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.进化论通常认为，进化通过随机突变推进，此类突变可提升个体的适合度。个体适合度提升会使其在种群中拥有更高的存活率，并在漫长的时间尺度上推动该变异位点趋于固定，最终产生新物种。我们近期在多个多样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假说模型：(i) 由该SSR引发的复制过程中链滑动错配，会提升此类位点的突变率；(ii) 蛋白质层面的功能约束会维持该SSR的存在，因此在漫长的时间尺度上维持该位点较高的突变率，进而推动进化。我们通过在既往研究的物种中鉴定线粒体编码蛋白内的SSR对该模型进行了验证，结果表明几乎所有正选择位点均被SSR所覆盖。此外，我们证实所提出的模型可解释中性位点上的绝大多数突变，且该机制大概率是正选择位点上的主要进化机制。这一发现表明，进化并非仅通过简单的随机过程推进，而是由DNA自身的物理特性以及DNA所编码蛋白质的功能约束共同引导的。