Origins Institute, McMaster University, Hamilton, Ontario, Canada.
Biol Direct. 2011 Jan 3;6:1. doi: 10.1186/1745-6150-6-1.
Horizontal Gene Transfer (HGT) is beneficial to a cell if the acquired gene confers a useful function, but is detrimental if the gene has no function, if it is incompatible with existing genes, or if it is a selfishly replicating mobile element. If the balance of these effects is beneficial on average, we would expect cells to evolve high rates of acceptance of horizontally transferred genes, whereas if it is detrimental, cells should reduce the rate of HGT as far as possible. It has been proposed that the rate of HGT was very high in the early stages of prokaryotic evolution, and hence there were no separate lineages of organisms. Only when the HGT rate began to fall, would lineages begin to emerge with their own distinct sets of genes. Evolution would then become more tree-like. This phenomenon has been called the Darwinian Threshold.
We study a model for genome evolution that incorporates both beneficial and detrimental effects of HGT. We show that if rate of gene loss during genome replication is high, as was probably the case in the earliest genomes before the time of the last universal common ancestor, then a high rate of HGT is favourable. HGT leads to the rapid spread of new genes and allows the build-up of larger, fitter genomes than could be achieved by purely vertical inheritance. In contrast, if the gene loss rate is lower, as in modern prokaryotes, then HGT is, on average, unfavourable.
Modern cells should therefore evolve to reduce HGT if they can, although the prevalence of independently replicating mobile elements and viruses may mean that cells cannot avoid HGT in practice. In the model, natural selection leads to gradual improvement of the replication accuracy and gradual decrease in the optimal rate of HGT. By clustering genomes based on gene content, we show that there are no separate lineages of organisms when the rate of HGT is high; however, as the rate of HGT decreases, a tree-like structure emerges with well-defined lineages. The model therefore passes through a Darwinian Threshold.
如果获得的基因赋予了有用的功能，那么水平基因转移 (HGT) 对细胞是有益的，但如果基因没有功能、与现有基因不兼容或如果它是自私复制的移动元件，则是有害的。如果这些影响的平衡平均是有益的，我们预计细胞会进化出高接受率的水平转移基因，而如果是有害的，细胞应该尽可能降低 HGT 的速度。有人提出，在原核生物进化的早期阶段，HGT 的速度非常高，因此没有单独的生物谱系。只有当 HGT 速度开始下降时，谱系才会开始出现自己独特的基因集。进化随后将变得更加像树。这种现象被称为达尔文阈值。
我们研究了一个包含 HGT 有益和有害影响的基因组进化模型。我们表明，如果在最后一个普遍共同祖先之前的最早基因组中，基因在基因组复制过程中的丢失率很高，那么高 HGT 率是有利的。HGT 导致新基因的快速传播，并允许构建比仅通过垂直遗传可以实现的更大、更健康的基因组。相比之下，如果基因丢失率较低，就像现代原核生物一样，那么平均而言，HGT 是不利的。
因此，如果可以的话，现代细胞应该进化以减少 HGT，尽管独立复制的移动元件和病毒的流行可能意味着细胞实际上无法避免 HGT。在该模型中，自然选择导致复制准确性的逐步提高和最佳 HGT 率的逐步降低。通过基于基因含量对基因组进行聚类，我们表明在 HGT 率较高时没有单独的生物谱系；然而，随着 HGT 率的降低，会出现具有明确定义谱系的树状结构。因此，该模型通过了达尔文阈值。
