Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.
Bioinformatics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands.
Mol Biol Evol. 2017 Oct 1;34(10):2613-2626. doi: 10.1093/molbev/msx185.
The rate of directional environmental change may have profound consequences for evolutionary dynamics and outcomes. Yet, most evolution experiments impose a sudden large change in the environment, after which the environment is kept constant. We previously cultured replicate Saccharomyces cerevisiae populations for 500 generations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium, nickel, and zinc. Here, we investigate how each of these treatments affected genomic evolution. Whole-genome sequencing of evolved clones revealed that adaptation occurred via a combination of SNPs, small indels, and whole-genome duplications and other large-scale structural changes. In contrast to some theoretical predictions, gradual and abrupt environmental change caused similar numbers of genomic changes. For cadmium, which is toxic already at comparatively low concentrations, mutations in the same genes were used for adaptation to both gradual and abrupt increase in concentration. Conversely, for nickel and zinc, which are toxic at high concentrations only, mutations in different genes were used for adaptation depending on the rate of change. Moreover, evolution was more repeatable following a sudden change in the environment, particularly for nickel and zinc. Our results show that the rate of environmental change and the nature of the selection pressure are important drivers of evolutionary dynamics and outcomes, which has implications for a better understanding of societal problems such as climate change and pollution.
环境变化的方向速率可能对进化动态和结果产生深远的影响。然而，大多数进化实验都是在环境发生突然的巨大变化后，将环境保持不变。我们之前在存在逐渐增加或恒定的高浓度重金属镉、镍和锌的情况下，对重复培养的酿酒酵母种群进行了 500 代的培养。在这里，我们研究了这些处理中的每一种是如何影响基因组进化的。进化后的克隆的全基因组测序表明，适应性是通过 SNP、小插入缺失和全基因组复制以及其他大规模结构变化的组合来实现的。与一些理论预测相反，渐进式和突发性的环境变化导致了相似数量的基因组变化。对于镉来说，即使在相对较低的浓度下也具有毒性，因此适应浓度的逐渐增加和突然增加都使用了相同基因中的突变。相反，对于镍和锌来说，只有在高浓度下才具有毒性，适应取决于变化的速度，因此使用了不同基因中的突变。此外，环境的突然变化后，进化的可重复性更高，特别是对于镍和锌。我们的研究结果表明，环境变化的速度和选择压力的性质是进化动态和结果的重要驱动因素，这对更好地理解气候变化和污染等社会问题具有重要意义。
