes or fine tuning of their expression states proves costly to the organism, noise can be useful in allowing access to more unique phenotypes.
进化需要生物种群中存在表型变异，以便选择发挥作用。参与生物体发育的基因调控过程会影响生物体的表型多样性。由于预计在发育结束时只能获得所有可能表型中的一小部分，生物体可能会进化出策略，利用环境线索和类似噪声的波动来产生额外的表型多样性，从而提高适应速度。我们使用了一个通用的生物体发育模型——基因调控网络，来研究基因表达状态（即表型）上不同程度的噪声如何影响对新的、独特表型的获取，进而影响表型多样性。我们研究了生物体可能采用的其他策略，以获得更大的表型多样性：要么增加其基因组，要么增加基因表达状态的数量。这是针对不同类型的基因调控网络进行的，这些网络对基因表达具有不同程度的调控影响，或者更有可能产生稳定的表型。我们发现，如果基因表达是二元的，对于所有研究的网络类型，增加噪声水平通常会降低表型可及性。如果考虑更多的基因表达状态，当允许三或四种基因表达状态，并且种群中有足够多不同的调控网络时，噪声可以适度提高发现速度。这些结果与所分析的网络类型无关，并且对噪声的不同实现方式具有鲁棒性。因此，要使噪声增加基因调控网络中可及表型的数量，需要满足非常特定的条件。如果参与生物体发育的不同调控网络数量足够多，并且获取更多基因或对其表达状态进行微调对生物体来说成本过高，那么噪声在允许获取更多独特表型方面可能会有用。
