Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

Because novel environmental conditions alter the selection pressure on genes or entire subgenomes, adaptive and nonadaptive changes will leave a measurable signature in the genomes, shaping their molecular evolution. We present herein a model of the trajectory of plastid genome evolution under progressively relaxed functional constraints during the transition from autotrophy to a nonphotosynthetic parasitic lifestyle. We show that relaxed purifying selection in all plastid genes is linked to obligate parasitism, characterized by the parasite’s dependence on a host to fulfill its life cycle, rather than the loss of photosynthesis. Evolutionary rates and selection pressure coevolve with macrostructural and microstructural changes, the extent of functional reduction, and the establishment of the obligate parasitic lifestyle. Inferred bursts of gene losses coincide with periods of relaxed selection, which are followed by phases of intensified selection and rate deceleration in the retained ...

由于新奇环境条件会改变基因乃至整个亚基因组所承受的选择压力，适应性与非适应性变化均会在基因组中留下可被检测的特征印记，进而塑造其分子演化进程。在此我们提出一套模型，用以阐释从自养型向非光合寄生生活方式过渡过程中，质体基因组（plastid genome）在功能约束逐步松弛状态下的演化轨迹。研究表明，所有质体基因的纯化选择（purifying selection）松弛均与专性寄生（obligate parasitism）相关：专性寄生的核心特征为寄生生物依赖宿主完成自身生命周期，而非仅丢失光合能力。演化速率与选择压力会随宏观结构与微观结构变化、功能缩减程度加深以及专性寄生生活方式的确立发生协同演化。推断得到的基因丢失爆发事件与选择松弛阶段相契合，随后则进入选择作用强化以及保留基因的演化速率减缓……