Data from: 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 functional complexes. Our findings suggest that the transition to obligate parasitism relaxes functional constraints on plastid genes in a stepwise manner. During the functional reduction process, the elevation of evolutionary rates reaches several new rate equilibria, possibly relating to the modified protein turnover rates in heterotrophic plastids.

由于新奇环境条件会改变基因或整个亚基因组所承受的选择压力，适应性与非适应性变化会在基因组中留下可被检测到的印记，进而塑造其分子演化进程。本文构建了从自养（autotrophy）生活方式向非光合寄生生活方式过渡期间，功能约束逐步放松条件下的质体基因组（plastid genome）演化轨迹模型。研究表明，所有质体基因的纯化选择（purifying selection）压力放松，与专性寄生（obligate parasitism）密切相关——专性寄生的核心特征为寄生生物依赖宿主完成自身生活史，而非仅发生光合功能的丢失。演化速率与选择压力会与宏观结构、微观结构变异，功能缩减程度以及专性寄生生活方式的建立协同演化。经推断的基因丢失集中爆发时段与选择压力放松的时期相吻合，随后保留的功能复合体便进入选择压力强化与演化速率减缓的阶段。本研究结果显示，向专性寄生的过渡会逐步放松质体基因所承受的功能约束。在功能缩减的过程中，演化速率的升高会达到多个新的速率平衡态，这可能与异养质体（heterotrophic plastids）中改变的蛋白质更新速率相关。