Data from: Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast

Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and in addition, constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the population converged towards a different multivariate phenotype. However, the evolution of most traits, including fitness components, was constrained by history. Phenotypic convergence was partly associated with the selection of mutations in genes involved in the same pathway. By further investigating the convergence in one gene, BMH1, mutated in 20% of the evolved populations, we show that both the history and the environment influenced the types of mutations (missense/nonsense), their location within the gene itself, as well as their effects on multiple traits. However, these effects could not be easily predicted from ancestors’ phylogeny or past-selection. Combined, our data highlight the role of pleiotropy and epistasis in shaping a rugged fitness landscape.

不同生物体在演化历史的不同节点上，独立且反复地演化出了相似的表型性状。这种表型趋同可能由基因型趋同所引发，同时还会受到历史偶然性的约束。为探究趋同演化如何受特定环境中的选择作用驱动、又受到历史因素的约束，我们对6株酵母菌株在4种不同环境下进行实验进化（experimental evolution）过程中的9项生活史性状（life-history traits）与4项代谢性状（metabolic traits）展开了分析。在每一种环境中，种群均趋同至一种独特的多变量表型（multivariate phenotype）。然而，包括适合度组分（fitness components）在内的多数性状的演化均受到历史因素的约束。表型趋同在一定程度上与同一通路相关基因的突变选择存在关联。通过进一步针对单基因BMH1的趋同演化展开研究——该基因在20%的进化种群中发生突变——我们证实，历史背景与环境因素共同影响了突变类型（错义突变/无义突变（missense/nonsense））、突变在基因内部的位置，以及它们对多重性状的效应。不过，这些效应无法通过祖先的系统发育或过往选择轻易预测。综合来看，我们的数据凸显了多效性（pleiotropy）与上位性（epistasis）在塑造崎岖适合度景观（fitness landscape）过程中的关键作用。