Huynen M A, Hogeweg P
Bioinformatics Group, Utrecht University, Netherlands.
J Mol Evol. 1994 Jul;39(1):71-9. doi: 10.1007/BF00178251.
Evolution of RNA secondary structure is studied using simulation techniques and statistical analysis of fitness landscapes. The transition from RNA sequence to RNA secondary structure leads to fitness landscapes that have local variations in their "ruggedness." Evolution exploits these variations. In stable environments it moves the quasispecies toward relatively "flat" peaks, where not only the master sequence but also its mutants have a high fitness. In a rapidly changing environment, the situation is reversed; evolution moves the quasispecies to a region where the correlation between secondary structures of "neighboring" RNA sequences is relatively low. In selection for simple secondary structures the movement toward flat peaks leads to pattern generation in the RNA sequences. Patterns are generated at the level of polynucleotide frequencies and the distribution of purines and pyrimidines. The patterns increase the modularity of the sequence. They thereby prevent the formation of alternative secondary structures after mutations. The movement of the quasispecies toward relatively rugged parts of the landscape results in pattern generation at the level of the RNA secondary structure. The base-pairing frequency of the sequences increases. The patterns that are generated in the RNA sequences and the RNA secondary structures are not directly selected for and can be regarded as a side effect of the evolutionary dynamics of the system.
利用模拟技术和适应度景观的统计分析来研究RNA二级结构的进化。从RNA序列到RNA二级结构的转变会导致适应度景观在其“崎岖度”上存在局部变化。进化利用了这些变化。在稳定环境中，它会将准种移向相对“平坦”的峰值，在那里不仅主序列而且其突变体都具有较高的适应度。在快速变化的环境中，情况则相反；进化会将准种移到一个“相邻”RNA序列的二级结构之间相关性相对较低的区域。在选择简单二级结构时，向平坦峰值的移动会导致RNA序列中产生模式。模式在多核苷酸频率以及嘌呤和嘧啶的分布水平上产生。这些模式增加了序列的模块化。从而防止突变后形成替代二级结构。准种向景观中相对崎岖部分的移动会导致在RNA二级结构水平上产生模式。序列的碱基配对频率增加。在RNA序列和RNA二级结构中产生的模式并非直接被选择，可以被视为系统进化动力学的一种副作用。
