Data from: Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ~150-fold, while the mutY mutations reduced the rate by ~40-60%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined.

突变是进化可遗传变异的终极来源。因此，要定量理解诸多进化过程，阐明突变率自身的演化规律至关重要。理论预测，生活在稳定环境中的高度适应种群，其突变率应被降至最低；而当环境发生改变时，突变增变株（hypermutator）可能会演化出现。然而，突变增变株的长期演化命运仍属未知。本研究采用系统发育基因组学（phylogenomic）方法，对一个正在适应环境的大肠杆菌（Escherichia coli）种群展开分析，发现该种群首先演化出mutT突变型的增变表型，之后又被两个独立演化的mutY突变谱系入侵——这些mutY突变可降低全基因组范围内的突变率。我们将中性理论应用于同义替换分析，以此估算这些突变的出现时间，并推断出mutT突变可使点突变率提升约150倍，而mutY突变则可使突变率降低约40%至60%，同时伴随遗传负荷（genetic load）的相应下降。由此可见，随着进一步适应的潜力逐渐降低，突变增变株的长期演化命运，将由突变率降低所带来的选择优势所决定。