Table_5_Experimental Evolution Expands the Breadth of Adaptation to an Environmental Gradient Correlated With Genome Reduction.XLSX

Whether and how adaptive evolution adjusts the breadth of adaptation in coordination with the genome are essential issues for connecting evolution with ecology. To address these questions, experimental evolution in five Escherichia coli strains carrying either the wild-type genome or a reduced genome was performed in a defined minimal medium (C0). The ancestral and evolved populations were subsequently subjected to fitness and chemical niche analyses across an environmental gradient with 29 combinations of eight chemical components of the minimal medium. The results showed that adaptation was achieved not only specific to the evolutionary condition (C0), but also generally, to the environmental gradient; that is, the breadth of adaptation to the eight chemical niches was expanded. The magnitudes of the adaptive improvement and the breadth increase were both correlated with genome reduction and were highly significant in two out of eight niches (i.e., glucose and sulfate). The direct adaptation-induced correlated adaptation to the environmental gradient was determined by only a few genome mutations. An additive increase in fitness associated with the stepwise fixation of mutations was consistently observed in the reduced genomes. In summary, this preliminary survey demonstrated that evolution finely tuned the breadth of adaptation correlated with genome reduction.

适应性进化能否以及如何协同基因组调控适应广度，是联结进化生物学与生态学的核心科学议题。为解答上述问题，本研究以5株分别携带野生型基因组与简化基因组的大肠杆菌（Escherichia coli）为实验材料，在限定性基本培养基（C0）中开展实验进化研究。随后，针对祖先种群与进化种群，基于由该基本培养基8种化学成分组合得到的29种环境梯度，开展适合度与化学生态位分析。研究结果表明，适应性进化不仅针对进化培养条件（C0）产生特异性适应，同时也对整体环境梯度产生广谱适应性：即菌株对8种化学生态位的适应广度得以拓展。适应性提升幅度与适应广度拓展程度均与基因组简化程度呈显著相关，且在8种生态位中的2种（葡萄糖与硫酸盐）中达到极显著水平。由直接适应性进化诱导产生的环境梯度广谱适应，仅由少量基因组突变所介导。在简化基因组菌株中，始终可观察到伴随突变逐步固定的适合度累加增长现象。综上，本初步研究表明，进化过程可精准调控适应广度，并使其与基因组简化程度呈协同关联。