Continued adaptation of C4 photosynthesis after an initial burst of changes in the Andropogoneae grasses

C4 photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C4 lineages is Andropogoneae, a group of ~ 1,200 grass species that includes some of the world's most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C4 evolution in the group have compared a few model C4 plants to distantly related C3 species, so that changes directly responsible for the transition to C4 could not be distinguished from those that preceded or followed it. In this study, we analyse the genomes of 66 grass species, capturing the earliest diversification within Andropogoneae as well as their C3 relatives. Phylogenomics combined with molecular dating and analyses of protein evolution show that many changes linked to the evolution of C4 photosynthesis in Andropogoneae happened in the Early Miocene, between 21 and 18 Ma, after the split from its C3 sister lineage, and before the diversification of the group. This initial burst of changes was followed by an extended period of modifications to leaf anatomy and biochemistry during the diversification of Andropogoneae, so that a single C4 origin gave birth to a diversity of C4 phenotypes during 18 million years of speciation events and migration across geographic and ecological spaces. Our comprehensive approach and broad sampling of the diversity in the group reveals that one key transition can lead to a plethora of phenotypes following sustained adaptation of the ancestral state.C4光合途径（C4 photosynthesis）是一类复杂的性状，能够在热带与亚热带环境中维持快速生长与高生产力，并在被子植物中独立演化多次。主要的C4演化支系之一为蜀黍族（Andropogoneae），该类群包含约1200种禾本科物种，囊括了全球若干最重要的农作物，以及主导热带与部分温带草原的优势物种。此前针对该类群C4演化的研究，多将少数模式C4植物与亲缘关系较远的C3物种进行对比，因此无法将直接参与C4途径转变的遗传变化，与该转变前后发生的变化区分开来。本研究对66个禾本科物种的基因组进行解析，涵盖了蜀黍族最早的分化事件及其C3近缘类群。结合系统发育基因组学（phylogenomics）、分子定年与蛋白质进化分析，研究结果显示：蜀黍族中与C4光合途径演化相关的诸多遗传改变，发生于中新世早期（2100万至1800万年前，Ma），即该类群与其C3姊妹支系分化之后、且在该类群发生辐射分化之前。这一初始的遗传改变爆发期之后，伴随着蜀黍族辐射分化过程中叶片解剖结构与生物化学通路的长期修饰，使得单次C4起源事件，在1800万年的物种形成过程与跨地理、生态空间的迁移过程中，衍生出了多样的C4表型。本研究采用的全面研究策略与对该类群多样性的广泛采样表明：祖先状态经过持续适应后，单次关键转变即可催生大量多样的表型。