Raas Maximilian W D, Dutheil Julien Y
Research Group Molecular Systems Evolution, Max Planck Institute for Evolutionary Biology, Plön, Germany.
Unité Mixte de Recherche 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.
Mol Ecol. 2024 May;33(10):e16980. doi: 10.1111/mec.16980. Epub 2023 May 8.
Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilisation during the Neolithic period, and the yeast remains of importance in industry and biotechnology, giving rise to bona fide domesticated populations. Here, we conduct a population genomic study of domesticated and wild populations of S. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence with S. paradoxus. We fitted models of distributions of fitness effects to infer the rate of adaptive ( ) and non-adaptive ( ) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated with and positively correlated with . However, the effect of recombination on was found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation with , suggesting that it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population's demography. Together, our results provide a detailed characterisation of adaptive mutations in protein-coding genes across S. cerevisiae populations.
通过其发酵能力，酿酒酵母在新石器时代文明发展中起着核心作用，并且这种酵母在工业和生物技术领域仍然具有重要意义，从而产生了真正的驯化群体。在此，我们对酿酒酵母的驯化群体和野生群体进行了群体基因组研究。通过溯祖分析，我们报告称自与奇异酵母分化以来，酵母群体的有效种群大小有所下降。我们拟合了适合度效应分布模型，以推断蛋白质编码基因中适应性（ ）和非适应性（ ）非同义替换的速率。我们报告称正选择对酿酒酵母蛋白质进化的总体贡献有限，尽管野生群体中的适应性进化速率高于驯化群体。我们的分析揭示了背景选择以及可能的希尔 - 罗伯逊干扰的特征，因为发现重组与 呈负相关，与 呈正相关。然而，发现重组对 的影响不稳定，因为只有在消除密码子使用偏好对同义位点频率谱的影响后才明显，并且如果我们控制与 的相关性，这种影响就会消失，这表明它可能是种群大小下降的一个假象。此外，适应性非同义替换的速率与残基溶剂暴露显著相关，这种关系无法用种群的人口统计学来解释。总之，我们的结果提供了酿酒酵母群体中蛋白质编码基因适应性突变的详细特征。
