The fitness landscape of the codon space across environments

Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and re-estimate selection coefficients of all possible codon mutations across 9 amino-acid positions in Saccharomyces cerevisiae Hsp90 across 6 environments. We quantify the distribution of fitness effects of synonymous mutations and show that it is dominated by many mutations of small or no effect and few mutations of larger effect. We then compare the shape of the codon fitness landscape across amino-acid positions and environments, and quantify how the consideration of synonymous fitness effects changes the evolutionary dynamics on these fitness landscapes. Toget...

适应度景观（fitness landscape）描述了基因型与适应度之间的关联关系。然而，绝大多数适应度景观研究都忽略了密码子表所构建的遗传架构，从而忽视了同义突变的潜在作用。为量化同义突变的适应度效应及其对适应度景观上适应性演化的潜在影响，我们采用一款基于贝叶斯蒙特卡洛马尔可夫链（Bayesian Monte Carlo Markov Chain）方法的全新软件，重新估算了酿酒酵母（Saccharomyces cerevisiae）Hsp90蛋白9个氨基酸位点上所有可能的密码子突变在6种环境下的选择系数。我们对同义突变的适应度效应分布进行了量化分析，结果显示该分布以大量弱效应或无效应突变为主体，仅伴随少量强效应突变。随后我们对比了不同氨基酸位点与环境下的密码子适应度景观形态，并量化了纳入同义突变适应度效应后，这些适应度景观上的演化动力学所发生的变化。Toget...