Data from: Evolution: are the monkeys’ typewriters rigged?

Evolution is presumed to proceed by random mutations, which increase an individual’s fitness. Increased fitness produces a higher survival rate for those individuals within populations and drives the variants to fixation over large timescales to produce new species. We recently identified positively selected sites in mitochondrial complex I in numerous, diverse taxa. In one taxon, a simple sequence repeat (SSR) encompassed the positively selected sites. We hypothesized a model in which: (i) slip-strand mis-pairing during replication due to the SSR increases the mutation rate at these sites, and (ii) a functional constraint at the protein level maintains the SSR and therefore a higher mutation rate at this site over large time scales to drive evolution. We tested this model by identifying SSRs in a mitochondrial-encoded protein in species from our previous work and determined that nearly all of the positively selected sites encompass an SSR. Furthermore, we show that our proposed model accounts for most of the mutations at neutral sites but it is probably the predominant mechanism at positively selected sites. This suggests that evolution does not proceed by simple random processes but is guided by physical properties of the DNA itself and functional constraint of the proteins encoded by the DNA.

演化通常被认为是通过随机突变推进的，此类突变可提升个体的适合度（fitness）。具备更高适合度的个体在种群中拥有更高的存活率，并在漫长的时间尺度上驱动相关变异被固定，进而产生新物种。我们近期在众多不同类群的线粒体复合物I（mitochondrial complex I）中鉴定出了正选择位点。在其中一个类群中，一段简单序列重复（simple sequence repeat, SSR）覆盖了这些正选择位点。我们据此提出了如下模型：(i) 由该简单序列重复引发的复制过程中链滑动错配，会提升这些位点的突变率；(ii) 蛋白质层面的功能约束会维持该简单序列重复，进而在漫长时间尺度上维持该位点的高突变率，以此推动演化。我们通过在前期研究的物种中鉴定线粒体编码蛋白内的简单序列重复验证了该模型，并发现几乎所有正选择位点均被简单序列重复所覆盖。此外，我们的研究表明，该模型可解释中性位点的绝大多数突变，且大概率是正选择位点处的主要演化机制。这一结果提示，演化并非仅通过简单的随机过程推进，而是受到DNA自身的物理特性以及DNA所编码蛋白质的功能约束的引导。