Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
Curr Biol. 2019 May 20;29(10):1584-1591.e3. doi: 10.1016/j.cub.2019.03.054. Epub 2019 May 2.
Mutation is the ultimate genetic source of evolution and biodiversity, but to what extent the environment impacts mutation rate and spectrum is poorly understood. Past studies discovered mutagenesis induced by antibiotic treatment or starvation, but its relevance and importance to long-term evolution is unclear because these severe stressors typically halt cell growth and/or cause substantial cell deaths. Here, we quantify the mutation rate and spectrum in Saccharomyces cerevisiae by whole-genome sequencing following mutation accumulation in each of seven environments with relatively rapid cell growths and minimal cell deaths. We find the point mutation rate per generation to differ by 3.6-fold among the seven environments, generally increasing in environments with slower cell growths. This trend renders the mutation rate per year more constant than that per generation across environments, which has implications for neutral evolution and the molecular clock. Additionally, we find substantial among-environment variations in mutation spectrum, such as the transition to transversion ratio and AT mutational bias. Other main mutation types, including small insertion or deletion, segmental duplication or deletion, and chromosome gain or loss also tend to occur more frequently in environments where yeast grows more slowly. In contrast to these findings from the nuclear genome, the yeast mitochondrial mutation rate rises with the growth rate, consistent with the metabolic rate hypothesis. Together, these observations indicate that environmental changes, which are ubiquitous in nature, influence not only natural selection, but also the amount and type of mutations available to selection, and suggest that ignoring the latter impact, as is currently practiced, may mislead evolutionary inferences.
突变是进化和生物多样性的终极遗传来源，但环境对突变率和突变谱的影响程度还不清楚。过去的研究发现了抗生素处理或饥饿诱导的诱变，但由于这些严重的应激因素通常会停止细胞生长和/或导致大量细胞死亡，因此其对长期进化的相关性和重要性尚不清楚。在这里，我们通过在每个具有相对较快细胞生长和最小细胞死亡的七种环境中进行突变积累后进行全基因组测序，来量化酿酒酵母中的突变率和突变谱。我们发现，在七种环境中，每个世代的点突变率差异高达 3.6 倍，通常在细胞生长较慢的环境中增加。这种趋势使得环境之间的突变率每年比每代更稳定，这对中性进化和分子钟都有影响。此外，我们发现突变谱在环境之间存在很大的差异，例如转换为颠换的比例和 AT 突变偏向。其他主要的突变类型，包括小插入或缺失、片段重复或缺失以及染色体增益或缺失，也往往更容易发生在酵母生长较慢的环境中。与核基因组的这些发现相反，酵母线粒体的突变率随着生长速率的提高而上升，这与代谢率假说一致。总之，这些观察结果表明，环境变化不仅影响自然选择，而且影响可供选择的突变数量和类型，这表明目前的实践中忽略后者的影响可能会误导进化推断。
